Systems-wide prediction of enzyme promiscuity reveals a new underground alternative route for pyridoxal 5'-phosphate production in E. coli

Oberhardt, Matthew A.; Zarecki, Raphy; Reshef, Leah; Xia, Fangfang; Duran Frigola, Miquel; Schreiber, Rachel; Henry, Christopher S.; Ben-Tal, Nir; Dwyer, Daniel J.; Gophna, Uri; Ruppin, Eytan

Systems-wide prediction of enzyme promiscuity reveals a new underground alternative route for pyridoxal 5'-phosphate production in E. coli

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dc.contributor.author Oberhardt, Matthew A.ca
dc.contributor.author Zarecki, Raphyca
dc.contributor.author Reshef, Leahca
dc.contributor.author Xia, Fangfangca
dc.contributor.author Duran Frigola, Miquelca
dc.contributor.author Schreiber, Rachelca
dc.contributor.author Henry, Christopher S.ca
dc.contributor.author Ben-Tal, Nirca
dc.contributor.author Dwyer, Daniel J.ca
dc.contributor.author Gophna, Urica
dc.contributor.author Ruppin, Eytanca
dc.date.accessioned 2016-06-06T13:47:01Z
dc.date.available 2016-06-06T13:47:01Z
dc.date.issued 2016
dc.description.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.ca
dc.description.sponsorship Funding agencies: (MO) Whitaker Foundation (Whitaker International Scholars Program) (http://www.whitaker.org/grants/fellows-scholars) (MO) Dan David Fellowship (http://www.dandavidprize.org/scholarship-applications) (ER) European Union FP7 INFECT project (http://www.fp7infect.eu/) ERA-Net Plant project (http://www.erapg.org/publicpage.m?key=everyone&trail=/everyone) (ER) I-CORE Program of the Planning and Budgeting Committee and The Israel Science Foundation (grant No 41/11) (www.i-core.org.il/ISF) (UG) McDonnell foundation (https://www.jsmf.org/) (UG) German-Israeli Project Cooperation (DIP) (http://www.dfg.de/en/research_funding/programmes/international_cooperation/german_israeli_cooperation/) (MD) Spanish FPU grant (http://cepima.upc.edu/positions/FPU_2013) (MD) FEBS short term fellowship (http://www.febs.org/our-activities/fellowships/febs-short-term-fellowships/guidelines-for-febs-short-term-fellowships) (NBT) Grant No. 1775/12 of the I-CORE Program of the Planning and Budgeting Committee and The Israel Science Foundation
dc.format.mimetype application/pdfca
dc.identifier.citation Oberhardt MA, Zarecki R, Reshef L, Xia F, Duran-Frigola M, Schreiber R et al. Systems-wide prediction of enzyme promiscuity reveals a new underground alternative route for pyridoxal 5'-phosphate production in E. coli. PLoS computational biology. 2016; 12(1): e1004705. DOI 10.1371/journal.pcbi.1004705ca
dc.identifier.doi http://dx.doi.org/10.1371/journal.pcbi.1004705
dc.identifier.issn 1553-734X
dc.identifier.uri http://hdl.handle.net/10230/26855
dc.language.iso engca
dc.publisher Public Library of Science (PLoS)ca
dc.relation.ispartof PLoS computational biology. 2016; 12(1): e1004705
dc.rights This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the/nCreative Commons CC0 public domain dedicationca
dc.rights.accessRights info:eu-repo/semantics/openAccessca
dc.rights.uri https://creativecommons.org/publicdomain/zero/1.0/ca
dc.subject.other Enzimsca
dc.subject.other Filogeniaca
dc.title Systems-wide prediction of enzyme promiscuity reveals a new underground alternative route for pyridoxal 5'-phosphate production in E. colica
dc.type info:eu-repo/semantics/articleca
dc.type.version info:eu-repo/semantics/publishedVersionca

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