Genetic and Biochemical Characterization of a Pathway for the Degradation of 2-Aminoethylphosphonate in Sinorhizobium meliloti 1021

Institute for Genomic Biology, Howard Hughes Medical Institute University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.
Journal of Biological Chemistry (Impact Factor: 4.57). 06/2011; 286(25):22283-90. DOI: 10.1074/jbc.M111.237735
Source: PubMed


A variety of microorganisms have the ability to use phosphonic acids as sole sources of phosphorus. Here, a novel pathway
for degradation of 2-aminoethylphosphonate in the bacterium Sinorhizobium meliloti 1021 is proposed based on the analysis of the genome sequence. Gene deletion experiments confirmed the involvement of the
locus containing phnW, phnA, and phnY genes in the conversion of 2-aminoethylphosphonate to inorganic phosphate. Biochemical studies of the recombinant PhnY and
PhnA proteins verified their roles as phosphonoacetaldehyde dehydrogenase and phosphonoacetate hydrolase, respectively. This
pathway is likely not limited to S. meliloti as suggested by the presence of homologous gene clusters in other bacterial genomes.

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    • "The pathways of 2-aminoethyl phosphonate degradation require the presence of either a phosphonatase that cleaves 2-phosphonoacetaldehyde to acetaldehyde and phosphate or the phosphonoacetaldehyde dehydrogenase coupled to phosphonoacetate hydrolase (PhnWY-PhnA) pathways [37, 38]. Strikingly, no gene homologous to phosphonatase (PhnX, EC "
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    ABSTRACT: The Delta-Proteobacterium Desulfotignum phosphitoxidans is a type strain of the genus Desulfotignum, which comprises to date only three species together with D. balticum and D. toluenicum. D. phosphitoxidans oxidizes phosphite to phosphate as its only source of electrons, with either sulfate or CO2 as electron acceptor to gain its metabolic energy, which is of exclusive interest. Sequencing of the genome of this bacterium was undertaken to elucidate the genomic basis of this so far unique type of energy metabolism. The genome contains 4,998,761 base pairs and 4646 genes of which 3609 were assigned to a function, and 1037 are without function prediction. Metabolic reconstruction revealed that most biosynthetic pathways of Gram negative, autotrophic sulfate reducers were present. Autotrophic CO2 assimilation proceeds through the Wood-Ljungdahl pathway. Additionally, we have found and confirmed the ability of the strain to couple phosphite oxidation to dissimilatory nitrate reduction to ammonia, which in itself is a new type of energy metabolism. Surprisingly, only two pathways for uptake, assimilation and utilization of inorganic and organic phosphonates were found in the genome. The unique for D. phosphitoxidans Ptx-Ptd cluster is involved in inorganic phosphite oxidation and an atypical C-P lyase-coding cluster (Phn) is involved in utilization of organophosphonates. We present the whole genome sequence of the first bacterium able to gain metabolic energy via phosphite oxidation. The data obtained provide initial information on the composition and architecture of the phosphite--utilizing and energy-transducing systems needed to live with phosphite as an unusual electron donor.
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    • "Cloning, Protein Expression, Purification, and Crystallization Cloning, expression, and purification of recombinant S. meliloti PhnA from E. coli has been described previously (Borisova et al., 2011). For crystallization, the hexahistidine tag was removed by digestion with thrombin (1 unit/mg of protein) followed by purification using anion exchange (5 ml of HiTrap Q-FF, GE Healthcare) and size exclusion chromatographies (Superdex 75 16/60, GE Healthcare). "
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    ABSTRACT: Bacteria have evolved pathways to metabolize phosphonates as a nutrient source for phosphorus. In Sinorhizobium meliloti 1021, 2-aminoethylphosphonate is catabolized to phosphonoacetate, which is converted to acetate and inorganic phosphate by phosphonoacetate hydrolase (PhnA). Here we present detailed biochemical and structural characterization of PhnA that provides insights into the mechanism of C-P bond cleavage. The 1.35 Å resolution crystal structure reveals a catalytic core similar to those of alkaline phosphatases and nucleotide pyrophosphatases but with notable differences, such as a longer metal-metal distance. Detailed structure-guided analysis of active site residues and four additional cocrystal structures with phosphonoacetate substrate, acetate, phosphonoformate inhibitor, and a covalently bound transition state mimic provide insight into active site features that may facilitate cleavage of the C-P bond. These studies expand upon the array of reactions that can be catalyzed by enzymes of the alkaline phosphatase superfamily.
    Preview · Article · Oct 2011 · Chemistry & biology
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    ABSTRACT: Phosphonates are compounds that contain the chemically stable carbon-phosphorus (C-P) bond. They are widely distributed amongst more primitive life forms including many marine invertebrates and constitute a significant component of the dissolved organic phosphorus reservoir in the oceans. Virtually all biogenic C-P compounds are synthesized by a pathway in which the key step is the intramolecular rearrangement of phosphoenolpyruvate to phosphonopyruvate. However C-P bond cleavage by degradative microorganisms is catalyzed by a number of enzymes - C-P lyases, C-P hydrolases, and others of as-yet-uncharacterized mechanism. Expression of some of the pathways of phosphonate catabolism is controlled by ambient levels of inorganic P (Pi) but for others it is Pi-independent. In this report we review the enzymology of C-P bond metabolism in bacteria, and also present the results of an in silico investigation of the distribution of the genes that encode the pathways responsible, in both bacterial genomes and in marine metagenomic libraries, and their likely modes of regulation. Interrogation of currently available whole-genome bacterial sequences indicates that some 10% contain genes encoding putative pathways of phosphonate biosynthesis while ∼40% encode one or more pathways of phosphonate catabolism. Analysis of metagenomic data from the global ocean survey suggests that some 10 and 30%, respectively, of bacterial genomes across the sites sampled encode these pathways. Catabolic routes involving phosphonoacetate hydrolase, C-P lyase(s), and an uncharacterized 2-aminoethylphosphonate degradative sequence were predominant, and it is likely that both substrate-inducible and Pi-repressible mechanisms are involved in their regulation. The data we present indicate the likely importance of phosphonate-P in global biogeochemical P cycling, and by extension its role in marine productivity and in carbon and nitrogen dynamics in the oceans.
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