RT Journal Article
SR Electronic
T1 Revisiting Demand Rules for Gene Regulation
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 014142
DO 10.1101/014142
A1 Mahendra Kumar Prajapat
A1 Kirti Jain
A1 Debika Choudhury
A1 Gauri S. Choudhary
A1 Supreet Saini
YR 2015
UL http://biorxiv.org/content/early/2015/01/22/014142.abstract
AB Starting with Savageau’s pioneering work from 1970s, here, we choose the simplest transcription network and ask: How does the cell choose a regulatory topology from the different available possibilities? We study the natural distribution of topologies at genome, systems, and micro-level in E. coli and perform stochastic simulations to help explain the differences in natural distributions. Analyzing regulation of amino acid biosynthesis and carbon utilization in E. coli and B. subtilis, we observe many deviations from the demand rules, and observe an alternate pattern emerging. Overall, our results indicate that choice of topology is drawn randomly from a pool of all networks which satisfy the kinetic requirements of the cell, as dictated by physiology. In short, simply, the cell picks “whatever works”.