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Protein quality control (PQC) systems are essential for cellular resilience to proteotoxic stress. Despite intensive study, functional redundancies in the system obscure the contributions of important individual genes. Here, we leverage transposon sequencing (Tn-seq) across bacterial strains lacking key chaperones and proteases to reveal hidden determinants of stress response in protein homeostasis. By profiling fitness under multiple proteotoxic stresses, we uncover stress-specific vulnerabilities and reveal how major players of PQC mask correlations between transcriptomic responses and gene fitness. We identify a heat-specific synthetic lethality between the ClpB disaggregase and DNA polymerase 1 mediated by prolific aggregation of the RecA recombinase and persistent induction of the heat shock regulon, supporting a conclusion that vulnerabilities in PQC are genetic- and environmental-context specific. Overall, our work presents a framework to reveal critical addressable fragilities in stress responses using gene fitness scores adaptable to a variety of systems.