PhpR, as a unique transcriptional regulator, represses the expression of pyridoxal 5′-phosphate-binding protein YggS in Alcaligenes

ABSTRACT YggS (COG0325 family) was widely conserved across the three domains of life and had been implicated in pyridoxal 5′-phosphate (PLP) homeostasis. However, transcriptional regulators that directly controlled yggS had remained unknown. Here, using Alcaligenes faecalis JQ135, PhpR, a previously unrecognized MocR-family regulator, was identified as a transcriptional regulator that directly controlled yggS . Deletion of yggS in strain JQ135 impaired cell growth and caused intracellular PLP imbalance. PhpR (PLP homeostasis-related protein regulator, phpR ) directly repressed yggS transcription by binding a conserved non-palindromic promoter motif in a PLP-dependent manner. Comparative genomic analyses further revealed that the adjacent yggS-phpR gene pair was divergently transcribed and highly conserved, but restricted to Alcaligenes species. Together, these findings established the first direct transcriptional regulatory mechanism for a YggS-family protein and revealed a PLP-responsive regulatory circuit linking cofactor homeostasis in bacteria. IMPORTANCE Pyridoxal 5′-phosphate (PLP), the main catalytically active form of vitamin B6, was an essential cofactor for many enzymes, particularly those involved in amino acid metabolism. PLP deficiency could impair the activity of PLP-dependent enzymes and disrupt cellular metabolism, whereas excessive accumulation of free PLP could also cause metabolic imbalance. YggS-family proteins were widely conserved PLP homeostasis factors, yet how their expression was regulated had remained largely unknown. Here, we identified PhpR as a previously uncharacterized MocR-family transcriptional regulator that directly repressed the expression of YggS in Alcaligenes , establishing a direct link between intracellular PLP availability and yggS expression. These findings revealed a previously unknown regulatory mechanism governing bacterial PLP homeostasis and provided new insight into how PLP-responsive transcriptional regulation coordinated cofactor balance with cellular metabolism.