Cells use multiple mechanisms for cell-cycle arrest upon withdrawal of individual amino acids

Amino acids are required for cell growth and proliferation, but it remains unclear when and how amino acid availability impinges on the proliferation-quiescence decision. Here, we used time-lapse microscopy and single-cell tracking of cyclin-dependent kinase 2 (CDK2) activity to assess the response of individual cells to withdrawal of single amino acids and found strikingly different cell-cycle effects depending on the amino acid. For example, upon leucine withdrawal, MCF10A cells complete two cell cycles and then enter a CDK2-low quiescence, whereas lysine withdrawal causes immediate cell-cycle stalling. Methionine withdrawal triggers a restriction point phenotype similar to serum starvation or Mek inhibition: upon methionine withdrawal, cells complete their current cell cycle and enter a CDK2-low quiescence after mitosis. Modulation of restriction point regulators p21/p27 or cyclin D1 enables short-term rescue of proliferation under methionine and leucine withdrawal, and to a lesser extent lysine withdrawal, revealing a checkpoint connecting nutrient signaling to cell-cycle entry. [Display omitted] •Withdrawal of different amino acids leads to different cell-cycle arrest phenotypes•Cells rapidly sense the drop of intracellular amino acid levels upon withdrawal•Methionine withdrawal triggers a restriction point phenotype•Lysine withdrawal triggers rapid cell-cycle arrest due to lack of protein synthesis Amino acids are key inputs for cell growth and proliferation. Using time-lapse single-cell microscopy, Rong et al. found that cell-cycle arrest upon methionine and leucine starvation is mainly regulated by restriction point regulators, while cell-cycle arrest upon lysine withdrawal is mainly caused by inhibition of protein synthesis.