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).homeostasis ͉ network motif ͉ regulation ͉ sugar uptake F eedback and biological regulation are two sides of the same coin, reflecting the need of the living cell to deal with changing environments, to generate cell to cell heterogeneity and to optimize cellular metabolism to a given external condition (1-6). The interplay between function and design of regulatory systems is a key issue in understanding cellular processes, and for engineering artificial biological circuits (7,8). In a few relatively simple biological circuits, like the genetic switch in phage lambda (9), the connection between the regulatory logic and its biological function has been partially clarified. For larger scale regulatory networks, it has also been suggested that feed-forward motifs are associated with particular functions (10). However, feedback loops are, in fact, the most common network motifs in cellular organization, especially when one considers the regulation of small molecules (11), ranging from minerals to nutrients required for proper cellular function. A large class of cellular response systems are designed to regulate the flux and concentration of these molecules by controlling, via two feedback loops, the transport and metabolism pathways. Typically, these two loops are connected by a common transcriptional regulator that senses the concentration of the small molecule. In fact, almost half the transcription factors in Escherichia coli are directly regulated by a small molecule (12, 13).Here we investigate the possible logical structures of such entangled loops involving small molecules and explicate, for these network motifs, a direct connection between structure and function of molecular regulation. There are four distinct logical structures for two entangled feedback loops, shown in Fig. 1. Inspired by their functional behavior we label the first two the socialist and the consumer motifs. The former balances the influx (transport) and outflux (metabolism) preventing large variations in the concentration of the small molecule. The latter, in contrast, responds by maximizing both influx and outflux.The other two logical ...

Genome-scale reconstruction of the Lrp regulatory network in Escherichia coli

“…For example, the AA(ϩ/ϩ) loop motif indicates that the transcription of both transport and metabolic genes are activated, whereas the RR(Ϫ/Ϫ) motif demonstrates that the transcription of both genes are repressed. The possible logical structures of the feedback loop motifs can be characterized depending on how Lrp (or Lrp-leucine complex) activates or represses both T and E in response to the exogenous leucine: homeostasis (Ϫ/ϩ), nutrition (ϩ/ϩ), flow homeostasis (Ϫ/Ϫ), and accumulation (ϩ/Ϫ) (1). Based on the feedback loop motifs, we analyzed the behavior of logical structures of the transporters and metabolic enzymes in response to the exogenous leucine (Table S4).…”

“…In many cases, these 2 feedback loops are connected by a common transcription factor (TF) that senses the concentration of the small molecule (1). Little is known at present about the transition between the regulatory modes in the feedback loop motifs for global TFs in bacteria.…”

Timing of Gene Transcription in the Galactose Utilization System of Escherichia coli

“…If the system did not reduce the rate of galactose utilization when the galactose influx decreases, the cell would quickly use up the intracellular galactose pool, leading to switching off of promoters by reactivated GalR and GalS and therefore reduced galactose transport and utilization. This effect can be overcome by changing the relative strengths of the transport and metabolism feedback loops (1). Limiting GalK production is an efficient way to block the metabolic feedback loop without compromising transport, allowing accumulation of intracellular galactose.…”

“…Assay of ␤-Glucuronidase Activity-Cells were grown overnight in LB medium containing 100 g/ml Zeocin and diluted 1000-fold for further growth in M63 medium containing 10 g/ml Zeocin and supplemented with 0.4% (w/v) D-galactose, 0.1% (w/v) casamino acids (Sigma A2427), and 0.004% (w/v) vitamin B 1 . At various times, aliquots of cells were removed, diluted in 1 ml of LB medium to OD 600 ϭ 0.2, pelleted, resuspended in M63 medium containing 100 g/ml chloramphenicol, and stored at Ϫ70°C.…”

“…Transport and metabolism of several sugars are controlled via two feedback loops connected by a common regulator that senses the intracellular concentration of the small molecule (1,2). The simplest systems (e.g.…”