Identification of Conserved, RpoS-Dependent Stationary-Phase Genes of Escherichia coli

Abstract

During entry into stationary phase, many free-living, gram-negative bacteria express genes that impart cellular resistance to environmental stresses, such as oxidative stress and osmotic stress. Many genes that are required for stationary-phase adaptation are controlled by RpoS, a conserved alternative sigma factor, whose expression is, in turn, controlled by many factors. To better understand the numbers and types of genes dependent upon RpoS, we employed a genetic screen to isolate more than 100 independent RpoS-dependent gene fusions from a bank of several thousand mutants harboring random, independent promoter-lacZ operon fusion mutations. Dependence on RpoS varied from 2-fold to over 100-fold. The expression of all fusion mutations was normal in an rpoS/rpoS ؉ merodiploid (rpoS background transformed with an rpoS-containing plasmid). Surprisingly, the expression of many RpoS-dependent genes was growth phase dependent, albeit at lower levels, even in an rpoS background, suggesting that other growth-phase-dependent regulatory mechanisms, in addition to RpoS, may control postexponential gene expression. These results are consistent with the idea that many growth-phase-regulated functions in Escherichia coli do not require RpoS for expression. The identities of the 10 most highly RpoS-dependent fusions identified in this study were determined by DNA sequence analysis. Three of the mutations mapped to otsA, katE, ecnB, and osmY-genes that have been previously shown by others to be highly RpoS dependent. The six remaining highly-RpoS-dependent fusion mutations were located in other genes, namely, gabP, yhiUV, o371, o381, f186, and o215.Like many other free-living bacteria, Escherichia coli lives in environments that may change rapidly with respect to both nutrients and physical conditions. To survive stresses associated with starvation, E. coli expresses many stationary-phasespecific genes whose expression depends largely on an alternative sigma factor, s , encoded by rpoS (27,30). Inactivation of this gene renders the cell sensitive to heat shock (25, 29), oxidative stress (25, 29), osmotic challenge (29), and near-UV light (40). Proteins that depend on RpoS include catalase HPII (33, 39, 42) and catalase HPI (32), exonuclease III (39), penicillin-binding proteins (15), and osmoprotective proteins (21,22,53). RpoS is required for virulence (17) and acid tolerance (6) in Salmonella typhimurium. Although the signal(s) giving rise to increased expression of RpoS itself is not completely understood, homoserine lactone (23), UDP-6-glucose (10), and weak acids, such as acetate (42), have been shown to be inducers of RpoS.Several approaches have been used to enumerate and identify RpoS-regulated functions. Many of these genes, however, are probably still unidentified. Two-dimensional gel electrophoresis studies of proteins expressed in wild-type and rpoS strains have revealed that the RpoS regulon is quite large (30). Mutagenesis with random lacZ (16,51) or lux insertions (46), coupled with screening for RpoS-related ch...

Formation of 100S ribosomes in Staphylococcus aureus by the hibernation promoting factor homolog SaHPF

“…When Escherichia coli cell growth reaches the stationary phase from the exponential phase, the cells undergo significant morphological and physiological changes. These changes are known to involve more than 100 genes (Hengge‐Aronis 1996; Schellhorn et al. 1998).…”

Bacterial transcription factors involved in global regulation

“…The sequestering of sigma factors by antisigmas, and their interactions with chaperones as a widespread mechanism of physiological control, deserve more investigation. Furthermore, not every change in gene expression during the onset of stationary phase can be traced to σ S (Schellhorn et al ., 1998), and new mechanisms hitherto undisclosed might reveal more surprises.…”

Cell-cell interactions influence resistance and survival of Salmonella serotype Typhimurium to environmental stress

“…These differences have been ascribed to an alternative sigma factor, σ S , encoded by rpoS that is active in the stationary phase of many bacteria, directing RNA polymerase to transcribe a large number of genes that encode proteins designed to respond to and protect cells from a variety of environmental stresses (Loewen and Hengge‐Aronis 1994; O'Neal et al 1994; Chen et al . 1996; Schellhorn et al . 1998; Hengge‐Aronis 1999).…”

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