ArticleNature chemical biology2018
Functional assignment of multiple catabolic pathways for D-apiose.
Article in Nature chemical biology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed, 41 citations in OpenAlex.
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- Deep ocean metagenomes provide insight into the metabolic architecture of bathypelagic microbial communities.Communications biology · 2021Article
- Discovery of novel pathways for carbohydrate metabolism.Current opinion in chemical biology · 2021Review
- Deciphering the enzymatic mechanism of sugar ring contraction in UDP-apiose biosynthesis.Nature catalysis · 2019Article
- The EFI Web Resource for Genomic Enzymology Tools: Leveraging Protein, Genome, and Metagenome Databases to Discover Novel Enzymes and Metabolic Pathways.Biochemistry · 2019Article
- Lateral Gene Transfer Shapes the Distribution of RuBisCO among Candidate Phyla Radiation Bacteria and DPANN Archaea.Molecular biology and evolution · 2019Article
- Revisiting the methionine salvage pathway and its paralogues.Microbial biotechnology · 2019Article
- Back to the future: Why we need enzymology to build a synthetic metabolism of the future.Beilstein journal of organic chemistry · 2019Review
- 'Democratized' genomic enzymology web tools for functional assignment.Current opinion in chemical biology · 2018Review
Corrections and comments
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Authors and funding
13 authors at 2 institutions in 1 country.
Funding
Abstract
Colocation of the genes encoding ABC, TRAP, and TCT transport systems and catabolic pathways for the transported ligand provides a strategy for discovering novel microbial enzymes and pathways. We screened solute-binding proteins (SBPs) for ABC transport systems and identified three that bind D-apiose, a branched pentose in the cell walls of higher plants. Guided by sequence similarity networks (SSNs) and genome neighborhood networks (GNNs), the identities of the SBPs enabled the discovery of four catabolic pathways for D-apiose with eleven previously unknown reactions. The new enzymes include D-apionate oxidoisomerase, which catalyzes hydroxymethyl group migration, as well as 3-oxo-isoapionate-4-phosphate decarboxylase and 3-oxo-isoapionate-4-phosphate transcarboxylase/hydrolase, which are RuBisCO-like proteins (RLPs). The web tools for generating SSNs and GNNs are publicly accessible ( http://efi.igb.illinois.edu/efi-est/ ), so similar 'genomic enzymology' strategies for discovering novel pathways can be used by the community.
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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.