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Theoretical investigation of a genetic switch for metabolic adaptation.

ABSTRACT: Membrane transporters carry key metabolites across the cell membrane and, from a resource standpoint, are hypothesized to be produced when necessary. The expression of membrane transporters in metabolic pathways is often upregulated by the transporter substrate. In E. coli, such systems include for example the lacY, araFGH, and xylFGH genes, which encode for lactose, arabinose, and xylose transporters, respectively. As a case study of a minimal system, we build a generalizable physical model of the xapABR genetic circuit, which features a regulatory feedback loop via membrane transport (positive feedback) and enzymatic degradation (negative feedback) of an inducer. Dynamical systems analysis and stochastic simulations show that the membrane transport makes the model system bistable in certain parameter regimes. Thus, it serves as a genetic "on-off" switch, enabling the cell to only produce a set of metabolic enzymes when the corresponding metabolite is present in large amounts. We find that the negative feedback from the degradation enzyme does not significantly disturb the positive feedback from the membrane transporter. We investigate hysteresis in the switching and discuss the role of cooperativity and multiple binding sites in the model circuit. Fundamentally, this work explores how a stable genetic switch for a set of enzymes is obtained from transcriptional auto-activation of a membrane transporter through its substrate.

SUBMITTER: Laxhuber KS

PROVIDER: S-EPMC7205307 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

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Theoretical investigation of a genetic switch for metabolic adaptation.

Laxhuber Kathrin S KS Morrison Muir J MJ Chure Griffin G Belliveau Nathan M NM Strandkvist Charlotte C Naughton Kyle L KL Phillips Rob R

PloS one 20200507 5

Membrane transporters carry key metabolites across the cell membrane and, from a resource standpoint, are hypothesized to be produced when necessary. The expression of membrane transporters in metabolic pathways is often upregulated by the transporter substrate. In E. coli, such systems include for example the lacY, araFGH, and xylFGH genes, which encode for lactose, arabinose, and xylose transporters, respectively. As a case study of a minimal system, we build a generalizable physical model of ...[more]

PMID: 32379825

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Project description:Hemianopic patients exhibit visual detection improvement in the blind field when audiovisual stimuli are given in spatiotemporally coincidence. Beyond this "online" multisensory improvement, there is evidence of long-lasting, "offline" effects induced by audiovisual training: patients show improved visual detection and orientation after they were trained to detect and saccade toward visual targets given in spatiotemporal proximity with auditory stimuli. These effects are ascribed to the Superior Colliculus (SC), which is spared in these patients and plays a pivotal role in audiovisual integration and oculomotor behavior. Recently, we developed a neural network model of audiovisual cortico-collicular loops, including interconnected areas representing the retina, striate and extrastriate visual cortices, auditory cortex, and SC. The network simulated unilateral V1 lesion with possible spared tissue and reproduced "online" effects. Here, we extend the previous network to shed light on circuits, plastic mechanisms, and synaptic reorganization that can mediate the training effects and functionally implement visual rehabilitation. The network is enriched by the oculomotor SC-brainstem route, and Hebbian mechanisms of synaptic plasticity, and is used to test different training paradigms (audiovisual/visual stimulation in eye-movements/fixed-eyes condition) on simulated patients. Results predict different training effects and associate them to synaptic changes in specific circuits. Thanks to the SC multisensory enhancement, the audiovisual training is able to effectively strengthen the retina-SC route, which in turn can foster reinforcement of the SC-brainstem route (this occurs only in eye-movements condition) and reinforcement of the SC-extrastriate route (this occurs in presence of survived V1 tissue, regardless of eye condition). The retina-SC-brainstem circuit may mediate compensatory effects: the model assumes that reinforcement of this circuit can translate visual stimuli into short-latency saccades, possibly moving the stimuli into visual detection regions. The retina-SC-extrastriate circuit is related to restitutive effects: visual stimuli can directly elicit visual detection with no need for eye movements. Model predictions and assumptions are critically discussed in view of existing behavioral and neurophysiological data, forecasting that other oculomotor compensatory mechanisms, beyond short-latency saccades, are likely involved, and stimulating future experimental and theoretical investigations.

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Theoretical investigation of a genetic switch for metabolic adaptation.

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Theoretical investigation of a genetic switch for metabolic adaptation.

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