Integrative analysis of CAM photosynthesis reveals its impact on primary metabolism in Yucca

Crassulacean Acid Metabolism (CAM) is an adaptation that temporally separates carbon uptake at night from photosynthesis during the day. CAM has evolved repeatedly across vascular plants, suggesting its emergence may depend on relatively simple changes to deeply conserved regulatory mechanisms. Modern CAM research relies heavily on the interpretation of transcriptomic data. This approach may bias mechanistic explanations of CAM toward transcriptional regulation, though regulation is known to occur at multiple levels following transcription. Additionally, while the majority of research to date has focused on a handful of genes and metabolites in the core CAM pathway, the co-option of conserved regulatory and functional genes is bound to have wide ranging effects on other aspects of primary metabolism. Thus, taking a broad and integrative approach to understanding the downstream effects associated with the emergence of CAM is essential to explaining its convergent evolution as well as to efforts to engineer carbon concentrating mechanisms in crops. In this study, we integrate genomic, transcriptomic, proteomic, and metabolomic data to compare primary metabolism between the CAM species Yucca aloifolia and closely related C ₃ species, Y. filamentosa . We observe minimal correlation between protein abundance and mRNA expression, suggesting significant post-transcriptional regulation in CAM species. We also find evidence of shifts in gene expression and metabolite accumulation outside of the central CAM pathway suggesting that the shift to CAM has cascading effects across primary metabolism, especially nitrogen metabolism. Our findings provide insights into the metabolic shifts associated with CAM evolution and highlight the complexity of its regulation at multiple biological levels.