Publications

• A general strategy for the discovery of metabolic pathways: D-threitol, L-threitol, and erythritol utilization in Mycobacterium smegmatis.

  Huang H., Carter M.S., Vetting M.W., Al-Obaidi N., Patskovsky Y., Almo S.C., Gerlt J.A.

  We describe a general integrated bioinformatic and experimental strategy to discover the in vitro enzymatic activities and in vivo functions (metabolic pathways) of uncharacterized enzymes discovered in microbial genome projects using the ligand specificities of the solute binding proteins (SBPs) ... >> More

  We describe a general integrated bioinformatic and experimental strategy to discover the in vitro enzymatic activities and in vivo functions (metabolic pathways) of uncharacterized enzymes discovered in microbial genome projects using the ligand specificities of the solute binding proteins (SBPs) for ABC transporters. Using differential scanning fluorimetry, we determined that the SBP for an ABC transporter encoded by the genome of Mycobacterium smegmatis is stabilized by d-threitol. Using sequence similarity networks and genome neighborhood networks to guide selection of target proteins for pathway enzymes, we applied both in vitro and in vivo experimental approaches to discover novel pathways for catabolism of d-threitol, l-threitol, and erythritol. << Less

  J. Am. Chem. Soc. 137:14570-14573(2015) [PubMed] [EuropePMC]

  This publication is cited by 5 other entries.

• Functional assignment of multiple catabolic pathways for D-apiose.

  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.

  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-ap ... >> More

  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. << Less

  Nat. Chem. Biol. 14:696-705(2018) [PubMed] [EuropePMC]

  This publication is cited by 13 other entries.

• Correction to 'A general strategy for the discovery of metabolic pathways: D-threitol, L-threitol, and erythritol utilization in Mycobacterium smegmatis'.

  Huang H., Carter M.S., Vetting M.W., Al-Obaidi N., Patskovsky Y., Almo S.C., Gerlt J.A.

  J. Am. Chem. Soc. 138:4267-4267(2016) [PubMed] [EuropePMC]