To understand high amount of production and detailed processing of antihypertensive peptides, Val-Pro-Pro (VPP) and Ile-Pro-Pro (IPP), in Lactobacillus helveticus CM4 fermented milk, whole genome sequence of the CM4 strain was completed and compared to previously reported whole genome sequence of L helveticus DPC4571. It revealed 2,028,493 bp of DNA sequence and encoding of 2174 open reading frames in the whole genome sequence with the highest homology to the genome sequence of L. helveticus DPC 4571. Comparative analysis focused on proteolytic enzymes between CM4 and DPC4571 strains revealed existence of 23 kinds of identical intracellular peptidase genes in both strains but no prtY type proteinase gene in DPC4571. Immunoblotting analysis with an antibody raised against the PrtY proteinase showed existence of the 45 kDa PrtY protein in CM4 but not in DPC4571 in the cell extracts. The cell wall-associated proteinase activity was higher in the CM4 than that in the DPC4571 throughout all fermentation period, and the amounts of VPP and IPP in CM4 and DPC4571 fermented milk were correlated with the proteinase activity on the cell wall. Moreover, slight difference of the beta-casein hydrolysates by cell wall-associated extracellular proteinases between CM4 and DPC4571 cells was detected by a MALDI-TOF/TOF analysis. These results suggest that the extracellular proteinase activity might affect on the productivity of VPP and IPP in L helveticus fermented milk and some peptidases might play important role in following precise processing to release VPP and IPP. (C) 2012, The Society for Biotechnology, Japan. All rights reserved.