read_status: annotated
type: paper
title: Riboregulation of Enolase 1 activity controls glycolysis and embryonic stem cell differentiation
year: 2022
authors:
- Huppertz, Ina
- Perez-Perri, Joel I.
- Mantas, Panagiotis
- Sekaran, Thileepan
- Schwarzl, Thomas
- Russo, Francesco
- Ferring-Appel, Dunja
- Koskova, Zuzana
- Dimitrova-Paternoga, Lyudmila
- Kafkia, Eleni
- Hennig, Janosch
- Neveu, Pierre A.
- Patil, Kiran
- Hentze, Matthias W.
journal: Molecular Cell
doi: 10.1016/j.molcel.2022.05.019
url: https://linkinghub.elsevier.com/retrieve/pii/S1097276522004865
project:
- IGP
system:
- glycolysis
- cellular_metabolism
- embryonic_stem_cells
disease:
- stem_cell_differentiation
genes:
- eno1
- sirt2
processes:
- rna_binding
- enzymatic_inhibition
- metabolic_rewiring
- protein_acetylation
methods:
- eclip
- rna_immunoprecipitation
- enzymatic_activity_assay
- stable_isotope_tracing
- proximity_ligation_assay
key_findings:
- rna_inhibits_enzyme_activity
- acetylation_enhances_rna_binding
- rna_binding_controls_glycolysis
- metabolic_state_controls_differentiation
limitations:
- structural_basis_undefined
- enzyme_specificity_unknown
- broader_metabolic_scope_unresolved
relevance:
- conceptual_shift_in_metabolic_control
- mechanism_linking_metabolism_and_fate
- regulatory_layer_beyond_transcription
concepts:
- Riboregulation_of_Metabolic_Enzymes
- RNA_Mediated_Enzyme_Inhibition
- Metabolic_Control_of_Cell_Fate
tags:
- metabolism
- rna_binding_proteins
- stem_cells
Differentiating stem cells must coordinate their metabolism and fate trajectories. Here, we report that the catalytic activity of the glycolytic enzyme Enolase 1 (ENO1) is directly regulated by RNAs leading to metabolic rewiring in mouse embryonic stem cells (mESCs). We identify RNA ligands that specifically inhibit ENO1’s enzymatic activity in vitro and diminish glycolysis in cultured human cells and mESCs. Pharmacological inhibition or RNAi-mediated depletion of the protein deacetylase SIRT2 increases ENO1’s acetylation and enhances its RNA binding. Similarly, induction of mESC differentiation leads to increased ENO1 acetylation, enhanced RNA binding, and inhibition of glycolysis. Stem cells expressing mutant forms of ENO1 that escape or hyper-activate this regulation display impaired germ layer differentiation. Our findings uncover acetylationdriven riboregulation of ENO1 as a physiological mechanism of glycolytic control and of the regulation of stem cell differentiation. Riboregulation may represent a more widespread principle of biological control.
ENO1 directly binds cellular mRNAs, functioning as an RNA-binding enzyme
RNA binding inhibits ENO1 catalytic activity by competing with substrate binding
Acetylation of ENO1 increases RNA binding, reducing glycolytic flux
Differentiation increases ENO1 acetylation and RNA association
RNA-sensitive ENO1 activity is required for proper germ layer differentiation
eCLIP to map transcriptome-wide ENO1 RNA-binding sites
In vitro ENO1 enzymatic assays with defined RNA ligands
RNA proximity ligation assay to detect protein–RNA interactions in cells
13C-glucose tracing to assess metabolic flux downstream of ENO1
CRISPR-based ENO1 mutant knock-in and auxin-inducible degradation
Establishes RNA as a direct regulator of enzyme activity, not just gene expression
Introduces riboregulation as a physiological metabolic control mechanism
Links post-translational modification to RNA-mediated enzymatic control
Provides a mechanistic bridge between metabolism and cell fate decisions
Figure 1: ENO1 binds specific mRNAs in cells and in vitro
Figure 2: RNA ligands inhibit ENO1 enzymatic activity
Figure 3: RNA binding inversely correlates with glycolytic output in cells
Figure 4: ENO1 acetylation enhances RNA binding
Figure 5: Riboregulation rewires glycolytic metabolites during differentiation
Figure 6: ENO1 riboregulation controls germ layer differentiation outcomes
Structural mechanism of RNA–ENO1 inhibition remains unresolved
Unknown whether riboregulation generalizes to other glycolytic enzymes in vivo
Limited exploration beyond embryonic stem cell systems