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 Alan Gerlt

Research output: Contribution to journalArticle

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

Fingerprint

Methylmalonyl-CoA carboxytransferase
Carrier Proteins
Phosphates
Genome
Pentoses
Carboxy-Lyases
Hydrolases
Protein Transport
Enzymes
Cell Wall
Ligands
Genes
apiose
Proteins

ASJC Scopus subject areas

  • Molecular Biology
  • Cell Biology

Cite this

Carter, M. S., Zhang, X., Huang, H., Bouvier, J. T., Francisco, B. S., Vetting, M. W., ... 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

Functional assignment of multiple catabolic pathways for d-apiose article. / Carter, Michael S.; Zhang, Xinshuai; Huang, Hua; Bouvier, Jason T.; Francisco, Brian San; Vetting, Matthew W.; Al-Obaidi, Nawar; Bonanno, Jeffrey B.; Ghosh, Agnidipta; Zallot, Rémi G.; Andersen, Harvey M.; Almo, Steven C.; Gerlt, John Alan.

In: Nature chemical biology, Vol. 14, No. 7, 01.07.2018, p. 696-705.

Research output: Contribution to journalArticle

Carter, MS, Zhang, X, Huang, H, Bouvier, JT, Francisco, BS, Vetting, MW, Al-Obaidi, N, Bonanno, JB, Ghosh, A, Zallot, RG, Andersen, HM, Almo, SC & Gerlt, JA 2018, 'Functional assignment of multiple catabolic pathways for d-apiose article', Nature chemical biology, vol. 14, no. 7, pp. 696-705. https://doi.org/10.1038/s41589-018-0067-7
Carter MS, Zhang X, Huang H, Bouvier JT, Francisco BS, Vetting MW et al. Functional assignment of multiple catabolic pathways for d-apiose article. Nature chemical biology. 2018 Jul 1;14(7):696-705. https://doi.org/10.1038/s41589-018-0067-7
Carter, Michael S. ; Zhang, Xinshuai ; Huang, Hua ; Bouvier, Jason T. ; Francisco, Brian San ; Vetting, Matthew W. ; Al-Obaidi, Nawar ; Bonanno, Jeffrey B. ; Ghosh, Agnidipta ; Zallot, Rémi G. ; Andersen, Harvey M. ; Almo, Steven C. ; Gerlt, John Alan. / Functional assignment of multiple catabolic pathways for d-apiose article. In: Nature chemical biology. 2018 ; Vol. 14, No. 7. pp. 696-705.
@article{dbf3735bfd304566b5345060a50d338b,
title = "Functional assignment of multiple catabolic pathways for d-apiose article",
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.",
author = "Carter, {Michael S.} and Xinshuai Zhang and Hua Huang and Bouvier, {Jason T.} and Francisco, {Brian San} and Vetting, {Matthew W.} and Nawar Al-Obaidi and Bonanno, {Jeffrey B.} and Agnidipta Ghosh and Zallot, {R{\'e}mi G.} and Andersen, {Harvey M.} and Almo, {Steven C.} and Gerlt, {John Alan}",
year = "2018",
month = "7",
day = "1",
doi = "10.1038/s41589-018-0067-7",
language = "English (US)",
volume = "14",
pages = "696--705",
journal = "Nature Chemical Biology",
issn = "1552-4450",
publisher = "Nature Publishing Group",
number = "7",

}

TY - JOUR

T1 - Functional assignment of multiple catabolic pathways for d-apiose article

AU - Carter, Michael S.

AU - Zhang, Xinshuai

AU - Huang, Hua

AU - Bouvier, Jason T.

AU - Francisco, Brian San

AU - Vetting, Matthew W.

AU - Al-Obaidi, Nawar

AU - Bonanno, Jeffrey B.

AU - Ghosh, Agnidipta

AU - Zallot, Rémi G.

AU - Andersen, Harvey M.

AU - Almo, Steven C.

AU - Gerlt, John Alan

PY - 2018/7/1

Y1 - 2018/7/1

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=85047978021&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85047978021&partnerID=8YFLogxK

U2 - 10.1038/s41589-018-0067-7

DO - 10.1038/s41589-018-0067-7

M3 - Article

C2 - 29867142

AN - SCOPUS:85047978021

VL - 14

SP - 696

EP - 705

JO - Nature Chemical Biology

JF - Nature Chemical Biology

SN - 1552-4450

IS - 7

ER -