Loss of nonsense mediated decay suppresses mutations in Saccharomyces cerevisiae TRA1

We screened for suppressors of the ethanol sensitivity caused by tra1-L3733A. Eleven extragenic recessive mutations, belonging to three complementation groups, were identified that partially suppressed a subset of the phenotypes caused by tra1-L3733A. Using whole genome sequencing we identified one of the mutations as an opal mutation at tryptophan 165 of UPF1/NAM7. Partial suppression of the transcriptional defect resulting from tra1-L3733A was observed at GAL10, but not at PHO5. Suppression was due to loss of nonsense mediated decay (NMD) since deletion of any one of the three NMD surveillance components (upf1/nam7, upf2/nmd2, or upf3) mediated the effect. Deletion of upf1 suppressed a second FATC domain mutation, tra1-F3744A, as well as a mutation to the PIK3 domain. In contrast, deletions of SAGA or NuA4 components were not suppressed.We have demonstrated a genetic interaction between TRA1 and genes of the NMD pathway. The suppression is specific for mutations in TRA1. Since NMD and Tra1 generally act reciprocally to control gene expression, and the FATC domain mutations do not directly affect NMD, we suggest that suppression occurs as the result of overlap and/or crosstalk in these two broad regulatory networks.Tra1 is a 3744 amino acid residue protein, essential for viability in Saccharomyces cerevisiae. It is a major constituent of the SAGA and NuA4 transcriptional regulatory complexes [1-3], both with significant roles in gene regulation and DNA repair [4-6]. More recently a putative complex based on mutual associations termed ASTRA, was also found to contain Tra1 [7]. Tra1's mammalian homolog TRRAP was identified because of its interactions with the transcription factors c-myc and E2F [8]. Similarly Tra1 interacts with yeast transcriptional activators to target SAGA and NuA4 to promoters [9-12]. Interestingly, Helmlinger et al. [13] have recently provided evidence that Tra1 also acts independently of SAGA and NuA4 to regulate gene expression.Tra1/TRRAP are