ATP-binding Cassette (ABC) Transport System Solute-binding Protein-guided Identification of Novel d-Altritol and Galactitol Catabolic Pathways in Agrobacterium tumefaciens C58

• Published in: The Journal of biological chemistry Vol. 290; no. 48; pp. 28963 - 28976
• Main Authors: Wichelecki, Daniel J., Vetting, Matthew W., Chou, Liyushang, Al-Obaidi, Nawar, Bouvier, Jason T., Almo, Steven C., Gerlt, John A.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 27.11.2015; American Society for Biochemistry and Molecular Biology
• Subjects: ABC transporter; Agrobacterium tumefaciens - genetics; Agrobacterium tumefaciens - metabolism; Agrobacterium tumefaciens C58; ATP-Binding Cassette Transporters - genetics; ATP-Binding Cassette Transporters - metabolism; Bacterial Proteins - genetics; Bacterial Proteins - metabolism; bioinformatics; carbohydrate metabolism; D-altritol catabolism; enzyme; Enzymology; Galactitol - genetics; Galactitol - metabolism; genome neighborhood networks; sequence similarity networks; Sugar Alcohols - metabolism; transcriptomics; enzyme; D-altritol catabolism; sequence similarity networks; carbohydrate metabolism; bioinformatics; transcriptomics; genome neighborhood networks; ABC transporter; Agrobacterium tumefaciens C58
• ISSN: 0021-9258; 1083-351X
• DOI: 10.1074/jbc.M115.686857

Innovations in the discovery of the functions of uncharacterized proteins/enzymes have become increasingly important as advances in sequencing technology flood protein databases with an exponentially growing number of open reading frames. This study documents one such innovation developed by the Enzyme Function Initiative (EFI; U54GM093342), the use of solute-binding proteins for transport systems to identify novel metabolic pathways. In a previous study, this strategy was applied to the tripartite ATP-independent periplasmic transporters. Here, we apply this strategy to the ATP-binding cassette transporters and report the discovery of novel catabolic pathways for d-altritol and galactitol in Agrobacterium tumefaciens C58. These efforts resulted in the description of three novel enzymatic reactions as follows: 1) oxidation of d-altritol to d-tagatose via a dehydrogenase in Pfam family PF00107, a previously unknown reaction; 2) phosphorylation of d-tagatose to d-tagatose 6-phosphate via a kinase in Pfam family PF00294, a previously orphan EC number; and 3) epimerization of d-tagatose 6-phosphate C-4 to d-fructose 6-phosphate via a member of Pfam family PF08013, another previously unknown reaction. The epimerization reaction catalyzed by a member of PF08013 is especially noteworthy, because the functions of members of PF08013 have been unknown. These discoveries were assisted by the following two synergistic bioinformatics web tools made available by the Enzyme Function Initiative: the EFI-Enzyme Similarity Tool and the EFI-Genome Neighborhood Tool. Background: Solute-binding proteins for ABC transport systems can be used to guide discovery of novel enzymes and metabolic pathways. Results: Novel metabolic pathways were discovered for d-altritol and galactitol catabolism. Conclusion: More than 2,000 proteins with previously unknown functions were annotated using this strategy. Significance: Strategies are described that can be used to address misannotation in protein databases.