The Conserved Family of the Pyridoxal Phosphate-Binding Protein (PLPBP) and Its Cyanobacterial Paradigm PipY

Abstract

The PLPBP family of pyridoxal phosphate-binding proteins has a high degree of sequence conservation and is represented in all three domains of life. PLPBP members, of which a few representatives have been studied in different contexts, are single-domain proteins with no known enzymatic activity that exhibit the fold type III of PLP-holoenzymes, consisting in an α/β barrel (TIM-barrel), where the PLP cofactor is solvent-exposed. Despite the constant presence of cofactor PLP (a key catalytic element in PLP enzymes), PLPBP family members appear to have purely regulatory functions affecting the homeostasis of vitamin B6 vitamers and amino/keto acids. Perturbation of these metabolites and pleiotropic phenotypes have been reported in bacteria and zebrafish after PLPBP gene inactivation as well as in patients with vitamin B6-dependent epilepsy that results from loss-of-function mutations at the PLPBP. Here, we review information gathered from diverse studies and biological systems, emphasizing the structural and functional conservation of the PLPBP members and discussing the informative nature of model systems and experimental approaches. In this context, the relatively high level of structural and functional characterization of PipY from Synechococcus elongatus PCC 7942 provides a unique opportunity to investigate the PLPBP roles in the context of a signaling pathway conserved in cyanobacteria.

Pleiotropic effects of PipX, PipY, or RelQ overexpression on growth, cell size, photosynthesis, and polyphosphate accumulation in the cyanobacterium Synechococcus elongatus PCC7942

“…A simple correlation between protein levels and cell size in S. elongatus was previously observed with the global transcriptional regulator RpaB ( Moronta-Barrios et al, 2013 ). However, pipX or pipY null mutants show no cell size defects ( Labella et al, 2017 and Supplementary Figure S6B ), thus ruling out a simple correlation between PipX or PipY protein levels and cell size ( Labella et al, 2020a , b ; Tremiño et al, 2022 ). PipX and/or PipY overexpression may have indirect effects on cell size due to metabolic perturbations, or they may alter protein–protein interactions involved in cell division.…”

“…In particular, the phenotypic features described here for PipY ox cultures should help studies on the structure–function relationship at PipY/PLPBP or concerning the regulatory complexities of accumulation of giant polyP granules in S. elongatus . For instances, PipY ox derivatives carrying mutations at functionally relevant or conserved residues ( Tramonti et al, 2022 ; Tremiño et al, 2022 ) can be easily compared in the presence of IPTG and further analyzed for traits of interest.…”

“…In S. elongatus pipX forms a bicistronic operon with the downstream gene pipY ( Labella et al, 2017 ), encoding a member of the widely distributed and highly conserved family of Pyridoxal-phosphate (PLP)-binding proteins (COG0325/PLPBP) that are involved in vitamin B 6 and amino acid homeostasis ( Ito, 2022 ; Tremiño et al, 2022 ). PLPBP deficiency altered the B 6 pool in different organisms ( Darin et al, 2016 ; Prunetti et al, 2016 ; Ito et al, 2019 , 2020 ; Johnstone et al, 2019 ; Vu et al, 2020 ).…”

“…PLPBP deficiency altered the B 6 pool in different organisms ( Darin et al, 2016 ; Prunetti et al, 2016 ; Ito et al, 2019 , 2020 ; Johnstone et al, 2019 ; Vu et al, 2020 ). Despite the obligate presence of the catalyst cofactor PLP in PipY and its orthologs, these proteins appear to have no enzymatic activity and are assumed to have purely regulatory functions ( Tremiño et al, 2022 ). Since no direct protein targets or cellular components directly interacting with PLPBP family members have been reported to date, the operonic association of pipY with pipX provides a unique opportunity to investigate the roles of PLPBP members in the context of a signaling pathway highly conserved in cyanobacteria.…”

“…Furthermore, the relatively short or non-existent intergenic distances found between contiguous pipX and pipY coding sequences are suggestive of tight co-regulation and translational coupling, thus supporting the idea of a functional interaction between PipX and PipY in cyanobacteria (Labella et al, 2017;Cantos et al, 2019), although the role played by PipY in the PipX interaction network and the molecular mechanisms involved remain to be established (Figure 1). PipY from S. elongatus is one of the best-characterized PLBPB members and can be regarded as a paradigm for these proteins (Labella et al, 2017;Tremiño et al, 2017Tremiño et al, , 2022Cantos et al, 2019). Inactivation of PLBPB members results in alterations of the relative levels of B 6 vitamers and amino/keto acids in all organisms investigated (Ito, 2022;Tremiño et al, 2022).…”