PLP, the active form of vitamin B6, is a key molecule for all living organisms, being an essential coenzyme especially involved in amino acid metabolism. Its mechanism of action depends on the reactivity of its aldehyde group, which binds free amino acids or target proteins’ lysine residues through a Schiff base. In the last years a PLP-binding protein (PLP-BP), with a high affinity for PLP but without any apparent enzymatic activity, captured our attention. PLP-BP is conserved among many species, but most studies have been performed on the E. coli PLP-BP, called YggS. An E. coli deletion strain lacking YggS grows normally, but it is more sensitive to B6-interfering compounds, such as 4-deoxypiridoxine. Moreover, it shows an imbalance in B6 and amino acid homeostasis. Therefore, PLP-BP is believed to play a crucial role in PLP homeostasis. While purifying recombinant YggS in E. coli, with the intention of clarifying its regulatory properties towards the vitamin B6 pool, we noticed that it co-purified with RNA stably bound to it. RNA-seq analysis of RNA co-purified with or captured by YggS revealed SsrA and RnpB RNAs, respectively involved in trans-translation and tRNA maturation, as the major molecular components. R-EMSA analyses using these RNAs and purified apo-YggS (i.e. free from PLP) revealed a binding affinity in the low micromolar range. When the PLP-bound form was used, the affinity for these RNA significantly decreased. This led us to speculate that YggS could “sense” a build-up of PLP and, consequently, modulate the function, or the stability, of its target RNAs. Considering the RNA-seq results, we hypothesised that YggS could be indirectly involved in regulating tRNA maturation and protein translation. These processes are controlled by the amino acid levels, which are in turn strictly connected to PLP metabolism and availability. Further studies are now being performed to gain insight into these hypothetical and scientifically appealing mechanisms.
The E. coli pyridoxal 5’-phosphate-binding protein is also an RNA-binding protein / Graziani, Claudio; Barile, Anna; Parroni, Alessia; Di Salvo, Martino Luigi; De Cecio, Irene; Colombo, Teresa; Babor, Jill; de Crécy-Lagard, Valérie; Tramonti, Angela; Contestabile, Roberto. - (2025). (Intervento presentato al convegno EMBL Conference: The expanding world of RBPs: from posttranscriptional control to riboregulation tenutosi a Heidelberg, Germany).
The E. coli pyridoxal 5’-phosphate-binding protein is also an RNA-binding protein
Claudio Graziani;Anna Barile;Alessia Parroni;Martino Luigi di Salvo;Irene De Cecio;Angela Tramonti;Roberto Contestabile
2025
Abstract
PLP, the active form of vitamin B6, is a key molecule for all living organisms, being an essential coenzyme especially involved in amino acid metabolism. Its mechanism of action depends on the reactivity of its aldehyde group, which binds free amino acids or target proteins’ lysine residues through a Schiff base. In the last years a PLP-binding protein (PLP-BP), with a high affinity for PLP but without any apparent enzymatic activity, captured our attention. PLP-BP is conserved among many species, but most studies have been performed on the E. coli PLP-BP, called YggS. An E. coli deletion strain lacking YggS grows normally, but it is more sensitive to B6-interfering compounds, such as 4-deoxypiridoxine. Moreover, it shows an imbalance in B6 and amino acid homeostasis. Therefore, PLP-BP is believed to play a crucial role in PLP homeostasis. While purifying recombinant YggS in E. coli, with the intention of clarifying its regulatory properties towards the vitamin B6 pool, we noticed that it co-purified with RNA stably bound to it. RNA-seq analysis of RNA co-purified with or captured by YggS revealed SsrA and RnpB RNAs, respectively involved in trans-translation and tRNA maturation, as the major molecular components. R-EMSA analyses using these RNAs and purified apo-YggS (i.e. free from PLP) revealed a binding affinity in the low micromolar range. When the PLP-bound form was used, the affinity for these RNA significantly decreased. This led us to speculate that YggS could “sense” a build-up of PLP and, consequently, modulate the function, or the stability, of its target RNAs. Considering the RNA-seq results, we hypothesised that YggS could be indirectly involved in regulating tRNA maturation and protein translation. These processes are controlled by the amino acid levels, which are in turn strictly connected to PLP metabolism and availability. Further studies are now being performed to gain insight into these hypothetical and scientifically appealing mechanisms.I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.
