Cellular proteins are decorated with a wide range of acetyl and other acyl modifications. Many studies have demonstrated regulation of site-specific acetylation by acetyltransferases and deacetylases. Acylation is emerging as a new type of lysine modification, but less is known about its overall regulatory role. Furthermore, the mechanisms of lysine acylation, its overlap with protein acetylation, and how it influences cellular function are major unanswered questions in the field. In this review, we discuss the known roles of acetyltransferases and deacetylases and the sirtuins as a conserved family of a nicotinamide adenine dinucleotide (NAD+)-dependent protein deacylases that are important for response to cellular stress and homeostasis. We also consider the evidence for an emerging idea of nonenzymatic protein acylation. Finally, we put forward the hypothesis that protein acylation is a form of protein “carbon stress” that the deacylases evolved to remove as a part of a global protein quality-control network. The sirtuins are protein deacylases that regulate cellular homeostasis and response to stress. In this review, Wagner and Hirschey highlight recent findings on new types of acyl lysine modifications and propose a model for protein acylation as a “carbon stress” that sirtuins remove as part of protein quality control.