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

doi:10.1371/journal.pcbi.1004705

Title: Systems-Wide Prediction of Enzyme Promiscuity Reveals a New Underground Alternative Route for Pyridoxal 5’-Phosphate Production in E. coli

Journal Article · 28 January 2016 · PLoS Computational Biology (Online)

DOI: https://doi.org/10.1371/journal.pcbi.1004705 · OSTI ID:1258643

Oberhardt, Matthew A. ^[1]; Zarecki, Raphy ^[2]; Reshef, Leah ^[3]; Xia, Fangfang ^[4]; Duran-Frigola, Miquel ^[5]; Schreiber, Rachel ^[2]; Henry, Christopher S. ^[4]; Ben-Tal, Nir ^[2]; Dwyer, Daniel J. ^[6]; Gophna, Uri ^[2]; Ruppin, Eytan ^[1]

Tel Aviv Univ., Tel Aviv (Israel); Univ. of Maryland, College Park, MD (United States)
Tel Aviv Univ., Tel Aviv (Israel)
Univ. of Maryland, College Park, MD (United States)
Argonne National Lab. (ANL), Argonne, IL (United States)
Inst. for Research in Biomedicine (IRB), Barcelona (Spain)
Univ. of Maryland, College Park, MD (United States). Maryland Pathogen Research Institute

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. Here, 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.

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Research Organization:: Argonne National Laboratory (ANL), Argonne, IL (United States)

Sponsoring Organization:: USDOE; European Union (EU)

Grant/Contract Number:: AC02-06CH11357

OSTI ID:: 1258643

Alternate ID(s):: OSTI ID: 1393162

Journal Information:: PLoS Computational Biology (Online), Vol. 12, Issue 1; ISSN 1553-7358

Publisher:: Public Library of ScienceCopyright Statement

Country of Publication:: United States

Language:: English

Citation Metrics:

Cited by: 15 works

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Multicopy Suppression Underpins Metabolic Evolvability Patrick, W. M.; Quandt, E. M.; Swartzlander, D. B. Molecular Biology and Evolution, Vol. 24, Issue 12 https://doi.org/10.1093/molbev/msm204	journal	June 2007
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SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information Biasini, Marco; Bienert, Stefan; Waterhouse, Andrew Nucleic Acids Research, Vol. 42, Issue W1 https://doi.org/10.1093/nar/gku340	journal	April 2014
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A retrosynthetic biology approach to metabolic pathway design for therapeutic production Carbonell, Pablo; Planson, Anne-Gaëlle; Fichera, Davide BMC Systems Biology, Vol. 5, Issue 1 https://doi.org/10.1186/1752-0509-5-122	journal	January 2011

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A Survey of Pyridoxal 5′-Phosphate-Dependent Proteins in the Gram-Positive Model Bacterium Bacillus subtilis Richts, Björn; Rosenberg, Jonathan; Commichau, Fabian M. Frontiers in Molecular Biosciences, Vol. 6 https://doi.org/10.3389/fmolb.2019.00032	journal	May 2019
Current status and applications of genome-scale metabolic models Gu, Changdai; Kim, Gi Bae; Kim, Won Jun Genome Biology, Vol. 20, Issue 1 https://doi.org/10.1186/s13059-019-1730-3	journal	June 2019

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