%0 Journal Article
%T Systems-Wide Prediction of Enzyme Promiscuity Reveals a New Underground Alternative Route for Pyridoxal 5¡¯-Phosphate Production in E. coli
%A Matthew A. Oberhardt&nbsp
%A Raphy Zarecki&nbsp
%A Leah Reshef&nbsp
%A Fangfang Xia&nbsp
%A Miquel Duran-Frigola&nbsp
%A Rachel Schreiber&nbsp
%A Christopher S. Henry&nbsp
%A Nir Ben-Tal&nbsp
%A Daniel J. Dwyer&nbsp
%A Uri Gophna
%J PLOS Computational Biology
%D 2016
%I Public Library of Science (PLoS)
%R 10.1371/journal.pcbi.1004705
%X 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.
%U http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1004705