ATO3 encoding a putative outward ammonium transporter is an RTG-independent retrograde responsive gene regulated by GCN4 and the Ssy1-Ptr3-Ssy5 amino acid sensor system.

Respiratory deficient yeast cells such as rhoo petites activate an inter-organelle signaling pathway called retrograde regulation. This results in changes in the expression of a subset of nuclear genes leading to major reconfigurations of metabolism that enable cells to adapt to the respiratory deficient state. Previous studies have focused on the role of three positive regulatory factors in the retrograde pathway, Rtg1p, Rtg2p, and Rtg3p, which are essential for both basal and elevated expressions of some, but not all, retrograde responsive genes. Here we characterize the retrograde regulation of one of those genes, ATO3, whose elevated expression in rhoo petites is largely independent of RTG gene function. ATO3 encodes a member of the YaaH family of proteins that is a putative outward ammonium transporter. We show that Ato3p-green fluorescent protein is preferentially localized to the plasma membrane of mother cells. rhoo petites express more Ato3p-green fluorescent protein in their plasma membrane than do rho+ cells, consistent with the elevated level of ATO3 transcripts in rhoo cells. We find that ATO3 expression has two levels of control, both of which are connected to amino acid sensing and regulation. The first involves GCN4, which is required for the bulk of ATO3 expression. The second involves the Ssy1-Ptr3-Ssy5 amino acid sensor system, which is preferentially required for elevated ATO3 expression in rhoo cells. We propose that ATO3 is induced in rhoo cells to eliminate the excess ammonia that arises because of a potential defect in ammonia assimilation in those cells.