Simultaneous cross-evaluation of heterogeneous <i>E. coli</i> datasets via mechanistic simulation
Derek N. Macklin, Travis A. Ahn-Horst, Heejo Choi, Nicholas A. Ruggero, Javier Carrera, J. C. Mason, Gwanggyu Sun, Eran Agmon, Mialy DeFelice, Inbal Maayan, Keara Lane, Ryan K. Spangler, Taryn E. Gillies, Morgan L Paull, Sajia Akhter, Samuel R. Bray, Daniel Weaver, Ingrid M. Keseler, Peter D. Karp, Jerry H. Morrison, Markus W. Covert
Abstract
enabled us to integrate and cross-evaluate a massive, heterogeneous dataset based on measurements reported by various groups over decades. We identified inconsistencies with functional consequences across the data, including that the total output of the ribosomes and RNA polymerases described by data are not sufficient for a cell to reproduce measured doubling times, that measured metabolic parameters are neither fully compatible with each other nor with overall growth, and that essential proteins are absent during the cell cycle-and the cell is robust to this absence. Finally, considering these data as a whole leads to successful predictions of new experimental outcomes, in this case protein half-lives.