Peptidoglycan Remodeling by an L,D-Transpeptidase, LdtD during Cold Shock in Escherichia coli

Peptidoglycan (PG) is a unique and essential component of the bacterial cell envelope. It is made up of several linear glycan polymers cross-linked through covalently attached stem peptides making it a fortified mesh-like sacculus around the bacterial cytosolic membrane. In most bacteria, including Escherichia coli, the stem peptide is made up of l-alanine (l-Ala¹), d-glutamate (d-Glu²), meso-diaminopimelic acid (mDAP³), d-alanine (d-Ala⁴), and d-Ala⁵ with cross-links occurring either between d-ala⁴ and mDAP³ or between two mDAP³ residues. Of these, the cross-links of the 4-3 (d-Ala⁴-mDAP³) type are the most predominant and are formed by penicillin-binding D,D-transpeptidases, whereas the formation of less frequent 3-3 linkages (mDAP³-mDAP³) is catalyzed by L,D-transpeptidases. In this study, we found that the frequency of the 3-3 cross-linkages increased upon cold shock in exponentially growing E. coli and that the increase was mediated by an L,D-transpeptidase, LdtD. We found that a cold-inducible RNA helicase DeaD enhanced the cellular LdtD level by facilitating its translation resulting in an increased abundance of 3-3 cross-linkages during cold shock. However, DeaD was also required for optimal expression of LdtD during growth at ambient temperature. Overall, our study finds that E. coli undergoes PG remodeling during cold shock by altering the frequency of 3-3 cross-linkages, implying a role for these modifications in conferring fitness and survival advantage to bacteria growing in diverse environmental conditions. IMPORTANCE Most bacteria are surrounded by a protective exoskeleton called peptidoglycan (PG), an extensively cross-linked mesh-like macromolecule. In bacteria, such as Escherichia coli, the cross-links in the PG are of two types: a major fraction is of 4-3 type whereas a minor fraction is of 3-3 type. Here, we showed that E. coli exposed to cold shock had elevated levels of 3-3 cross-links due to the upregulation of an enzyme, LdtD, that catalyzed their formation. We showed that a cold-inducible RNA helicase DeaD enhanced the cellular LdtD level by facilitating its translation, resulting in increased 3-3 cross-links during cold shock. Our results suggest that PG remodeling contributes to the survival and fitness of bacteria growing in conditions of cold stress.