Structure of PhnP, a Phosphodiesterase of the Carbon-Phosphorus Lyase Pathway for Phosphonate Degradation

Podzelinska, Kateryna; He, Shikun; Wathier, Matthew; Yakunin, Alexander F.; Proudfoot, Michael; Hove‐Jensen, Bjarne; Zechel, David L.; Jia, Zongchao

doi:10.1074/jbc.m808392200

Cited by 38 publications

(77 citation statements)

References 52 publications

(59 reference statements)

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“…This enzyme is a member of the ␤-lactamase family of metal iondependent hydrolases, and, typically for this family of enzymes, it is a homodimer and contains a dinuclear active site with two Mn 2ϩ ions as well as a structural Zn 2ϩ ion. The enzyme has activity toward a number of phosphodiesters besides the physiological substrate (49,50). Mutants defective in phnP have proven valuable in elucidating the structure of the components of the C-P lyase pathway.…”

Section: Mesorhizobium Lotimentioning

confidence: 99%

Utilization of Glyphosate as Phosphate Source: Biochemistry and Genetics of Bacterial Carbon-Phosphorus Lyase

Hove‐Jensen

Zechel

Jochimsen

2014

Microbiol Mol Biol Rev

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185

157

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SUMMARY After several decades of use of glyphosate, the active ingredient in weed killers such as Roundup, in fields, forests, and gardens, the biochemical pathway of transformation of glyphosate phosphorus to a useful phosphorus source for microorganisms has been disclosed. Glyphosate is a member of a large group of chemicals, phosphonic acids or phosphonates, which are characterized by a carbon-phosphorus bond. This is in contrast to the general phosphorus compounds utilized and metabolized by microorganisms. Here phosphorus is found as phosphoric acid or phosphate ion, phosphoric acid esters, or phosphoric acid anhydrides. The latter compounds contain phosphorus that is bound only to oxygen. Hydrolytic, oxidative, and radical-based mechanisms for carbon-phosphorus bond cleavage have been described. This review deals with the radical-based mechanism employed by the carbon-phosphorus lyase of the carbon-phosphorus lyase pathway, which involves reactions for activation of phosphonate, carbon-phosphorus bond cleavage, and further chemical transformation before a useful phosphate ion is generated in a series of seven or eight enzyme-catalyzed reactions. The phn genes, encoding the enzymes for this pathway, are widespread among bacterial species. The processes are described with emphasis on glyphosate as a substrate. Additionally, the catabolism of glyphosate is intimately connected with that of aminomethylphosphonate, which is also treated in this review. Results of physiological and genetic analyses are combined with those of bioinformatics analyses.

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Section: Mesorhizobium Lotimentioning

confidence: 99%

Utilization of Glyphosate as Phosphate Source: Biochemistry and Genetics of Bacterial Carbon-Phosphorus Lyase

Hove‐Jensen

Zechel

Jochimsen

2014

Microbiol Mol Biol Rev

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185

157

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“…The reason for three apparent ABCs (PhnC, PhnK, and PhnL) in Pn transport remains to be established. The phnN cistron encodes ribosyl 1,5-bisphosphate phosphokinase (12), the phnO cistron encodes aminophosphonate N-acetyltransferase (13), whereas phnP encodes phosphoribosyl cyclic phosphodiesterase (14,15). Pn degradation by the CP lyase pathway involves a number of intermediates, which presumably are ribose derivatives.…”

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confidence: 99%

Five phosphonate operon gene products as components of a multi-subunit complex of the carbon-phosphorus lyase pathway

Jochimsen

Lolle

McSorley

et al. 2011

Proc. Natl. Acad. Sci. U.S.A.

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Organophosphonate utilization by Escherichia coli requires the 14 cistrons of the phnCDEFGHIJKLMNOP operon, of which the carbon-phosphorus lyase has been postulated to consist of the seven polypeptides specified by phnG to phnM . A 5,660-bp DNA fragment encompassing phnGHIJKLM is cloned, followed by expression in E. coli and purification of Phn-polypeptides. PhnG, PhnH, PhnI, PhnJ, and PhnK copurify as a protein complex by ion-exchange, size-exclusion, and affinity chromatography. The five polypeptides also comigrate in native-PAGE. Cross-linking of the purified protein complex reveals a close proximity of PhnG, PhnI, PhnJ, and PhnK, as these subunits disappear concomitant with the formation of large cross-linked protein complexes. Two molecular forms are identified, a major form of molecular mass of approximately 260 kDa, a minor form of approximately 640 kDa. The stoichiometry of the protein complex is suggested to be PhnG 4 H 2 I 2 J 2 K. Deletion of individual phn genes reveals that a strain harboring plasmid-borne phnGHIJ produces a protein complex consisting of PhnG, PhnH, PhnI, and PhnJ, whereas a strain harboring plasmid-borne phnGIJK produces a protein complex consisting of PhnG and PhnI. We conclude that phnGHIJK specify a soluble multisubunit protein complex essential for organophosphonate utilization.

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“…An alternative approach is to target genes in the C-P lyase clusters that are not required for phosphonate catabolism but encode auxiliary functions such as phnN, phnO, and phnP . For example, phnP encodes a phosphodiesterase with high cyclic nucleotide activity (Podzelinska et al, 2009). It is possible that PhnP also exhibits phosphodiesterase activity towards HMW DOM phosphonates since these are linked to sugar residues by ester bonds (Repeta et al, unpublished Fig.…”

Section: Resultsmentioning

confidence: 99%

Microbial cycling of marine high molecular weight dissolved organic matter

Sosa¹

2016

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Microorganisms play a central role mediating biogeochemical cycles in the ocean. Marine dissolved organic matter (DOM) -a reservoir of organic solutes and colloids derived from plankton is a major source of carbon, nutrients, and energy to microbial communities. The biological transformation and remineralization of DOM sustains marine productivity by linking the microbial food web to higher trophic levels (the microbial loop) and exerts important controls over the cycles of carbon and bioessential elements, such as nitrogen and phosphorus, in the sea. Yet insight into the underlying metabolism and reactions driving the degradation of DOM is limited partly because its exact molecular composition is difficult to constrain and appropriate microbial model systems known to decompose marine DOM are lacking. This thesis identifies marine microorganisms that can serve as model systems to study the metabolic pathways and biochemical reactions that control an important ecosystem function, DOM turnover. To accomplish this goal, bacterial isolates were obtained by enriching seawater in dilution-to-extinction culturing experiments with a natural source of DOM, specifically, the high molecular weight (HMW) fraction (>1 kDa nominal molecular weight) obtained by ultrafiltration. Because it is relatively easy to concentrate and it is fairly uniform in its chemical composition across the global ocean and other aquatic environments, HMW DOM has the potential to serve as a model growth substrate to study the biological breakdown of DOM. The phylogeny, genomes, and growth characteristics of the organisms identified through this work indicate that HMW DOM contains bioavailable substrates that may support widespread microbial populations in coastal and open-ocean environments. The availability of ecologically relevant isolates in culture can now serve to test hypothesis emerging from cultivation-independent studies pertaining the potential role of microbial groups in the decomposition of organic matter in the sea. Detailed studies of the biochemical changes exerted on DOM by selected bacterial strains will provide new insight into the processes driving the aerobic microbial food chain in the upper ocean. AcknowledgmentsI owe my deepest gratitude to those who mentored me in the lab. My advisers Ed DeLong and Dan Repeta really changed my life and career trajectory in a way I never imagined bringing me on as a JP student, giving me the opportunity to take part in research at sea and an important collaborative project as part of my dissertation. Thank you to my thesis committee members Martin Polz and Tracy Mincer who always provided constructive discussion and advice that helped me progress. Thank you to my friend and collegue Jamie Becker, my reference in the JP, who convinced my advisers Ed and Dan I should help him out with his research in Hawaii as he was finishing up his thesis, an experience that would be invaluable down the road as a continued my work there when our lab moved to C-MORE at the University of Hawaii. A big mahalo al...

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Structure of PhnP, a Phosphodiesterase of the Carbon-Phosphorus Lyase Pathway for Phosphonate Degradation

Cited by 38 publications

References 52 publications

Utilization of Glyphosate as Phosphate Source: Biochemistry and Genetics of Bacterial Carbon-Phosphorus Lyase

Utilization of Glyphosate as Phosphate Source: Biochemistry and Genetics of Bacterial Carbon-Phosphorus Lyase

Five phosphonate operon gene products as components of a multi-subunit complex of the carbon-phosphorus lyase pathway

Microbial cycling of marine high molecular weight dissolved organic matter

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