Beyond the Primary-Secondary Dichotomy: Toward a Unified Metabolic Perspective.

Abstract

The distinction between primary and secondary metabolism has long provided a useful conceptual and pedagogical framework in biochemistry, particularly in plant sciences, but it increasingly fails as a literal description of how metabolites are produced and function. Pathways share precursors, cofactors, regulatory mechanisms, transport systems, and recycling routes, while metabolites conventionally assigned to different categories can contribute to growth, signaling, defense, nutrient acquisition, structure, or stress responses depending on context. Here, we review the historical origins of the primary-secondary dichotomy and synthesize biochemical, genetic, ecological, metabolomic, and systems-level evidence for a more integrated interpretation of plant metabolism. We do not argue that established terms must be abolished: they remain useful descriptors of broad tendencies in conservation, distribution, and pathway organization. Instead, we argue against treating them as fixed functional categories. We develop an operational framework in which network position, flux and resource coupling, phylogenetic distribution, spatiotemporal localization, conditional essentiality, and experimentally demonstrated function are evaluated together. We then show how this perspective changes the analysis of untargeted metabolomic data and the design of metabolic-engineering strategies. A unified metabolic perspective provides a practical way to connect plant physiology, environmental responses, and ecological interactions without replacing established terminology with a new rigid vocabulary.

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