The cortex peptidoglycan from endospores of Bacillus subtilis is responsible for the maintenance of dormancy. LytH (YunA) has been identified as a novel sporulation-specific component with a role in cortex structure determination. The lytH gene was expressed only during sporulation, under the control of the mother cellspecific sigma factor K . Spores of a lytH mutant have slightly reduced heat resistance and altered staining when viewed by electron microscopy. Analysis of the peptidoglycan structure of lytH mutant spores shows the loss of muramic acid residues substituted with L-alanine and a corresponding increase in muramic acid residues substituted with tetrapeptide compared to those in the parent strain. In a lytH cwlD mutant, the lack of muramic acid residues substituted with L-alanine and ␦-lactam leaves 97% of residues substituted with tetrapeptide. These results suggest that lytH encodes an L-Ala-D-Glu peptidase involved in production of single L-alanine side chains from tetrapeptides in the spore cortex. The lack of di-or tripeptides in a lytH mutant reveals the enzyme is an endopeptidase.Bacterial endospores are characterized by their extreme dormancy and high-level resistance to a range of stresses, in particular heat (7). The specialized spore structure determines resistance properties, with the dehydrated spore core being crucial for heat resistance. The spore cell wall peptidoglycan, known as the spore cortex, is essential for the maintenance of the dehydrated core, heat resistance, and dormancy (7). The cortex has a unique, spore-specific structure, and recent analysis has begun to identify features important in its role during differentiation and to reveal components responsible for cortex synthesis, modification during sporulation, and hydrolysis during germination (1, 2). Spore cortex is characterized by an extremely low level of cross-linking, which is important for the maintenance of heat resistance (1, 15). A unique feature of the dormant spore cortex is the presence of muramic acid ␦-lactam residues. This modification has a specific role during germination, because the putative germination-specific lytic enzymes SleB and CwlJ, which are responsible for cortex degradation, require the presence of muramic acid ␦-lactam for substrate recognition, since cortex lacking this modification is unable to be hydrolyzed during germination (2).During cortex maturation, a sporulation-specific amidase, CwlD, and a recently described polysaccharide deacetylase, PdaA, are responsible for the formation of the characteristic ␦-lactam residues of bacterial endospores (1,8,15). Although cwlD or pdaA mutants and a cwlD pdaA double mutant can produce resistant endospores, no cortex hydrolysis is observed during germination, and the spores do not outgrow (1,2,8,16,18). The final characteristic feature of the cortex is that about 25% of the muramic acid side chains are substituted for with single L-alanine residues (1, 17). These may be formed by the action of an L-Ala-D-Glu endopeptidase on nascent stem peptides. ...