Divergent transcription of pdxB and homology between the pdxB and serA gene products in Escherichia coli K-12

We report the DNA sequence and in vivo transcription start of the pdxB, which encodes a protein required for de novo biosynthesis of pyridoxine (vitamin B₆). The DNA sequence confirms results from previous minicell experiments showing that pdxB encodes a 41-kilodalton polypeptide. RNase T2 mapping of in vivo transcripts and corroborating experiments with promoter expression vector pKK232-8 demonstrated that the pdxB promoter shares its -10 region with an overlapping, divergent promoter. Thus, pdxB must be the first gene in the complex pdxB-hisT operon. The steady-state transcription level from these divergent promoters, which probably occlude each other, is approximately equal in bacteria growing in rich medium at 37°C. The divergent transcript could encode a polypeptide whose amino-terminal domain is rich in proline and glutamine residues. Similarity searches of protein data bases revealed a significant number of amino acid matches between the pdxB gene product and D-3-phosphoglycerate dehydrogenase, which is encoded by serA and catalyzes the first step in the phosphorylated pathway of serine biosynthesis. FASTA and alignment score analyses indicated that PdxB and SerA are indeed homologs and share a common ancestor. The amino acid alignment between PdxB and SerA implies that PdxB is a 2-hydroxyacid dehydrogenase and suggests possible NAD⁺, substrate binding, and active sites of both enzymes. Furthermore, the fact that 4-hydroxythreonine, a probable intermediate in pyridoxine biosynthesis, is structurally related to serine strongly suggests that the pdxB gene product is erythronate-4-phosphate dehydrogenase. The homology between PdxB and SerA provides considerable support for Jensen's model of enzyme recruitment as the basis for the evolution of different biosynthetic pathways.