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Functional assignment of multiple catabolic pathways for d-apiose

by Brian San Francisco , Bouvier, Jason T , Carter, Michael S , Andersen, Harvey M , Ghosh, Agnidipta , Vetting, Matthew W , Gerlt, John A , Zallot, Rémi G , Zhang, Xinshuai , Almo, Steven C , Al-Obaidi, Nawar , Bonanno, Jeffrey B , Huang, Hua

in Cell walls / Chemical reactions / Enzymes / Enzymology / Genomes / Hydrolase / Microorganisms / Neighborhoods / Nucleotide sequence / Pentose / Proteins / Ribulose-bisphosphate carboxylase / Transport

2018

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Functional assignment of multiple catabolic pathways for d-apiose

2018

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2018

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Journal Article

Functional assignment of multiple catabolic pathways for d-apiose

Brian San Francisco,

Bouvier, Jason T,

Carter, Michael S,

Andersen, Harvey M,

Ghosh, Agnidipta,

Vetting, Matthew W,

Gerlt, John A,

Zallot, Rémi G,

Zhang, Xinshuai,

Almo, Steven C,

Al-Obaidi, Nawar,

Bonanno, Jeffrey B,

Huang, Hua

2018

Overview

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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Publisher

Nature Publishing Group

Subject

/ Enzymes

/ Genomes