A systems-level atlas of carbon-response transcriptional states in <i>Escherichia coli</i>.

Abstract

<i>Escherichia coli</i> encounters chemically diverse carbon sources, and the observed outputs of its transcriptional regulatory network (TRN) vary with substrate chemistry, metabolic entry route, and growth physiology. Here, we compiled PRECISE-NP881, an 881-condition transcriptome compendium comprising 346 RNA-seq profiles generated for this study during growth on 43 individual carbon sources, and used independent component analysis to quantify condition-specific activities of 137 iModulons, defined here as statistically independent gene-expression modules. We identified 25 carbon-catabolism iModulons and summarized their activity patterns across the 43 substrates into four activity-defined substrate groups. These activity patterns were associated with measured growth rates, substrate chemical classes, central-metabolic entry routes, carbon-normalized stoichiometric yield, and model-estimated proteome allocation. Faster-growing sugar conditions showed low CRP-linked iModulon activity, whereas slower-growing conditions showed elevated, condition-specific activity of CRP-linked and substrate-specific catabolic iModulons. TCA-entry and amino acid-associated conditions were linked with NtrC-1 and Propionate iModulon activities, with targeted knock-out assays supporting the conditional physiological relevance of selected propionyl-CoA-associated genes. A subset of nitrogen-containing, slower-growth conditions with predicted ammonium release induced the cryptic prophage-associated SgcABCEQX iModulon. Projection of an independent glucose starvation/refeeding time-course dataset revealed overlapping dynamics among selected carbon-catabolism iModulons and coordinated changes in growth- and stress-associated TRN outputs. Together, these results provide a systems-level atlas of observed carbon-responsive transcriptional states and systematize carbon physiology at scale.