The NRF2-related interactome and regulome contain multifunctional proteins and fine-tuned autoregulatory loops

Abstract

NRF2 is a well-known, master transcription factor (TF) of oxidative and xenobiotic stress responses. Recent studies uncovered an even wider regulatory role of NRF2 influencing carcinogenesis, inflammation and neurodegeneration. Prompted by these advances here we present a systems-level resource for NRF2 interactome and regulome that includes 289 protein-protein, 7469 TF-DNA and 85 miRNA interactions. As systems-level examples of NRF2-related signaling we identified regulatory loops of NRF2 interacting proteins (e.g., JNK1 and CBP) and a fine-tuned regulatory system, where 35 TFs regulated by NRF2 influence 63 miRNAs that down-regulate NRF2. The presented network and the uncovered regulatory loops may facilitate the development of efficient, NRF2-based therapeutic agents.

Fig. 1.

Components and interaction types of the NRF2 interactome and regulome. (a) Structure of the database with the numbers of the components and the regulatory loops. Regulators of NRF2 are shown with blue color. Purple arrows highlight the number of those target genes that regulate NRF2 (termed as regulatory loops). (b) Venn-diagram of the source types used to build the NRF2 interactome. Numbers represent the number of NRF2 interactions/interactors from the given source type. The “imported databases” represent the following sources: BioGRID, MINT, IntACT, HPRD and Innate DB. “Predictions” represent both domain–motif and domain–domain interactions. The asterisk notes that from the 125 predicted interactions we found 13 already described in the literature (but not found during the manual curation step).

Fig. 2.

Manually curated network of NRF2. The high-density NRF2 interactome with interactions among NRF2 interactors. Activation links are shown in green, inhibitory links are shown in red color. Undirected interactions have gray color. Direct interactions are presented with solid lines, indirect interactions with dashed lines. See Fig. 4 for an enlarged subnetwork and Supplementary material 8 for a searchable network image.

Fig. 3.

Functional overlap in the NRF2 interactome. The 8 major Gene Ontology Biological Processes are shown among the NRF2 interactors. The numbers in the main diagonal represent the total number of the NRF2 interactors involved in the given function, while the numbers in the matrix represent the overlap between the given function. The colors of the cells illustrate the level of the overlap between the functional groups. Two functions, “immune system” and “reproduction” is highlighted with red as they are not among the NRF2 Gene Ontology terms (see Supplementary material 4. for the whole dataset and functional analysis).

Fig. 4.

Feedforward loops in the manually curated NRF2 interactome. The subnetwork of the HD NRF2 interactome containing only feedforward interaction loops. Activation links are shown with delta arrows, inhibitory links with T-arrows, while undirected interactions have no arrows. Direct interactions are presented with solid lines, indirect interaction with dashed lines. Note the 4 smaller loops marked with different colors on the left side of the image and the more complex intertwined motif-system with KEAP1 (orange) and NF-kB (green) on the right side, enlarged in colored boxes.

Fig. 5.

NRF2 regulatory loops. (a) The regulatory loop of NRF2 and JNK1. (b) The regulatory loops of NRF2 and CBP, where the NRF2 regulation is predicted. (c) The mutual regulatory loop between NRF2 and PPARγ.