title: Systems-Wide Prediction of Enzyme Promiscuity Reveals a New Underground Alternative Route for Pyridoxal 5'-Phosphate Production in E. coli.
abstract: Recent insights suggest that non-specific and/or promiscuous enzymes are common and active across life. Understanding the role of such enzymes is an important open question in biology. Here we develop a genome-wide method, PROPER, that uses a permissive PSI-BLAST approach to predict promiscuous activities of metabolic genes. Enzyme promiscuity is typically studied experimentally using multicopy suppression, in which over-expression of a promiscuous 'replacer' gene rescues lethality caused by inactivation of a 'target' gene. We use PROPER to predict multicopy suppression in Escherichia coli, achieving highly significant overlap with published cases (hypergeometric p = 4.4e-13). We then validate three novel predicted target-replacer gene pairs in new multicopy suppression experiments. We next go beyond PROPER and develop a network-based approach, GEM-PROPER, that integrates PROPER with genome-scale metabolic modeling to predict promiscuous replacements via alternative metabolic pathways. GEM-PROPER predicts a new indirect replacer (thiG) for an essential enzyme (pdxB) in production of pyridoxal 5'-phosphate (the active form of Vitamin B6), which we validate experimentally via multicopy suppression. We perform a structural analysis of thiG to determine its potential promiscuous active site, which we validate experimentally by inactivating the pertaining residues and showing a loss of replacer activity. Thus, this study is a successful example where a computational investigation leads to a network-based identification of an indirect promiscuous replacement of a key metabolic enzyme, which would have been extremely difficult to identify directly.
authors.affiliation: School of Computer Sciences and Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel.|Department of Molecular Microbiology and Biotechnology, Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel.|Center for Bioinformatics and Computational Biology, Department of Computer Science, University of Maryland, College Park, Maryland, United States of America.
authors.forename: Matthew A
authors.initials: MA
authors.lastname: Oberhardt
authors.affiliation: School of Computer Sciences and Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel.
authors.forename: Raphy
authors.initials: R
authors.lastname: Zarecki
authors.affiliation: Department of Molecular Microbiology and Biotechnology, Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel.
authors.forename: Leah
authors.initials: L
authors.lastname: Reshef
authors.affiliation: Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, United States of America.
authors.forename: Fangfang
authors.initials: F
authors.lastname: Xia
authors.affiliation: Joint IRB-BSC-CRG Program in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), Barcelona, Spain.
authors.forename: Miquel
authors.initials: M
authors.lastname: Duran-Frigola
authors.affiliation: Department of Molecular Microbiology and Biotechnology, Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel.
authors.forename: Rachel
authors.initials: R
authors.lastname: Schreiber
authors.affiliation: Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, United States of America.
authors.forename: Christopher S
authors.initials: CS
authors.lastname: Henry
authors.affiliation: Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel.
authors.forename: Nir
authors.initials: N
authors.lastname: Ben-Tal
authors.affiliation: Department of Cell Biology and Molecular Genetics, Institute for Physical Science and Technology, Department of Bioengineering, Maryland Pathogen Research Institute, University of Maryland, College Park, Maryland, United States of America.
authors.forename: Daniel J
authors.initials: DJ
authors.lastname: Dwyer
authors.affiliation: Department of Molecular Microbiology and Biotechnology, Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel.
authors.forename: Uri
authors.initials: U
authors.lastname: Gophna
authors.affiliation: School of Computer Sciences and Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel.|Center for Bioinformatics and Computational Biology, Department of Computer Science, University of Maryland, College Park, Maryland, United States of America.
authors.forename: Eytan
authors.initials: E
authors.lastname: Ruppin
mesh_terms: D002237:Carbohydrate Dehydrogenases / Q000235:genetics / Q000378:metabolism; D019295:Computational Biology / Q000379:methods*; D004926:Escherichia coli / Q000201:enzymology* / Q000235:genetics / Q000378:metabolism*; D029968:Escherichia coli Proteins / Q000235:genetics / Q000378:metabolism; D008958:Models, Molecular; D011732:Pyridoxal Phosphate / Q000378:metabolism*
chemical_list: D029968:Escherichia coli Proteins; C450942:ThiG protein, E coli; D011732:Pyridoxal Phosphate; D002237:Carbohydrate Dehydrogenases; C061651:pdxB protein, E coli
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