Functional assignment of multiple catabolic pathways for d-apiose article

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

Research output: Contribution to journalArticle

8 Scopus citations

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.

Original languageEnglish (US)
Pages (from-to)696-705
Number of pages10
JournalNature Chemical Biology
Volume14
Issue number7
DOIs
StatePublished - Jul 1 2018

ASJC Scopus subject areas

  • Molecular Biology
  • Cell Biology

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    Carter, M. S., Zhang, X., Huang, H., Bouvier, J. T., Francisco, B. S., Vetting, M. W., Al-Obaidi, N., Bonanno, J. B., Ghosh, A., Zallot, R. G., Andersen, H. M., Almo, S. C., & Gerlt, J. A. (2018). Functional assignment of multiple catabolic pathways for d-apiose article. Nature Chemical Biology, 14(7), 696-705. https://doi.org/10.1038/s41589-018-0067-7