Three distinct proteases are responsible for overall cell surface proteolysis in Streptococcus thermophilus .

The lactic acid bacterium Streptococcus thermophilus was believed to display only two distinct proteases at the cell surface, namely the cell-envelope protease PrtS and the house-keeping protease HtrA. Using peptidomics, we demonstrate here the existence of an additional active cell-surface protease, which shares significant homology with the SepM protease of Streptococcus mutans . Although all three proteases—PrtS, HtrA, and SepM—are involved in the turnover of surface proteins, they demonstrate distinct substrate specificities. In particular, SepM cleaves proteins involved in cell wall metabolism and cell elongation, and its inactivation has consequences for cell morphology. When all three proteases are inactivated, the residual cell-surface proteolysis of S. thermophilus is approximately 5% of that of the wild-type strain. Importance Streptococcus thermophilus is a lactic acid bacterium widely used as a starter in the dairy industry. Due to its "generally recognized as safe" status and its weak cell-surface proteolytic activity, it is also considered to be a potential bacterial vector for heterologous protein production. Our identification of a new cell surface protease made it possible to construct a mutant strain with a 95% reduction in surface proteolysis, which could be useful in numerous biotechnological applications.