Substrate complex competition is a regulatory motif that allows NFκB RelA to license but not amplify NFκB RelB

Abstract

Significance Inflammation-responsive canonical NFκB induces many genes, two of which encode noncanonical NFκB pathway components that control developmental processes. This suggests potentially perilous cross-regulation by which inflammatory conditions could derail immune organ developmental decisions. We use mathematical modeling to propose a mechanism that functions as a brake on this connection. We report that the key enzyme mediating developmental NFκB is subject to competition from two forms of its single substrate. Termed substrate complex competition, this regulatory motif can lead to a counterintuitive decrease of signaling product in conditions of elevated substrate abundance. We propose that although noncanonical NFκB requires intact inflammatory NFκB signaling, substrate complex competition allows developmental signals to be reliably transduced without inappropriate amplification by inflammation. Signaling pathways often share molecular components, tying the activity of one pathway to the functioning of another. In the NFκB signaling system, distinct kinases mediate inflammatory and developmental signaling via RelA and RelB, respectively. Although the substrates of the developmental, so-called noncanonical, pathway are induced by inflammatory/canonical signaling, crosstalk is limited. Through dynamical systems modeling, we identified the underlying regulatory mechanism. We found that as the substrate of the noncanonical kinase NIK, the nfkb2 gene product p100, transitions from a monomer to a multimeric complex, it may compete with and inhibit p100 processing to the active p52. Although multimeric complexes of p100 (IκBδ) are known to inhibit preexisting RelA:p50 through sequestration, here we report that p100 complexes can inhibit the enzymatic formation of RelB:p52. We show that the dose–response systems properties of this complex substrate competition motif are poorly accounted for by standard Michaelis–Menten kinetics, but require more detailed mass action formulations. In sum, although tonic inflammatory signaling is required for adequate expression of the noncanonical pathway precursors, the substrate complex competition motif identified here can prevent amplification of the active RelB:p52 dimer in elevated inflammatory conditions to ensure reliable RelB-dependent developmental signaling independent of inflammatory context.