To adapt quickly to the environmental change, bacteria have evolved a protein quality control (PQC) network to remove unwanted proteins. AAA + ( ATPases associated with diverse cellular activities) proteases form a major part of this PQC network, and the discovery of Pup ( prokaryotic ubiquitin-like protein ) -proteasome system revealed a novel mechanism of prokaryotic protein degradation. Proteolytic machines only degrade substrates bearing a degradation tag or degron to insure the proteolysis specificity. In addition, bacteria adopt different strategies to regulate the protein degradation. With the discovery of Ubiquitin-mediated protein degradation in eukaryotes, it has become evident that regulated protein degradation plays a crucial role in the cell response to environment change among eukaryotes and prokaryotes. Regulation by proteolysis has been shown to be involved in diverse bacterial cellular processes including growth, division, differentiation, pathogenesis and stress response. This review will focus on the structure, degradation process, and the function of AAA + proteolytic machines in bacteria.