ArticleProceedings of the National Academy of Sciences of the United States of America2013
Diversity and abundance of phosphonate biosynthetic genes in nature.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 82 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
82 citing papers in PubMed, 182 citations in OpenAlex.
- Article
- A metabolite extracted from Escherichia coli suppresses tau aggregation.The Biochemical journal · 2026Article
- From Discovery to Manufacturing: A Quantitative Review of Phosphonates and Strategies for High-Titer Production.Microorganisms · 2026Review
- The Factors Governing Metal Dependence of an Emergent Superfamily of Bimetallic Oxygenases.Journal of the American Chemical Society · 2026Article
- Discovery of the Phosphonate Flavophos Produced byJournal of the American Chemical Society · 2026Article
- Article
- Discovery of the Phosphonate Flavophos Produced bybioRxiv : the preprint server for biology · 2026Article
- Physicochemistry and comparative metagenomics of a tropical estuary persistently inundated with anthropogenic pollutants.Folia microbiologica · 2025Article
- Genomic context analysis enables the discovery of an unusual NAD-dependent racemase in phosphonate catabolism.The FEBS journal · 2025Article
- Unveiling novel features and phylogenomic assessment of indigenousMicrobiology spectrum · 2025Article
- The microbial phosphorus cycle in aquatic ecosystems.Nature reviews. Microbiology · 2025Review
- Determining biosynthetic gene cluster boundaries through comparative bioinformatics.Methods in enzymology · 2025Article
- Enzymatic Synthesis of Biologically ActiveBiomolecules · 2024Article
- Phosphonoalamides Reveal the Biosynthetic Origin of Phosphonoalanine Natural Products and a Convergent Pathway for Their Diversification.Angewandte Chemie (International ed. in English) · 2024Article
- Biosynthesis ofACS chemical biology · 2024Article
- Discovery of a glyphosate oxidase in nature.FEMS microbiology letters · 2024Article
- Oxic methane production from methylphosphonate in a large oligotrophic lake: limitation by substrate and organic carbon supply.Applied and environmental microbiology · 2023Article
- Phosphonate consumers potentially contributing to methane production in Brazilian soda lakes.Extremophiles : life under extreme conditions · 2023Article
- Deciphering the role of recurrent FAD-dependent enzymes in bacterial phosphonate catabolism.iScience · 2023Article
- The Microbial Degradation of Natural and Anthropogenic Phosphonates.Molecules (Basel, Switzerland) · 2023Review
22 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors at 2 institutions in 1 country.
Funding
Abstract
Phosphonates, molecules containing direct carbon-phosphorus bonds, compose a structurally diverse class of natural products with interesting and useful biological properties. Although their synthesis in protozoa was discovered more than 50 y ago, the extent and diversity of phosphonate production in nature remains poorly characterized. The rearrangement of phosphoenolpyruvate (PEP) to phosphonopyruvate, catalyzed by the enzyme PEP mutase (PepM), is shared by the vast majority of known phosphonate biosynthetic pathways. Thus, the pepM gene can be used as a molecular marker to examine the occurrence and abundance of phosphonate-producing organisms. Based on the presence of this gene, phosphonate biosynthesis is common in microbes, with ~5% of sequenced bacterial genomes and 7% of genome equivalents in metagenomic datasets carrying pepM homologs. Similarly, we detected the pepM gene in ~5% of random actinomycete isolates. The pepM-containing gene neighborhoods from 25 of these isolates were cloned, sequenced, and compared with those found in sequenced genomes. PEP mutase sequence conservation is strongly correlated with conservation of other nearby genes, suggesting that the diversity of phosphonate biosynthetic pathways can be predicted by examining PEP mutase diversity. We used this approach to estimate the range of phosphonate biosynthetic pathways in nature, revealing dozens of discrete groups in pepM amplicons from local soils, whereas hundreds were observed in metagenomic datasets. Collectively, our analyses show that phosphonate biosynthesis is both diverse and relatively common in nature, suggesting that the role of phosphonate molecules in the biosphere may be more important than is often recognized.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.