Global regulation of gene expression

Microorganisms such as Escherichia coli live in environments subject to rapid changes in the availability of the carbon and nitrogen compounds necessary to provide energy and building blocks for the synthesis of cell material. Their survival depends on their ability to regulate the expression of genes coding for the enzymes and transport proteins required for growth in the altered environment. The availability of microarrays of the entire genome of E. coli has made it possible to measure the expression of all genes by determining the levels of the corresponding species of RNA. As reported in this issue of PNAS, Sydney Kustu, Robert A. Bender, and their coworkers (1) have used this method to identify all of the genes whose expression is activated in response to the replacement of the preferred nitrogen source, ammonia, by a non-preferred source of nitrogen (nitrogen regulation) (2). Their study revealed that the products of many genes that had previously not been known to be subject to nitrogen regulation are responsible for the scavenging of amino acids and peptides, among them the dipeptide d-alanyl-d-alanine. Under conditions of stress, probably including nitrogen limitation, E. coli switches the mechanism for crosslinking the peptidoglycan layer of the cell wall to one that releases d-alanyl-d-alanine into the growth medium. The activation of the expression …