Search bioRxiv⌕ Search

bioRxiv · 10.1101/2025.11.09.687434

Flux organizations and control modes in antagonistically combined negative feedback loops

Abstract

The purpose of this paper is to show the different compensatory responses and control models towards environmental perturbations when two antagonistic integral controllers are combined at the level of the controlled variable. Dependent on the controllers relative setpoints two types of compensatory flux regulations occur, which have been termed delegated and isolated control. In delegated control one of the feedbacks submits its entire compensatory flux to the system, while the other feedback is the actual controller by neutralizing the excess flux of its antagonistic partner. In isolated control the compensatory flux of one of the controllers is negligible while the other feedback regulates the controlled variable alone. One of the findings is that these interacting feedbacks can exhibit environmentally driven setpoint changes known as rheostasis. A striking example is the photoperiodic control of Siberian hamsters body weights, which can be rationalized by the interacting feedbacks between circadian morning (M) and evening (E) oscillators. A third control type is metastable control. Here, additions or removals of the controller variable can cause a switch to the antagonistic partners control regime, but resets to its original control mode once additions or removals stop. Integral windup can induce temporary metastable setpoint changes or even lead to robust perfect adaptation without integral feedback! How the setpoint in blood glucose homeostasis arises is still debated. A dual-controller approach with two setpoints can describe many properties of blood glucose homeostasis and the roles of insulin, glucagon, and somatostatin. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=183 SRC="FIGDIR/small/687434v2_ufig1.gif" ALT="Figure 1"> View larger version (46K): org.highwire.dtl.DTLVardef@1f984b9org.highwire.dtl.DTLVardef@78c409org.highwire.dtl.DTLVardef@8e6ab6org.highwire.dtl.DTLVardef@233_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIA set of 16 inflow/outflow controllers (negative feedbacks) combined by a common controlled variable have been studied. C_LIO_LIDependent on the relationship between the inflow/outflow controllers setpoints two distinct regulatory modes termed delegated control and isolated control have been identified. C_LIO_LIRegions of control and their extensions are visualized by a perturbation phase diagram. C_LIO_LIMetastable control may temporarily occur when one of the controller variables are environmentally increased or decreased. C_LIO_LIRobust perfect or near-perfect adaptation may occur even in the absence of integral feedback. C_LIO_LIThe combined controllers can show homeostatic as well as rheostatic behaviors. A striking biological example of rheostasis is found in the photoperiodic regulation of the Siberian hamsters body weight. C_LIO_LIThe origin of the glycemic setpoint in blood glucose homeostasis is still debated. A glucagon- and insulin-based two-setpoint model suggests that in diabetic individuals the upper insulin-dependent setpoint increases with decreasing insulin generation rates. This setpoint is defended irrespective of its value, but the accuracy of regulation depends how tightly the insulin degrading enzyme (IDE, insulysin) binds to insulin. In addition, both glucagon- and insulin-based setpoints depend (rheostatically) on the level of somatostatin. C_LI

Source connections

Explore related subjects

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Ruoff, H. P.. 2025-11-10. Flux organizations and control modes in antagonistically combined negative feedback loops. https://doi.org/10.1101/2025.11.09.687434

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

Deep reinforcement learning-driven discovery of a MsbA-targeted small-molecule antibiotic for the treatment of Acinetobacter baumannii infection

Antibiotics with new mechanisms are highly pursued to address the threat of infections caused by drug-resistant Gram-negative bacteria. Targeting MsbA, a key protein of the lipopolysaccharide biosynthesis pathway, represents a promising strategy to discover new classes of antibiotics. However, currently available MsbA-targeted molecules either lack sufficient potency or have unfavorable properties, necessitating expansion of chemical space. In this study, we chose the most promising cerastecin Cpd 4 as the template, and used two Artificial Intelligence (AI)-based tools, i.e. Link-INVENT and AutoMolDesigner for molecular design, performed chemical derivatization and antibacterial activity evaluation, which led to the discovery of Y-11 (MIC for A. baumannii: 0.5 g/mL). Encouragingly, Y-11 showed equivalent potency to Cpd4 for carbapenem-resistant A. baumannii, and less cytotoxicity and hemolysis as well as lower spontaneous resistance frequency. In vivo efficacy study demonstrated that Y-11 could effectively reduce bacterial loads in the mice infected by A. baumannii. The following mechanism study including molecular dynamics simulation, biochemical assay, and transmission electron microscope (TEM) analysis suggested that Y-11 inhibited the transport of lipooligosaccharide and impaired the formation of outer membrane, probably by competitively binding to the substrate binding site of MsbA and modulating ATPase activity. Taken together, we have discovered a MsbA-targeted small molecule Y-11 via AI-driven drug design, which provides a foundation for future antibiotic development.

biochemistry↗

Dynamic architecture of the Rixosome reveals mechanism of activation and ITS2 processing

Eukaryotic ribosome assembly requires the coordinated processing and extensive remodeling of pre-rRNAs. During late nuclear maturation of the 60S subunit, sequential removal of the internal transcribed spacer 2 (ITS2) is initiated by endonucleolytic cleavage at site C2 by the conserved Las1 nuclease. Las1 acts together with the kinase Grc3 and the Rix1 complex to form the Rixosome, which also functions in transcriptional regulation. However, the assembly of the Rixosome, its recruitment to pre-ribosomes, and its activation for ITS2 cleavage remain unclear. Here, we present cryo-EM structures of the human LAS1 complex, two structures of the isolated Rixosome and nine transition states of Rix1-bound pre-60S particles from Schizosaccharomyces pombe. These structures reveal a dynamic Rixosome architecture in which the heterotetrameric Las1 complex engages one or two copies of the Rix1 complex. Rix1 binding is highly flexible in the human Rixosome but rigid in the yeast complex. The isolated yeast Rixosome remains inactive, but binding to the pre-60S particle triggers a structural rearrangement that allows for substrate engagement and activation of the nuclease. Together, our results define the dynamic architecture of the Rixosome and provide a structural framework for ITS2 processing during nuclear maturation of the eukaryotic 60S ribosomal subunit.

biochemistry↗

SGFP-Grid Split GFP Graphene Grids

Affinity graphene grids provide a promising approach for selective protein capture in cryo-EM. Here, we introduce a split-GFP graphene grid platform(SGFP-G), in which graphene-conjugated GFP 1-10 selectively captures GFP11 tagged proteins from low concentration samples or cell lysates. This platform enables rapid assessment of target protein enrichment and particle distribution before vitrification via fluorescence imaging, while the grid design positions captured proteins away from the graphene surface and air-water interface. We also introduce a unique strategy to minimize nonspecific protein adsorption, thereby improving the selective enrichment of target proteins on this grid. Using GFP11-tagged apoferritin, we demonstrate fluorescence guided protein capture and obtain a 2.58 [A] cryoEM reconstruction, establishing SGFP-G as an affinity grid platform for high resolution structural studies with reduced sample requirements.

biochemistry↗