title: Combinatorics of feedback in cellular uptake and metabolism of small molecules.
abstract: We analyze the connection between structure and function for regulatory motifs associated with cellular uptake and usage of small molecules. Based on the boolean logic of the feedback we suggest four classes: the socialist, consumer, fashion, and collector motifs. We find that the socialist motif is good for homeostasis of a useful but potentially poisonous molecule, whereas the consumer motif is optimal for nutrition molecules. Accordingly, examples of these motifs are found in, respectively, the iron homeostasis system in various organisms and in the uptake of sugar molecules in bacteria. The remaining two motifs have no obvious analogs in small molecule regulation, but we illustrate their behavior using analogies to fashion and obesity. These extreme motifs could inspire construction of synthetic systems that exhibit bistable, history-dependent states, and homeostasis of flux (rather than concentration).
authors: Department of Genetics, Eotvos Lorand University, Budapest H-1117, Hungary. sandeep@nbi.dk
authors: Sandeep
authors: S
authors: Krishna
authors: Szabolcs
authors: S
authors: Semsey
authors: Kim
authors: K
authors: Sneppen
mesh_terms: D020816:Amino Acid Motifs; D001671:Biochemistry / Q000379:methods*; D001692:Biological Transport; D002241:Carbohydrates / Q000493:pharmacokinetics; D004926:Escherichia coli / Q000378:metabolism; D025461:Feedback, Physiological; D015964:Gene Expression Regulation, Bacterial; D006706:Homeostasis; D053858:Metabolic Networks and Pathways; D008660:Metabolism; D008954:Models, Biological; D015233:Models, Statistical
chemical_list: D002241:Carbohydrates