Genome-wide identification of genes required for alternative peptidoglycan cross-linking in Escherichia coli

The D,D-transpeptidase activity of penicillin-binding proteins (PBPs) is the well-known primary target of beta-lactam antibiotics that block peptidoglycan polymerization. beta-lactam-induced bacterial killing involves complex downstream responses whose causes and consequences are difficult to resolve. Here, we use the functional replacement of PBPs by a beta-lactam-insensitive L,D-transpeptidase to identify genes essential to mitigate the effects of PBP inactivation by beta-lactams in actively dividing bacteria. The functions of the 179 conditionally essential genes identified by this approach extend far beyond L,D-transpeptidase partners for peptidoglycan polymerization to include proteins involved in stress response and in the assembly of outer membrane polymers.