8The metabolism of most organisms is controlled by a diverse cast of regulatory processes, including 9transcriptional regulation and post-translational modifications (PTMs). Yet how metabolic control is 10 distributed between these regulatory processes is unknown. Here we present Comparative Analysis of 11Regulators of Metabolism (CAROM), an approach that compares regulators based on network 12 connectivity, flux, and essentiality of their reaction targets. Using CAROM, we analyze transcriptome, 13proteome, acetylome and phospho-proteome dynamics during transition to stationary phase in E. coli 14 and S. cerevisiae. CAROM uncovered that the targets of each regulatory process shared unique 15 metabolic properties: growth-limiting reactions were regulated by acetylation, while isozymes and futile-16 cycles were preferentially regulated by phosphorylation. Reversibility, essentiality, and molecular-17weight further distinguished reactions controlled through diverse mechanisms. While every enzyme can 18 be potentially regulated by multiple mechanisms, analysis of context-specific datasets reveals a 19 conserved partitioning of metabolic regulation based on reaction attributes.
20Author summary
21There are several ways to regulate an enzyme's activity in a cell. Yet, the design principles that 22determine when an enzyme is regulated by transcription, translation or post-translational modifications 23 are unknown. Each control mechanism, such as transcription, comprises several regulators that control 24 a distinct set of targets. So far, it is unclear if similar partitioning of targets occurs at a higher level, 25between different control mechanisms. Here we systematically analyze patterns of metabolic regulation 26 in model microbes. We find that five key parameters can distinguish the targets of each mechanism. 27These key parameters provide insights on specific roles played by each mechanism in determining 28 overall metabolic activity. This approach may help define the basic regulatory architecture of metabolic 29 networks.
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