Proline-P5C biosynthesis and catabolism

Eukaryotic proline metabolism interconverts L-glutamate, L-ornithine, delta-1-pyrroline-5-carboxylate (P5C) and L-proline. In the biosynthetic arm, L-glutamate is phosphorylated to L-glutamyl 5-phosphate and reduced with NADPH to L-glutamate 5-semialdehyde, which cyclizes spontaneously to P5C; P5C reductase then forms L-proline. The two glutamate-activating reactions are catalyzed either by two separate enzymes, a glutamate 5-kinase and a gamma-glutamyl-phosphate reductase (as in fungi), or by the kinase and reductase domains of a single bifunctional P5C synthase (as in animals and plants). Ornithine aminotransferase can feed the same semialdehyde/P5C pool from L-ornithine. In the catabolic arm, a FAD-dependent proline dehydrogenase associated with the mitochondrial respiratory chain oxidizes L-proline back to P5C, and a mitochondrial NAD-dependent P5C dehydrogenase oxidizes the semialdehyde to L-glutamate, so that proline can serve as a carbon and nitrogen source. Biosynthesis and degradation are separated by compartment and by regulation (feedback control of glutamate 5-kinase, proline-induced expression of the catabolic enzymes).

GENERALIZE (YeastPathways project, 2026-10): the former mammal-only module was broadened to the eukaryotic proline-P5C cycle. The chemistry is shared across fungi, animals and plants; the main architectural difference is in the glutamate-activating arm, now an EXACTLY_ONE variant set: a split route with separate glutamate 5-kinase (S. cerevisiae PRO1, S. pombe pro2, PANTHER PTHR43654) and gamma-glutamyl-phosphate reductase (S. cerevisiae PRO2, S. pombe pro1, PTHR11063) versus the fused P5CS of animals and plants (ALDH18A1, PTHR11063:SF8). The previous mammalian ALDH18A1 leaves are kept unchanged as the fused variant. Note the confusing gene names: S. pombe pro1 is the reductase and pro2 the kinase, the reverse of S. cerevisiae. The remaining steps are shared and gained fungal representatives. The P5C dehydrogenase role no longer carries a PANTHER id because the orthologous enzymes fall in different PANTHER families (human ALDH4A1 PTHR14516, yeast PUT2 and S. pombe put2 PTHR42862, Arabidopsis ALDH12A1 PTHR43521), so no single family contains the representatives. Locations are generalized: P5C reductase is given cytoplasm (yeast PRO3 and pro3 are cytosolic, while human PYCR1/PYCR2 are mitochondrial; mitochondrion is part of cytoplasm), proline dehydrogenase is given mitochondrion (inner-membrane association is curated for human PRODH, whereas for PUT1 the direct evidence is mitochondrial import plus a requirement for a functional respiratory chain), and ornithine aminotransferase carries no module location (cytosolic in yeasts, matrix in animals and plants). In S. cerevisiae the biosynthetic enzymes are cytosolic and the catabolic enzymes mitochondrial, which is why arginine-derived P5C must pass through proline before it is oxidized (PMID:6997271, PMID:7009582, PMID:25112878); that route is modelled in arginine_catabolism_arginase_pathway, which reuses the P5C reductase, proline dehydrogenase and P5C dehydrogenase roles. OAT is retained here as an alternative P5C input in its reversible role; in Arabidopsis it feeds only catabolism (PMID:18419821), and in yeast it contributes to proline only in pro1/pro2 mutants under derepressed conditions, so its proline-biosynthetic process annotation is lineage-dependent. YeastCyc corrections: PUT2 added as catalyst of RXN-14116 (no gene in YeastCyc). GO-CAM disagreements: both YeastPathways models place every activity in cytosol, including mitochondrial PUT1 and PUT2; the PomBase model 678073a900003902 places put1 in the mitochondrial matrix rather than at the inner membrane, includes an unidentified mitochondrial proline transporter, glutamine synthetase, glutamine transport and mitochondrial tRNA charging (outside this module), and places arginase activities in the urea cycle process. Bacterial ProB-ProA-ProC and fused PutA architectures are modelled separately (bacterial_fused_puta_proline_catabolism). OAT and PRODH cofactors are retained explicitly as pyridoxal 5'-phosphate and FAD. GO:0010133, the former proline-to-glutamate catabolism term, is obsolete, so GO:0006562 is used. Disease and signaling consequences remain outside this reaction chain.