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Synopses of Research Articles Finding Sigma-Controlled Promoters DOI: 10.1371/journal.pbio.0040013 For bacteria, a change in the environment often causes physiological stress. Bacteria cope with that stress by altering the expression of suites of genes, and manufacturing new proteins, which may allow the cell to repair damage or protect itself in the future. This stress-induced gene expression response is often mediated by proteins called sigma factors. Sigma factors bind to the gene-transcribing machinery and direct this machinery to the promoter sites of the target genes. Identifying the binding sites for sigma factors that direct stress responses thus provides an important window on understanding how bacteria behave. Unfortunately, sigma factor binding sequences (otherwise known as promoters) vary from gene to gene, and current identifi cation methods are tedious and prone to error. In a new study, Virgil Rhodius, Carol Gross, and their colleagues describe a novel model that fi nds these sites quickly and accurately. Their results show that in Escherichia coli bacteria, the main targets for one type of sigma factor, called sigma factor E, are genes that increase production of cell envelope components (inner membrane, periplasm, and outer membrane). The authors fi rst found sigma factor E sites the hard way—by comparing gene expression in two strains of E. coli that differed in their intrinsic level of sigma E–induced activity. They looked for genes DOI: 10.1371/journal.pbio.0040013.g001 whose expression in the high sigma E activity strain differed most from genes in Escherichia coli (visualized with transmission electron microscopy, above) was used as a the low sigma E activity strain, and then model system to predict the regulatory DNA targets of sigma factors, bacterial proteins searched upstream of these genes for induced by stress. Image: CDC/Elizabeth H. Whit