Filamentation modulates allosteric regulation of PRPS

Abstract

Phosphoribosyl pyrophosphate (PRPP) is a key intermediate in the biosynthesis of purine and pyrimidine nucleotides, histidine, tryptophan, and cofactors NAD and NADP. Abnormal regulation of PRPP synthase (PRPS) is associated with human disorders, including Arts syndrome, retinal dystrophy, and gouty arthritis. Recent studies have demonstrated that PRPS can form filamentous cytoophidia in eukaryotes. Here, we show that PRPS forms cytoophidia in prokaryotes both in vitro and in vivo. Moreover, we solve two distinct filament structures of E. coli PRPS at near-atomic resolution using Cryo-EM. The formation of the two types of filaments is controlled by the binding of different ligands. One filament type is resistant to allosteric inhibition. The structural comparison reveals conformational changes of a regulatory flexible loop, which may regulate the binding of the allosteric inhibitor and the substrate ATP. A noncanonical allosteric AMP/ADP binding site is identified to stabilize the conformation of the regulatory flexible loop. Our findings not only explore a new mechanism of PRPS regulation with structural basis, but also propose an additional layer of cell metabolism through PRPS filamentation.

Structural basis of human PRPS2 filaments

“…Point mutations at the interface can destroy filament assembly, resulting in decreased enzyme activity. This result supports the views we previously observed in prokaryotic cells (Hu et al ., 2022).…”

“…Taking advantage of cryo-EM and laser-scanning confocal microscopy, we have recently found that PRPS in E. coli forms cytoophidia as well. E. coli PRPS forms two types of filament in vitro and in vivo (Hu et al ., 2022). The E. coli PRPS type A filament attenuates the allosteric inhibition by ADP, while the E. coli PRPS type B filament may influence the binding of ATP.…”

“…Using light microscopy, Wilhelm et al found that PRPS formed filamentous structures in a variety of eukaryotic cells such as yeast, Drosophila oocytes, rat neurons, human fibroblasts and zebrafish retinal epithelial cells (Begovich et al, 2020; Noree et al, 2019). Recently, we also found that PRPS can form filamentous structures in prokaryotes such as Escherichia coli in vitro and in vivo (Hu et al, 2022). We further understood the structure E. coli PRPS at near atomic resolution through cryo-EM.…”

Light-sensitive phosphorylation regulates enzyme activity and filament assembly of human IMPDH1 retinal splice variants

“…More than 20 different metabolic enzymes form filaments in cells, suggesting that filament assembly is a general mechanism for regulating multiple metabolic pathways (Hvorecny and Kollman, 2023; Lynch et al, 2020; Narayanaswamy et al, 2009; Noree et al, 2010; Park and Horton, 2019; Park and Horton, 2020; Shen et al, 2016; Simonet et al, 2020). For many metabolic enzymes, filament formation is an important mechanism for fine-tuning catalytic activity (Barry et al, 2014; Hansen et al, 2021; Hu et al, 2022; Hunkeler et al, 2018; Hvorecny et al, 2023; Lu et al, 2023; Lynch and Kollman, 2020; Lynch et al, 2017; Polley et al, 2019; Stoddard et al, 2020; Zhong et al, 2022). Here, we demonstrate that filament assembly itself can be directly tuned by phosphorylation, adding an additional layer to an already complex mode of regulation for IMPDH that occurs at different levels.…”

Structural basis of human PRPS2 filaments

“…PRPS formed filamentous structures in a variety of eukaryotic cells such as yeast, Drosophila oocytes, rat neurons, human fibroblasts [ 25 ] and zebrafish retinal epithelial cells [ 26 ]. Recently, we also found that PRPS can form filamentous structures in prokaryotes such as Escherichia coli in vitro and in vivo [ 1 ]. We further understood the filament structure E. coli PRPS (ecPRPS) at near atomic resolution using cryo-electron microscopy (cryo-EM).…”