title: Prediction and characterization of enzymatic activities guided by sequence similarity and genome neighborhood networks.
abstract: Metabolic pathways in eubacteria and archaea often are encoded by operons and/or gene clusters (genome neighborhoods) that provide important clues for assignment of both enzyme functions and metabolic pathways. We describe a bioinformatic approach (genome neighborhood network; GNN) that enables large scale prediction of the in vitro enzymatic activities and in vivo physiological functions (metabolic pathways) of uncharacterized enzymes in protein families. We demonstrate the utility of the GNN approach by predicting in vitro activities and in vivo functions in the proline racemase superfamily (PRS; InterPro IPR008794). The predictions were verified by measuring in vitro activities for 51 proteins in 12 families in the PRS that represent ∼85% of the sequences; in vitro activities of pathway enzymes, carbon/nitrogen source phenotypes, and/or transcriptomic studies confirmed the predicted pathways. The synergistic use of sequence similarity networks3 and GNNs will facilitate the discovery of the components of novel, uncharacterized metabolic pathways in sequenced genomes.
authors: Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, United States.
authors: Suwen
authors: S
authors: Zhao
authors: Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, United States.
authors: Ayano
authors: A
authors: Sakai
authors: Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, United States.
authors: Xinshuai
authors: X
authors: Zhang
authors: Department of Biochemistry, Albert Einstein College of Medicine, New York, United States.
authors: Matthew W
authors: MW
authors: Vetting
authors: Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, United States.
authors: Ritesh
authors: R
authors: Kumar
authors: Department of Biochemistry, Albert Einstein College of Medicine, New York, United States.
authors: Brandan
authors: B
authors: Hillerich
authors: Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, United States.
authors: Brian
authors: B
authors: San Francisco
authors: Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, United States.
authors: Jose
authors: J
authors: Solbiati
authors: Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, United States.
authors: Adam
authors: A
authors: Steves
authors: Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, United States.
authors: Shoshana
authors: S
authors: Brown
authors: Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, United States.
authors: Eyal
authors: E
authors: Akiva
authors: Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, United States.
authors: Alan
authors: A
authors: Barber
authors: Department of Biochemistry, Albert Einstein College of Medicine, New York, United States.
authors: Ronald D
authors: RD
authors: Seidel
authors: Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, United States.
authors: Patricia C
authors: PC
authors: Babbitt
authors: Department of Biochemistry, Albert Einstein College of Medicine, New York, United States.
authors: Steven C
authors: SC
authors: Almo
authors: Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, United States.
authors: John A
authors: JA
authors: Gerlt
authors: Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, United States.
authors: Matthew P
authors: MP
authors: Jacobson
mesh_terms: D000465:Algorithms; D000591:Amino Acid Isomerases / Q000737:chemistry*; D019295:Computational Biology / Q000379:methods*; D018360:Crystallography, X-Ray; D016680:Genome, Bacterial; D009682:Magnetic Resonance Spectroscopy; D013058:Mass Spectrometry; D053858:Metabolic Networks and Pathways; D008968:Molecular Conformation; D008969:Molecular Sequence Data; D005810:Multigene Family; D010957:Plasmids / Q000378:metabolism; D012313:RNA / Q000737:chemistry; D021241:Spectrometry, Mass, Electrospray Ionization; D014158:Transcription, Genetic
chemical_list: D012313:RNA; D000591:Amino Acid Isomerases; C022451:proline racemase
keywords: biochemistry; functional assignment; genome neighborhood network; sequence similarity network