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Condition-dependent transcriptome reveals high-level regulatory architecture in
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Dr Olivier Delumeau
Professor Colin Harwood
Dr Georg Homuth
Dr Susanne Pohl
Nicolas P, Mäder U, Dervyn E, Rochat T, Leduc A, Pigeonneau N, Bidnenko E, Marchadier E, Hoebeke M, Aymerich S, Becher D, Bisicchia P, Botella E, Delumeau O, Doherty G, Denham EL, Fogg M, Fromion V, Goelzer A, Hansen A, Härtig E, Harwood CR, Homuth G, Jarmer H, Jules M, Klipp E, Le Chat L, Lecointe F, Lewis P, Liebemeister W, March A, Mars RAT, Nannapaneni P, Noone D, Pohl S, Rinn B, Rügheimer F, Sappa PK, Samson F, Schaffer M, Schwikowski B, Steil L, Stülke J, Wiegert T, Devine K, Wilkinson AJ, van Dijl JM, Hecker M, Völker U, Bessières P, Noirot P
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The adaptation of cells to environmental changes requires dynamic interactions between metabolic and regulatory networks, but studies typically address only one or a few layers of regulation. For nutritional shifts between two preferred carbon sources of
, we combined statistical and model-based data analyses of dynamic transcript, protein, and metabolite abundances and promoter activities. Adaptation to malate was rapid and primarily post-transcriptionally controlled compared to the slow, predominantly transcriptionally controlled adaptation to glucose that entailed nearly half of the known transcription regulation network. Interactions across multiple levels of regulation were involved in adaptive changes that could be achieved by controlling single genes. Our analysis suggests that global trade-offs or evolutionary constraints provide incentives to favor substantially more complex control programs.
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