The root apical meristem (RAM) of plants can be divided into a proliferation domain (PD) and a transition domain (TD). In the PD, slow-growing cells proliferate before being displaced into the TD, where proliferation decreases but cells grow at the same pace and enter endoreduplication. The passage of cells from the PD to the TD indicates that the two domains are connected. Now, however, Joseph Dubrovsky and colleagues reveal that threonine metabolism alteration uncouples these domains. In the methionine overaccumulator 2 (mto2-2) Arabidopsis mutant, which lacks THREONINE SYNTHASE 1, the RAM is exhausted during development thus arresting root growth. The authors show that in the RAM of mto2-2 mutants only the TD is present. Interestingly, this phenotype is independent of auxin synthesis and classical pathways of RAM maintenance, related to PLETHORA and WOX5 genes. Constructing a mathematical model of threonine synthesis and breakdown, the researchers predict that threonine distribution is compartmentalised by domains, which is crucial for RAM organisation. Together, these data show that threonine metabolism is essential for establishing the PD and, similarly to mammalian embryonic stem cells, is crucial for plant stem cell function.