Overcoming redundancy in the Arabidopsis TREHALOSE‐6‐PHOSPHATE PHOSPHATASE family reveals connections to development and iron homeostasis

Arabidopsis encodes 10 TREHALOSE-6-PHOSPHATE PHOSPHATASE (TPP) genes, homologous to maize RAMOSA3 (RA3), which controls shoot branching. Here, we explored the functions of the Arabidopsis TPPs. We used expression profiling, multiplex CRISPR-Cas9 editing and metabolite profiling to explore the function of Arabidopsis TPP genes. The Arabidopsis TPP genes had distinct expression patterns in shoot apices, with TPPI and TPPJ expressed in shoot meristem boundaries, reminiscent of RA3 expression. Single and double mutants in these genes lacked obvious phenotypes; however, a CRISPR-Cas9 knockout of all 10 TPP genes led to increased branching and earlier flowering. Native expression of GFP-tagged TPPI partially complemented these defects, with protein localization in meristems, vascular tissues and in nuclei. Metabolite profiling revealed higher trehalose 6-phosphate (Tre6P), lower trehalose and altered sugar and iron-associated metabolites. The 10× tpp mutants were also chlorotic, had low iron levels and could be rescued by iron supplementation. Consistently, developmental and iron-responsive genes were upregulated in the 10× tpp mutants, while photosynthesis-related genes were repressed. Our findings suggest that TPP genes redundantly regulate shoot architecture, sugar metabolism, iron homeostasis and photosynthesis in Arabidopsis, and support a role for TPP-mediated Tre6P signaling in coordinating developmental and physiological pathways.