A surprising complexity of ubiquitin signaling has emerged with identification of different ubiquitin chain topologies. However, mechanisms of how the diverse ubiquitin codes control biological processes remain poorly understood. Here, we use a SILAC label-swap approach that combines high-resolution protein fractionation and an LC–MS/MS platform to examine the proteomes of two yeast strains, a wild-type (WT) strain and a ubiquitin mutant (K11R) strain, which could be used to identify yeast proteins that are regulated by lysine 11 (K11)-linked ubiquitin chains. Our results reveal a profound downregulation of methionine biosynthesis enzymes in the K11R mutant strain, indicating a so far unappreciated role of K11-linked ubiquitin chains in regulating the SCFMet30-Met4 network. The entire Met4 pathway, which links cell proliferation with sulfur amino acid metabolism, was selected for mechanistic studies. Previously we demonstrated that a K48-linked ubiquitin chain represses the transcription factor Met4. Here we show that efficient Met4 activation requires a K11-linked topology. Mechanistically our results propose that the K48 chain binds to a topology-selective tandem ubiquitin binding region in Met4 and competes with binding of the basal transcription machinery to the same region. The change to K11 enriched chain architecture releases this competition and permits binding of the basal transcription complex to activate transcription.