Transcriptional repression of autophagy and lysosome biogenesis

Abstract

The microphthalmia/transcription factor E (MiT/TFE) family activates macroautophagy/autophagy and lysosomal genes during acute nutrient deficiency. However, the mechanisms that suppress transcription of these genes under steady-state, nutrient-rich conditions to prevent unnecessary expression remain unclear. In this study, we identified a previously unrecognized mechanism of transcriptional repression for autophagy and lysosomal genes. Under nutrient-rich conditions, USF2 (upstream transcription factor 2) binds to the coordinated lysosomal expression and regulation (CLEAR) motif, recruiting a repressive complex containing HDAC (histone deacetylase). In contrast, during nutrient deficiency, TFEB (transcription factor EB) displaces USF2 at the same motif, activating transcription. This switch is regulated by USF2 phosphorylation at serine 155 by GSK3B (glycogen synthase kinase 3 beta). Reduced phosphorylation under nutrient-deprived conditions weakens USF2's DNA binding affinity, allowing TFEB to competitively bind and activate target genes. Knockdown or knockout of Usf2 upregulates specific autophagy and lysosomal genes, leading to enhanced lysosomal functionality and increased autophagic flux. In USF2-deficient cells, the SERPINA1 Z variant/antitrypsin Z - an aggregation-prone mutant protein used as a model - is rapidly cleared via the autophagy-lysosome pathway. Therefore, modulation of USF2 activity may be a therapeutic strategy for managing diseases associated with autophagy and lysosomal dysfunction.Abbreviation: CLEAR: coordinated lysosomal expression and regulation; GSK3B: glycogen synthase kinase 3 beta; HDAC: histone deacetylase; MiT/TFE: microphthalmia/transcription factor E; NuRD: nucleosome remodeling and deacetylation; SERPINA1 Z variant/ATZ/antitrypsin Z; TFE3: transcription factor E3; TFEB: transcription factor EB; USF2: upstream transcription factor 2.

Keywords: Autophagy; MiT/TFE; TFEB; USF2; lysosome; transcriptional repressor.

Figure 1.

USF2-mediated transcriptional regulation of autophagy and lysosomal genes in response to nutrient availability. Under nutrient-rich conditions (left panel), USF2 binds to the CLEAR motif of autophagy and lysosomal gene promoters and recruits HDAC1, leading to histone H3K27 deacetylation. USF2 phosphorylation at S155 by GSK3B enhances its dna-binding affinity, reinforcing transcriptional suppression. TFEB undergoes continuous nucleocytoplasmic shuttling, with a small portion present in the nucleus, even under nutrient-rich conditions. However, USF2 acts as a gatekeeper, preventing TFEB from activating autophagy and lysosomal genes by occupying the CLEAR motif. This repression maintains a low transcriptional state, leading to the reduced expression of autophagy and lysosomal genes. Under nutrient-deprived conditions (right panel), decreased GSK3B activity, as evident by phosphorylation at S9, leads to reduced USF2 phosphorylation at S155, weakening its dna-binding affinity. Consequently, TFEB replaces USF2 at the CLEAR motif, facilitating histone H3K27 acetylation and the transcriptional activation of autophagy and lysosomal genes. This shift enhances autophagic flux and lysosomal biogenesis.