The universal stress protein paralogues of Escherichia coli are co-ordinately regulated and co-operate in the defence against DNA damage

We have cloned, characterized and inactivated genes encoding putative UspA paralogues in Escherichia coli. The yecG (uspC), yiiT (uspD) and ydaA (uspE) genes were demonstrated to encode protein products and these were mapped to spots in the E. coli proteomic database. Expression analysis using chromosomal transcriptional lacZ fusions and two-dimensional gels revealed that all usp genes analysed are regulated in a similar fashion. Thus, uspC, D and E are all induced in stationary phase and by a variety of stresses causing growth arrest of cells. Induction is independent of rpoS but is abolished in a DeltarelA DeltaspoT (ppGpp(0)) background and rescued by suppressor mutations rendering the P-subunit of RNA polymerase to behave like a stringent polymerase. Ectopic elevation of ppGpp levels in growing cells, by overproducing the ReIA protein, triggered the induction of all usp genes. The expression of all usp genes was also elevated by a mutation in the ftsK cell division gene, and this super-induction could be suppressed by inactivating recA indicating that the usp paralogues are involved in the management of DNA. Indeed, uspC, uspD and uspE deletion mutants were all found to be sensitive to UV exposure. Overexpression of UspD could compensate for the lack of a chromosomal uspD gene but not a uspA gene. Similarly, UspA overproduction could only compensate for the lack of chromosomal uspA. Moreover, combination of usp mutations had no additive effect on UV sensitivity indicating that they are all cooperating and required in the same pathway, which could explain the co-ordinated regulation of the genes.