Name
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 B-6), 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. |
Year | DOI | Venue |
|---|---|---|
2016 | 10.1371/journal.pcbi.1004705 | PLOS COMPUTATIONAL BIOLOGY |
Field | DocType | Volume |
Sequence alignment,Pyridoxal,Enzyme,Gene,Biology,Metabolic pathway,Pyridoxal phosphate,Active site,Bioinformatics,Genetics,Enzyme promiscuity | Journal | 12 |
Issue | ISSN | Citations |
1 | 1553-734X | 0 |
PageRank | References | Authors |
0.34 | 6 | 11 |
Name | Order | Citations | PageRank |
|---|---|---|---|
| Matthew A Oberhardt | 1 | 74 | 5.55 |
| Raphy Zarecki | 2 | 1 | 0.72 |
| Leah Reshef | 3 | 1 | 0.72 |
| Fangfang Xia | 4 | 0 | 0.34 |
| Miquel Duran-Frigola | 5 | 5 | 1.38 |
| Rachel Schreiber | 6 | 0 | 0.34 |
| Christopher S Henry | 7 | 0 | 0.34 |
| Nir Ben-Tal | 8 | 474 | 42.20 |
| Daniel J Dwyer | 9 | 0 | 0.34 |
| Uri Gophna | 10 | 16 | 2.11 |
| Eytan Ruppin | 11 | 1954 | 173.51 |