The general stress response of alphaproteobacteria is regulated by a partner-switching mechanism that involves the alternative sigma factor σ(EcfG), the anti-sigma factor NepR and the anti-sigma factor antagonist PhyR. To address the question of how the PhyR-NepR-σ(EcfG) cascade is activated and modulated in Methylobacterium extorquens, a forward genetic screen was applied. The screen identified the single-domain response regulator Mext_0407 as a novel regulatory element in the general stress response of M. extorquens. Analysis of phenotypes and of transcriptional fusions of PhyR-dependent genes shows that the mext_0407 deletion mutant fails to respond to various stresses. Mext_0407 requires the putative phosphorylatable aspartate-64 for its activity in vivo and genetic evidence indicates that Mext_0407 operates upstream of the PhyR-NepR-σ(EcfG) cascade.