Carbon-Phosphorus Lyase—the State of the Art

Stosiek, Natalia; Talma, Michał; Klimek‐Ochab, Magdalena

doi:10.1007/s12010-019-03161-4

Cited by 32 publications

(26 citation statements)

References 118 publications

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“…In oligotrophic surface waters with low concentrations of P i , microbes supplement their P needs using AP to hydrolyze organic phosphate esters (Dyhrman and Ruttenberg 2006;Duhamel et al 2011;Ivanči c et al 2016). However, the ubiquity of phosphonate degradation pathways in environmental genomes (Stosiek et al 2019), as well as the high rates of methane production from methylphosphonate in lakes (Wang et al 2017;Li et al 2020) and marine surface waters (Repeta et al 2016;Sosa et al 2020), suggests that microbes also supplement their P needs through the hydrolysis and oxidation of phosphonates. A method comparable to the AP fluorescent assay that specifically targets the microbial utilization of phosphonates is not currently available.…”

Section: Discussionmentioning

confidence: 99%

A sensitive fluorescent assay for measuring carbon‐phosphorus lyase activity in aquatic systems

Granzow

Sosa

Gonnelli

et al. 2021

Limnology & Ocean Methods

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In the oligotrophic ocean where inorganic phosphate (P i ) concentrations are low, microorganisms supplement their nutrient requirements with phosphorus (P) extracted from dissolved organic matter (DOM). Most P in DOM is bound as phosphate esters, which are hydrolyzed by phosphoesterases to P i . However, a large fraction of DOM-P occurs as phosphonates, reduced organophosphorus compounds with a C P bond that do not yield P i through simple ester hydrolysis alone. Phosphonates require an additional step that cleaves the C P bond and oxidizes P(III) to P(V) to yield P i . Most phosphonates are metabolized by the C-P lyase pathway, which cleaves C P bonds and oxidizes phosphonates to P i , enabling microbial assimilation. While the activity of common phosphoesterases such as alkaline phosphatase and phosphodiesterase can be measured by a fluorescent assay, a comparable method to assess C-P lyase activity (CLA) in natural water samples does not exist. To address this, we synthesized a dansyl-labeled phosphonate compound, and measured its hydrolysis by C-P lyase using high performance liquid chromatography. We found that laboratory cultures of marine bacteria expressing the C-P lyase pathway are able to hydrolyze the dansyl phosphonate, while bacteria expressing other phosphonate degradation pathways do not. Finally, we performed several field tests of the assay to measure water column profiles of CLA at Sta. ALOHA in the North Pacific Subtropical Gyre. Activity was elevated near the deep chlorophyll maximum suggesting high levels of phosphonate degradation in that region.

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Section: Discussionmentioning

confidence: 99%

A sensitive fluorescent assay for measuring carbon‐phosphorus lyase activity in aquatic systems

Granzow

Sosa

Gonnelli

et al. 2021

Limnology & Ocean Methods

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“…There was a complex pattern of insertions in the phn operon ( phnC-phnP ; Fig. 3 and Supplementary Material S1) encoding the enzymes of the CP-lyase pathway which cleaves carbon-phosphorous bonds of a variety of substrates and is upregulated under conditions of phosphate starvation (Kamat and Raushel 2013 ; Stosiek, Talma and Klimek-Ochab 2019 ). With fosfomycin at the highest tested concentrations, strong unidirectional insertion signals were observed in phnF —the transcriptional repressor of the phn operon—with the mini-transposon outward-transcribing promoter oriented towards phnG .…”

Section: Resultsmentioning

confidence: 99%

“…Insertions within phnGHIJK are predicted to abolish the ability of the bacteria to cleave the C–P bond but they must still confer a selective advantage for growth, presumably by increasing expression of phnMNOP (within which insertions were not selected for), although the mechanism for this advantage is unclear. The phn operon is part of the pho regulon (Stosiek, Talma and Klimek-Ochab 2019 ), expression of which can be rendered constitutive by mutation in the pst operon (Wanner 1993 ) within which we observed selection for inactivating insertions (Supplementary Material S1). These results are consistent with those published in a recent study using transposon-mediated insertion of a regulated promoter (Turner et al .…”

Section: Resultsmentioning

confidence: 99%

High-density transposon libraries utilising outward-oriented promoters identify mechanisms of action and resistance to antimicrobials

Coward

Dharmalingham

Abdulle

et al. 2020

FEMS Microbiology Letters

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The use of bacterial transposon mutant libraries in phenotypic screens is a well-established technique for determining which genes are essential or advantageous for growth in conditions of interest. Standard, inactivating, transposon libraries cannot give direct information about genes whose over-expression gives a selective advantage. We report the development of a system wherein outward-oriented promoters are included in mini-transposons, generation of transposon mutant libraries in E. coli and P. aeruginosa, and their use to probe genes important for growth under selection with the antimicrobial fosfomycin, and a recently-developed leucyl-tRNA synthase inhibitor. In addition to the identification of known mechanisms of action and resistance, we identify the carbon-phosphorous lyase complex as a potential resistance liability for fosfomycin in E. coli and P. aeruginosa. The use of this technology can facilitate the development of novel mechanism-of-action antimicrobials that are urgently required to combat the increasing threat worldwide from antimicrobial-resistant pathogenic bacteria.

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“…For instance, the pstB and pstS are part of periplasmic transport system which are respectively ATP-binding and ATP-hydrolysis sites [27]. The phnC which was annotated for several species in the FN1 metagenome is encoded by the phn operon which is a member of the Pho regulon normally induced under phosphate starvation [28]. This suggests that these organisms were able to circumvent the shortage of inorganic phosphate in the polluted soil by activating the genes for acquisition and metabolism of less readily available organic sources requiring the activity of phosphate-carbon lyase.…”

Section: Discussionmentioning

confidence: 99%

Remarkable shift in structural and functional properties of an animal charcoal-polluted soil accentuated by inorganic nutrient amendment

Salam¹,

Obayori

2020

Journal of Genetic Engineering and Biotechnology

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Background Soils polluted with animal charcoal from skin and hide cottage industries harbour extremely toxic and carcinogenic hydrocarbon pollutants and thus require a bio-based eco-friendly strategy for their depuration. The effects of carbon-free mineral medium (CFMM) amendment on hydrocarbon degradation and microbial community structure and function in an animal charcoal-polluted soil was monitored for 6 weeks in field moist microcosms consisting of CFMM-treated soil (FN4) and an untreated control (FN1). Hydrocarbon degradation was monitored using gas chromatography-flame ionization detector (GC-FID), and changes in microbial community structure were monitored using Kraken, while functional annotation of putative open reading frames (ORFs) was done using KEGG KofamKOALA and NCBI’s conserved domain database (CDD). Results Gas chromatographic analysis of hydrocarbon fractions revealed the removal of 84.02% and 82.38% aliphatic and 70.09% and 70.14% aromatic fractions in FN4 and FN1 microcosms in 42 days. Shotgun metagenomic analysis of the two metagenomes revealed a remarkable shift in the microbial community structure. In the FN4 metagenome, 92.97% of the population belong to the phylum Firmicutes and its dominant representative genera Anoxybacillus (64.58%), Bacillus (21.47%) and Solibacillus (2.39%). In untreated FN1 metagenome, the phyla Proteobacteria (56.12%), Actinobacteria (23.79%) and Firmicutes (11.20%), and the genera Xanthobacter (9.73%), Rhizobium (7.49%) and Corynebacterium (7.35%), were preponderant. Functional annotation of putative ORFs from the two metagenomes revealed the detection of degradation genes for aromatic hydrocarbons, benzoate, xylene, chlorocyclohexane/chlorobenzene, toluene and several others in FN1 metagenome. In the FN4 metagenome, only seven hydrocarbon degradation genes were detected. Conclusion This study revealed that though CFMM amendment slightly increases the rate of hydrocarbon degradation, it negatively impacts the structural and functional properties of the animal charcoal-polluted soil. It also revealed that intrinsic bioremediation of the polluted soil could be enhanced via addition of water and aeration.

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Carbon-Phosphorus Lyase—the State of the Art

Cited by 32 publications

References 118 publications

A sensitive fluorescent assay for measuring carbon‐phosphorus lyase activity in aquatic systems

A sensitive fluorescent assay for measuring carbon‐phosphorus lyase activity in aquatic systems

High-density transposon libraries utilising outward-oriented promoters identify mechanisms of action and resistance to antimicrobials

Remarkable shift in structural and functional properties of an animal charcoal-polluted soil accentuated by inorganic nutrient amendment

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