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 PSIBLAST 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 successfulmore »
- Authors:
-
- 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
- Publication Date:
- Research Org.:
- Argonne National Laboratory (ANL), Argonne, IL (United States)
- Sponsoring Org.:
- USDOE; European Union (EU)
- OSTI Identifier:
- 1258643
- Alternate Identifier(s):
- OSTI ID: 1393162
- Grant/Contract Number:
- AC02-06CH11357
- Resource Type:
- Accepted Manuscript
- Journal Name:
- PLoS Computational Biology (Online)
- Additional Journal Information:
- Journal Name: PLoS Computational Biology (Online); Journal Volume: 12; Journal Issue: 1; Journal ID: ISSN 1553-7358
- Publisher:
- Public Library of Science
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 60 APPLIED LIFE SCIENCES
Citation Formats
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, and Ruppin, Eytan. Systems-Wide Prediction of Enzyme Promiscuity Reveals a New Underground Alternative Route for Pyridoxal 5’-Phosphate Production in E. coli. United States: N. p., 2016.
Web. doi:10.1371/journal.pcbi.1004705.
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. United States. https://doi.org/10.1371/journal.pcbi.1004705
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, and Ruppin, Eytan. Thu .
"Systems-Wide Prediction of Enzyme Promiscuity Reveals a New Underground Alternative Route for Pyridoxal 5’-Phosphate Production in E. coli". United States. https://doi.org/10.1371/journal.pcbi.1004705. https://www.osti.gov/servlets/purl/1258643.
@article{osti_1258643,
title = {Systems-Wide Prediction of Enzyme Promiscuity Reveals a New Underground Alternative Route for Pyridoxal 5’-Phosphate Production in E. coli},
author = {Oberhardt, Matthew A. and Zarecki, Raphy and Reshef, Leah and Xia, Fangfang and Duran-Frigola, Miquel and Schreiber, Rachel and Henry, Christopher S. and Ben-Tal, Nir and Dwyer, Daniel J. and Gophna, Uri and Ruppin, Eytan},
abstractNote = {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 PSIBLAST 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.},
doi = {10.1371/journal.pcbi.1004705},
journal = {PLoS Computational Biology (Online)},
number = 1,
volume = 12,
place = {United States},
year = {Thu Jan 28 00:00:00 EST 2016},
month = {Thu Jan 28 00:00:00 EST 2016}
}
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Works referencing / citing this record:
Current status and applications of genome-scale metabolic models
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A Survey of Pyridoxal 5′-Phosphate-Dependent Proteins in the Gram-Positive Model Bacterium Bacillus subtilis
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