The mutual interaction of glycolytic enzymes and RNA in post-transcriptional regulation

Abstract

About three decades ago, researchers suggested that metabolic enzymes participate in cellular processes that are unrelated to their catalytic activity, and the term "moonlighting functions" was proposed. Recently developed advanced technologies in the field of RNA interactome capture now unveil the unexpected RNA binding activity of many metabolic enzymes, as exemplified here for the enzymes of glycolysis. Although for most of these proteins a precise binding mechanism, binding conditions, and physiological relevance of the binding events still await in-depth clarification, several well explored examples demonstrate that metabolic enzymes hold crucial functions in post-transcriptional regulation of protein synthesis. This widely conserved RNA-binding function of glycolytic enzymes plays major roles in controlling cell activities. The best explored examples are glyceraldehyde 3-phosphate dehydrogenase, enolase, phosphoglycerate kinase, and pyruvate kinase. This review summarizes current knowledge about the RNA-binding activity of the ten core enzymes of glycolysis in plant, yeast, and animal cells, its regulation and physiological relevance. Apparently, a tight bidirectional regulation connects core metabolism and RNA biology, forcing us to rethink long established functional singularities.

Keywords: RNA-binding; enolase; glyceraldehyde-3-phosphate dehydrogenase; glycolytic enzymes; moonlighting; post-transcriptional regulation.

FIGURE 1.

Moonlighting functions of core glycolytic enzymes. Enzymes involved in the conversion of glucose to pyruvate during glycolysis exhibit additional functions unrelated to their catalytic activity. These moonlighting functions regulate cellular processes like RNA biology, cytoskeleton dynamics, cell cycle control, apoptosis, autophagy, or gene expression. Due to space limitations, the number of given examples and references is limited to one.

FIGURE 2.

Strategies to identify the RBPome. (A) Increasing number of publications concerning RNA binding proteins. (B) General workflow of RNA-interactome capture with cross-linking, affinity purification and final identification of interaction molecules. (C) Current RNA binding proteome in Arabidopsis thaliana, Saccharomyces cerevisiae, and Homo sapiens according to RBP2GO database and its assignment to different gene ontology terms.

FIGURE 3.

Overview of glycolytic enzymes and their identification as RNA-binding proteins. According to the RBP2GO database, glycolytic enzymes are highlighted with a light gray box when one isoform of the enzyme was identified in global RIC approaches, a dark gray box when additionally RNA binding was validated and characterized beyond global approaches, and with white boxes when a protein is not listed as an RNA-binding protein in the RBP2GO database. Multiple amino acid alignments were conducted using the UniProt alignment tool. For every glycolytic enzyme, all isoforms were compared. Shown are always the lowest values for protein sequence similarity. For a detailed percentage identity matrix, see Supplemental Figure 1.

FIGURE 4.

Examples for enzyme-mediated regulation of protein synthesis and riboregulation of metabolic activity through RNAs based on data from (A) Shetty et al. (2004), (B) Simsek et al. (2017), (C) Chang et al. (2013), (D) Huppertz et al. (2022), and (E) Fuller et al. (2020).

FIGURE 5.

Summary of interconnection between RNA biology and metabolism. The schematics illustrate the diverse implications (in black letters) of RNA–enzyme interactions on mRNA features and enzyme activity and potential targets (in red letters) to regulate the binding event.