Non-peroxisomal allantoin biosynthesis reveals unexpected flexibility in plant purine catabolism

Allantoin, a central intermediate of purine catabolism, plays key roles in nitrogen remobilization and is also implicated in stress protection in plants. As in other eukaryotes, allantoin biosynthesis in land plants has long been considered restricted to peroxisomes, where this process is catalyzed by ALLANTOIN SYNTHASE (ALNS). However, angiosperms produce not only the canonical peroxisomal isoform but also a shorter splice variant lacking a type 2 peroxisomal targeting signal (PTS2), raising the question of whether allantoin biosynthesis can occur outside peroxisomes. Through comparative sequence analyses across Archaeplastida, we show that PTS2-lacking ALNS exhibits a patchy distribution within Viridiplantae, including species without identifiable PTS2-containing ALNS homologs, suggesting the evolutionary significance of non-peroxisomal allantoin biosynthesis. Fluorescent protein fusion analysis showed that PTS2-lacking ALNS proteins from the angiosperm Arabidopsis thaliana, the monilophyte Dryopteris erythrosora, and the bryophyte Marchantia polymorpha localize outside peroxisomes, consistent with cytosolic localization. Furthermore, recombinant proteins from all three species catalyzed stereospecific (S)-allantoin formation. Arabidopsis alns knockout mutants accumulated racemic allantoin, indicating that ALNS ensures the stereospecific formation of (S)-allantoin while preventing the generation of poorly metabolizable (R)-allantoin, which likely arises through spontaneous decomposition of the unstable ALNS substrate 5-hydroxyisourate. Importantly, expression of either ALNS isoform restored normal allantoin metabolism and largely rescued the growth and physiological defects of the alns mutants. These findings demonstrate the functional equivalence of cytosolic and peroxisomal ALNS in Arabidopsis and reveal previously unrecognized flexibility in the subcellular organization of purine catabolism in plants.