Evidence that COG0325 proteins are involved in PLP homeostasis

Abstract

Pyridoxal 59-phosphate (PLP) is an essential cofactor for nearly 60 Escherichia coli enzymes but is a highly reactive molecule that is toxic in its free form. How PLP levels are regulated and how PLP is delivered to target enzymes are still open questions. The COG0325 protein family belongs to the fold-type III class of PLP enzymes and binds PLP but has no known biochemical activity although it occurs in all kingdoms of life. Various pleiotropic phenotypes of the E. coli COG0325 (yggS) mutant have been reported, some of which were reproduced and extended in this study. Comparative genomic, genetic and metabolic analyses suggest that these phenotypes reflect an imbalance in PLP homeostasis. The E. coli yggS mutant accumulates the PLP precursor pyridoxine 59-phosphate (PNP) and is sensitive to an excess of pyridoxine but not of pyridoxal. The pyridoxine toxicity phenotype is complemented by the expression of eukaryotic yggS orthologs. It is also suppressed by the presence of amino acids, specifically isoleucine, threonine and leucine, suggesting the PLP-dependent enzyme transaminase B (IlvE) is affected. These genetic results lay a foundation for future biochemical studies of the role of COG0325 proteins in PLP homeostasis.

Studies on cyanobacterial protein PipY shed light on structure, potential functions, and vitamin B6‐dependent epilepsy

“…The complementation of yggS − E. coli by COG0325 genes of other species and the phenotypic similarities of this E. coli mutant and of the S. elongatus pipY − mutant are strong indications that the function of COG0325 genes is conserved across phyla. The alleviation by PLP or by vitamin B 6 supplementation of the alterations observed in these mutants , best illustrated by the vitamin B 6 dependence of the epilepsy due to PROSC deficiency , indicates that this conserved function is related to PLP, in line with the fact that COG0325 products are PLP‐containing proteins. Yet, previous work has not favored an enzymatic role of COG0325 proteins.…”

“…A, inset). Similarly to the E. coli and yeast COG0325 gene products, YggS, and YBL036C , PipY was monomeric, judged from its behavior in size exclusion chromatography assays (Fig. A).…”

“…The movement of helix 9 might be the best candidate for triggering the PLP exchange required for the proposed role of PipY in PLP homeostasis . Due to its exposed nature, helix 9 could interact with other macromolecular players, acting as a trigger for PLP exchange, since a change in the position of helix 9 could importantly weaken PLP binding to PipY, given the PLP‐anchoring role of this helix.…”

Diagnostic pitfalls in vitamin B6‐dependent epilepsy caused by mutations in the PLPBP gene

“…Enzymes utilizing PLP as a cofactor are found in all organisms and catalyze diverse reactions mostly associated with amino acid as well as neurotransmitter metabolism among other pathways . Little is known about regulation of PLP‐homeostasis …”

“…PLPHP is likely to be a protein with dual localization, in both cytoplasm and mitochondria . It has a PLP‐binding domain, but no enzymatic activity . Darin et al suggested that PLPHP acts as a PLP‐carrier that prevents PLP from reacting with other molecules, supplies it to apo‐enzymes, and protects it from intracellular phosphatases .…”