Reference - Detail
| RRC ID | 53746 |
|---|---|
| Author | Oberhardt MA, Zarecki R, Reshef L, Xia F, Duran-Frigola M, Schreiber R, Henry CS, Ben-Tal N, Dwyer DJ, Gophna U, Ruppin E. |
| Title | Systems-Wide Prediction of Enzyme Promiscuity Reveals a New Underground Alternative Route for Pyridoxal 5'-Phosphate Production in E. coli. |
| Journal | PLoS Comput Biol |
| 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. |
| Volume | 12(1) |
| Pages | e1004705 |
| Published | 2016-1-1 |
| DOI | 10.1371/journal.pcbi.1004705 |
| PII | PCOMPBIOL-D-15-00971 |
| PMID | 26821166 |
| PMC | PMC4731195 |
| MeSH | Carbohydrate Dehydrogenases / genetics Carbohydrate Dehydrogenases / metabolism Computational Biology / methods* Escherichia coli / enzymology* Escherichia coli / genetics Escherichia coli / metabolism* Escherichia coli Proteins / genetics Escherichia coli Proteins / metabolism Models, Molecular Pyridoxal Phosphate / metabolism* |
| IF | 4.7 |
| Times Cited | 11 |
| Altmetric score |
オルトメトリクス指標項目
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| The most frequently cited source | X(Twitter) |
| Total number of mentions | 2 |
| Altmetric score changes over past 6months | 0.0 |
| Resource | |
| Prokaryotes E. coli | |