The rapid atrophy of skeletal muscles upon fasting or denervation is due largely to an increased rate of protein breakdown. Blocking the lysosomal or the Ca (2+)-dependent pathways did not prevent increased proteolysis in muscles from fasted animals or following denervation. In contrast, upon food deprivation, the nonlysosomal ATP-dependent process increased by 150-350%. After refeeding, this process returned to control levels by 24 h. Similarly, within one day after denervation of the soleus, proteolysis increased by 50-250%. By contrast, the residual energy-independent process did not change in fasting or denervation. Because the ATP-dependent process might involve activation of the ubiquitin-ATP-dependent pathway, we measured the levels of mRNA for ubiquitin [Ub] in the atrophying muscles. After food deprivation, the levels of polyUb transcripts increased 2-to 4-fold in the soleus and extensor digitorum longus (EDL) muscles, and returned to control levels within 1 day of refeeding. After denervation of the soleus, a 2-to 3-fold increase in polyUb mRNA also occurred within 1 day. The muscle content of ubiquitinated protein also changed in parallel with Ub mRNA levels under these conditions. Thus, polyUb genes appear to be selectively induced in atrophying muscle, and levels of Ub mRNA and ubiquitin-protein conjugates change coordinately with the rate of ATP-dependent proteolysis. These data suggest that in atrophying muscle the ATP-Ub-dependent system plays an important physiological role in the degradation of the bulk of cell proteins.