Molecular genetics of carbon-phosphorus bond cleavage in bacteria

Phosphonates (Pn) are a large class of organophosphorus molecules that have direct carbon-phosphorus (C - P) bonds in place of the carbon-oxygen-phosphorus ester bond. In bacteria two pathways exist for Pn breakdown for use as a P source: the phosphonatase and C - P lyase pathways. These pathways differ both in regard to their substrate specificity and their cleavage mechanism. The phosphonatase pathway acts on the natural Pn -aminoethylphosphonate(AEPn). In a two-step process it leads to cleavage of the C - P bond by a hydrolysis reaction requiring an adjacent carbonyl group. In contrast the C - P lyase pathway has a broad substrate specificity. It leads to cleavage of substituted Pn (such as AEPn) as well as unsubstituted Pn by a mechanism involving redox or radical chemistry. Due to its broad substrate specificity, the C - P lyase pathway is generally thought to be responsible for the breakdown of Pn herbicides (such as glyphosate) by bacteria. As a way to gain a more in-depth understanding of these Pn degradative pathways, their respective genes have been isolated and characterized. In the absence of a biochemical assay for the C - P lyase pathway such molecular approaches have been especially valuable. The roles of individual genes have been inferred from DNA sequence analysis and mutational effects. Genes for the C - P lyase pathway exist in a fourteen-gene operon that appears to encode both a binding protein-dependent Pn transporter and a C - P lyase. Genes for the phosphonatase pathway also exist in a gene cluster containing Pn uptake and degradative genes. A combination of biochemistry, molecular biology, and molecular genetics approaches has provided more detailed understanding of the mechanisms of C - P bond cleavage. Such basic information may provide a new handle for improvement of Pn degradation capabilities in bacteria, or in other cells in which the respective genes may be introduced and expressed.Abbreviations AEPn -aminoethylphosphonate - C carbon - kbp kilobase pair - kDa kilodalton - MPn methylphosphonate - P phosphorus - P _i inorganic phosphate - Pn phosphonate - psi phosphate starvation inducible     

A microbial carbon-phosphorus bond cleavage enzyme requires two protein components for activity.

Enterobacter aerogenes IFO 12010 contains a carbon-phosphorus (C-P) bond cleavage enzyme catalyzing the liberation of inorganic phosphate from various alkyl- and phenylphosphonic acids. The enzyme in the bacterium was found to be composed of two physically different protein components, E2 and E3. The molecular weights of E2 and E3 were 560,000 and 110,000, respectively, and E3 was resolved into two apparently homogeneous subunits. Neither component alone could catalyze the C-P bond cleavage reaction, but the reaction was efficiently catalyzed when the components were mixed.     

In vitro characterization of a phosphate starvation-independent carbon-phosphorus bond cleavage activity in Pseudomonas fluorescens 23F.

A novel, metal-dependent, carbon-phosphorus bond cleavage activity, provisionally named phosphonoacetate hydrolase, was detected in crude extracts of Pseudomonas fluorescens 23F, an environmental isolate able to utilize phosphonoacetate as the sole carbon and phosphorus source. The activity showed unique specificity toward this substrate; its organic product, acetate, was apparently metabolized by the glyoxylate cycle enzymes of the host cell. Unlike phosphonatase, which was also detected in crude extracts of P. fluorescens 23F, phosphonoacetate hydrolase was inducible only in the presence of its sole substrate and did not require phosphate starvation.     

Detection of a novel carbon-phosphorus bond cleavage activity in cell-free extracts of an environmental Pseudomonas fluorescens isolate.

Cell-free extracts of Pseudomonas fluorescens strain 23F catalyzed the hydrolysis of phosphonoacetate to acetate and inorganic phosphate; the products were detected in almost equimolar quantities. The stable in vitro activity responsible was distinct from phosphonoacetaldehyde hydrolase and appears to represent a novel mode of carbon-phosphorus bond cleavage.     

Homolytic carbon to phosphorus bond scission of some phosphonates catalyzed by bacterial carbon-phosphorus lyase

The production of volatile degradation products of phosphonates was monitored to investigate the mechanism involved in the biodegradation of propylphosphonic acid and phenylphosphonic acid byRhizobium sp MMM101a. The biodegradation of propylphosphonic acid gave rise to the production, in decreasing order, of propane, methane, ethane, 1-butene, propene, isobutene, butane and ethene. The formation of these degradation products was strongly reduced by adding catalase to the growing cultures indicating the involvement of peroxides in the biodegradation mechanism. OH⁰ radical scavengers did not reduce the rate of biodegradation, and therefore these radicals appear not to be involved. Addition of ascorbate, a known hydroxylating agent in biological systems, increased the amount of biodegradation products. The involvement of iron in the degradation was indicated and was optimal at a concentration of 950 µM. This suggests the involvement of a metalloenzyme involving iron and peroxide. The decomposition of phenylphosphonic acid yielded benzene and biphenyl. No phenol could be detected, again suggesting that OH⁰ radicals were not involved in the biodegradation. The presence of deuterated benzene did not result in the occurrence of biphenyl consisting of one nondeuterated and a deuterated ring, which is chemically more likely. It therefore appears that the degradation of the phosphonates occurs on a multicentered enzyme. The diversity of the products generated by this bacterium from phosphonates, many of them due to rearrangement of the carbon moiety of the substrate molecule, suggests an overall involvement of superoxide radicals in the homolytic carbon to phosphorus bond scission.     

The purification and characterization of phosphonopyruvate hydrolase,a novel carbon-phosphorus bond cleavage enzyme from Variovorax sp Pal2

Phosphonopyruvate hydrolase, a novel bacterial carbon-phosphorus bond cleavage enzyme, was purified to homogeneity by a series of chromatographic steps from cell extracts of a newly isolated environmental strain of Variovorax sp. Pal2. The enzyme was inducible in the presence of phosphonoalanine or phosphonopyruvate; unusually, its expression was independent of the phosphate status of the cell. The native enzyme had a molecular mass of 63 kDa with a subunit mass of 31.2 kDa. Activity of purified phosphonopyruvate hydrolase was Co2+-dependent and showed a pH optimum of 6.7-7.0. The enzyme had a Km of 0.53 mm for its sole substrate, phosphonopyruvate, and was inhibited by the analogues phosphonoformic acid, 3-phosphonopropionic acid, and hydroxymethylphosphonic acid. The nucleotide sequence of the phosphonopyruvate hydrolase structural gene indicated that it is a member of the phosphoenolpyruvate phosphomutase/isocitrate lyase superfamily with 41% identity at the amino acid level to the carbon-to-phosphorus bond-forming enzyme phosphoenolpyruvate phosphomutase from Tetrahymena pyriformis. Thus its apparently ancient evolutionary origins differ from those of each of the two carbon-phosphorus hydrolases that have been reported previously; phosphonoacetaldehyde hydrolase is a member of the haloacetate dehalogenase family, whereas phosphonoacetate hydrolase belongs to the alkaline phosphatase superfamily of zinc-dependent hydrolases. Phosphonopyruvate hydrolase is likely to be of considerable significance in global phosphorus cycling, because phosphonopyruvate is known to be a key intermediate in the formation of all naturally occurring compounds that contain the carbon-phosphorus bond.     

Fragmentative and stereochemical isomerization probes for homolytic carbon to phosphorus bond scission catalyzed by bacterial carbon-phosphorus lyase

Three bacterial strains, Agrobacterium radiobacter, Klebsiella oxytoca, and Kluyvera ascorbata, isolated by enrichment culture for carbon to phosphorus bond cleavage ability, were analyzed for the mode of C---P bond fission. The cleavage of alkyl phosphonic acids to alkanes and inorganic phosphates proceeded both aerobically and anaerobically, and growth on trideuteromethylphosphonic acid yielded trideuteromethane as product. These data indicate that functionalization of the organic moiety does not precede carbon to phosphorus bond cleavage. As probes for radical intermediates, cyclopropylmethylphosphonic acid and cis-1,2-dideutero-1-propenylphosphonic acid were used in growth experiments and the gaseous hydrocarbon products were examined. With the cyclopropylmethylphosphonic acid probe, all three bacteria produced methylcyclopropane, but only K. oxytoca and K. ascorbata also generated the acyclic olefin 1-butene, and then only in very low quantity (0.6 and 0.3% versus methylcyclopropane, respectively). With the propenylphosphonic acid probe, cis-1,2-dideuteropropene was formed with greater than 98% retention of configuration with each bacterial strain. Only for K. oxytoca was the alternate product, in this case trans-1,2-dideuteropropene, clearly detected at 1.5%. Thus, C---P bond fission may yield radical intermediates that are trapped efficiently at the enzyme active site or, alternatively, homolysis of the C---P bond may occur as a minor reaction pathway.     

Initial in vitro characterisation of phosphonopyruvate hydrolase, a novel phosphate starvation-independent, carbon-phosphorus bond cleavage enzyme in Burkholderia cepacia Pal6

A novel, inducible carbon-phosphorus bond cleavage enzyme, phosphonopyruvate hydrolase, was detected in cell-free extracts of Burkholderia cepacia Pal6, an environmental isolate capable of mineralising L-phosphonoalanine as carbon, nitrogen and phosphorus source. The activity was induced only in the presence of phosphonoalanine, did not require phosphate starvation for induction and was uniquely specific for phosphonopyruvate, producing equimolar quantities of pyruvate and inorganic phosphate. The native enzyme had a molecular mass of some 232 kDa and showed activation by metal ions in the order Co2+ > Ni2+ > Mg2+ > Zn2+ > Fe2+ > Cu2+. Temperature and pH optima in crude cell extracts were 50 degrees C and 7.5, respectively, and activity was inhibited by EDTA, phosphite, sulfite, mercaptoethanol and sodium azide. Phosphonopyruvate hydrolase is the third bacterial C-P bond cleavage enzyme reported to date that proceeds via a hydrolytic mechanism.     

Stereospecific cleavage of carbon-phosphorus bonds: stereochemical course of the phosphinoyl curtius (Harger) reaction

The homochiral phosphinic azides (R,R)-1 and (S,S)-1 were prepared in enantiomerically pure form by resolution of diastereomeric phosphinamides derived from (S)-l-phenylethylamine and (R)-phenylglycine. Irradiation of the azides in methanol induced a photo-Curtius rearrangement to phosphonamidates in which the stereogenic carbon unit migrated to a nitrogen atom. Hydrolysis of the phosphonamidates produced 1-phenylethylamine, which was 99.0% e.e. and of the same configuration as the carbon unit in the starting azide (99.0% retention).     

Sugars containing a carbon-phosphorus bond : Part V. 5-deoxy-5-(ethylphosphinyl)-D-ribopyranose

The Michaelis-Arbuzov reaction of methyl 5-deoxy-5-iodo-2,3-O-isopropylidene-β-D-ribofuranoside (4) with diethyl ethylphosphonite gave methyl 5-deoxy-5-(ethoxyethylphosphinyl)-2,3-O-isopropylidene-β-D-ribofuranoside (5) which, on treatment with sodium dihydrobis(2-methoxyethoxy)aluminate, afforded methyl-5-deoxy-5-(ethylphosphinyl)-2,3-O-isopropylidene-β-D-ribofuranoside (9). Hydrolysis of 9 with hydrochloric acid yielded a mixture of the anomeric 5-deoxy-5-(ethylphosphinyl)-D-ribopyranoses (10). The hygroscopic, syrupy mixture 10 was converted into a syrup consisting of the two 1,2,3,4-tetra-O-acetyl-5-deoxy-5-(ethylphosphinyl)-D-ribopyranoses (11).     

Aminoacyl-tRNA synthetase-catalyzed cleavage of the glycosidic bond of 5-halogenated uridines.

Because of previous data suggesting that aminoacyl-tRNA synthetases make a transient Michael adduct with a specific uridine residue in the tRNA structure, (Schoemaker, H.J.P., and Schimmel, P.R. (1977) Biochemistry 16, 5454-5460) attempts were made to find simple model systems in which this reaction might be studied in more detail. In the course of these investigations, it was found that Escherichia coli Ile-tRNA synthetase catalyzes cleavage of the glycosidic bond of 5-bromouridine. At pH 7.5, ambient temperatures, the turnover number is roughly 5/h. 5-Fluoro-, 5-chloro-, and 5-iodouridine are also cleaved in an analogous way by Ile-tRNA synthetase. In the case of uridine, conversion of uridine to uracil and ribose was also detected, but with a smaller turnover number. Three other E. coli and one mammalian aminoacyl-tRNA synthetases were also examined and all were found to catalyze glycosidic bond cleavage of 5-bromouridine. The data indicate that, in general, synthetases have a catalytic center that shows an unusual reactivity for uridine.     

Mechanism of ribonucleoside diphosphate reductase from Escherichia coli. Evidence for 3'-C--H bond cleavage

Incubation of the pyrimidine [3'-3H]UDP with ribonucleotide reductase resulted in an isotope effect on the conversion to dUDP which varied as a function of pH and allosteric effectors (pH, kH/kT, effector): 6.6, 4.7, ATP; 7.6, 3.3, ATP; 7.6, 2.6, dATP; 7.6, 2.0, TTP; 8.4, 2.8, ATP. During this reaction 3H2O was also released. The lower the pH of the reaction, the larger the isotope effect, and the smaller the amount of 3H2O produced. At 50% conversion of UDP to dUDP and at pH 7.6, approximately 0.5% of total 3H present in solution was volatilized, while at pH 8.4, approximately 0.9% was volatilized. Similar experiments in which the purine [3'-3H]ADP was incubated with ribonucleotide reductase also resulted in an isotope effect on its conversion to dATP which varied as a function of pH (pH, kH/kT with dGTP as an effector); 6.6, 1.9; 7.6, 1.7; 8.6, 1.4. Furthermore, 3H2O was also released as a function of the extent of the reaction. At 50% turnover and pH 7.6, approximately 0.6% of 3H2O was volatilized, while at pH 8.6 approximately 1.25% was released. Two control experiments in which either the B1 subunit of ribonucleotide reductase was inactivated with 2'-chloro-2'-deoxyuridine 5'-diphosphate or the B2 subunit of ribonucleotide reductase was inactivated with 2'-azido-2'-deoxyuridine 5'-diphosphate and then the enzyme incubated with [3'-3H]ADP or [3'-3H]UDP indicated that in neither case was 3H released. Both B1 and B2 subunits are required for cleavage of the 3'-C--H bond. Incubation of [3'-3H]dADP or [3'-3H]dUDP with ribonucleotide reductase produced no measurable release of 3H. These data clearly indicate that conversion of a purine or pyrimidine diphosphate to a deoxynucleotide diphosphate by Escherichia coli ribonucleotide reductase requires cleavage of the 3'-C--H bond of the substrate. The fate of the 3'-H of the substrate was also determined. Incubation of [3'-2H]UDP with ribonucleotide reductase resulted in the production of [3'-2H]dUDP.