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Photorespiration is the second largest carbon flux in most leaves and is integrated into metabolism broadly including one-carbon (C1) metabolism. Photorespiratory intermediates such as serine and others may serve as sources of C1 units, but it is unclear to what degree this happens in vivo, whether altered photorespiration changes flux to C1 metabolism, and if so through which intermediates. To clarify these questions, we quantified carbon flux from photorespiration to C1 metabolism using 13CO2 labelling and isotopically non-stationary metabolic flux analysis in Arabidopsis thaliana under different O2 concentrations which modulate photorespiration. The results revealed that ~5.8% of assimilated carbon passes to C1 metabolism under ambient photorespiratory conditions, but this flux greatly decreases under limited photorespiration. Furthermore, the primary carbon flux from photorespiration to C1 metabolism is through serine. Our results provide fundamental insight into how photorespiration is integrated into C1 metabolism, with possible implications for C1 metabolic response to climate change. 

Since they emerged approximately 125 million years ago, flowering plants have evolved to dominate the terrestrial landscape and survive in the most inhospitable environments on earth. At their core, these adaptations have been shaped by changes in numerous, interconnected pathways and genes that collectively give rise to emergent biological phenomena. Linking gene expression to morphological outcomes remains a grand challenge in biology, and new approaches are needed to begin to address this gap. Here, we implemented topological data analysis (TDA) to summarize the high dimensionality and noisiness of gene expression data using lens functions that delineate plant tissue and stress responses. Using this framework, we created a topological representation of the shape of gene expression across plant evolution, development, and environment for the phylogenetically diverse flowering plants. The TDA-based Mapper graphs form a well-defined gradient of tissues from leaves to seeds, or from healthy to stressed samples, depending on the lens function. This suggests that there are distinct and conserved expression patterns across angiosperms that delineate different tissue types or responses to biotic and abiotic stresses. Genes that correlate with the tissue lens function are enriched in central processes such as photosynthetic, growth and development, housekeeping, or stress responses. Together, our results highlight the power of TDA for analyzing complex biological data and reveal a core expression backbone that defines plant form and function.