Key messageThe function and components of l-glutamate signaling pathways in plants have just begun to be elucidated. Here, using a combination of genetic and biochemical strategies, we demonstrated that a MAPK module is involved in the control of root developmental responses to this amino acid.AbstractRoot system architecture plays an essential role in plant adaptation to biotic and abiotic factors via adjusting signal transduction and gene expression. l-Glutamate (l-Glu), an amino acid with neurotransmitter functions in animals, inhibits root growth, but the underlying genetic mechanisms are poorly understood. Through a combination of genetic analysis, in-gel kinase assays, detailed cell elongation and division measurements and confocal analysis of expression of auxin, quiescent center and stem cell niche related genes, the critical roles of l-Glu in primary root growth acting through the mitogen-activated protein kinase 6 (MPK6) and the dual specificity serine–threonine–tyrosine phosphatase MKP1 could be revealed. In-gel phosphorylation assays revealed a rapid and dose-dependent induction of MPK6 and MPK3 activities in wild-type Arabidopsis seedlings in response to l-Glu. Mutations in MPK6 or MKP1 reduced or increased root cell division and elongation in response to l-Glu, possibly modulating auxin transport and/or response, but in a PLETHORA1 and 2 independent manner. Our data highlight MPK6 and MKP1 as components of an l-Glu pathway linking the auxin response, and cell division for primary root growth.