Sequences in the -35 region of Escherichia coli rpoS-dependent genes promote transcription by E sigma S

Abstract

Bacterial cells must be able to efficiently induce transcription of a number of genes whose products are required to survive environmental stresses. Escherichia coli can survive environments characterized by nutrient scarcity, limited oxygen availability, toxic chemicals, and high osmolarity. Several of the genes induced by environmental stress rely on the rpoS gene for induction (2, 9, 22-25, 30, 36, 61, 64).rpoS encodes an alternate sigma factor (47) which acts as a principal regulator of E. coli's stress response by modifying the promoter recognition capacity of core RNA polymerase. Stationary-phase induction is characteristic of rpoS-dependent genes (9, 22-24, 30, 34-36, 45, 58, 60, 61, 64). Several rpoSdependent genes (bolA, otsBA, treA, osmB, osmY, and pexB) are also induced by hyperosmotic stress during exponential growth in a defined minimal medium (24,25,30,34,35,38,64). The cellular content of the S protein correlates with Sdependent gene induction, increasing during stationary phase and following hyperosmotic shock (37). Thus far, no DNAbinding protein that acts specifically as an activator of Sdependent genes has been identified. However, a mutation in hns, which encodes a nonspecific DNA-associated protein, leads to accumulation of the S protein during exponential growth (4, 63). An increase in the level of the alarmone ppGpp correlates with increased amounts of S protein (16). UDPglucose and homoserine lactone have also been proposed as signal molecules that influence production of S (5, 27 , which is encoded by the rpoD gene, is the chief determinant of promoter recognition by RNA polymerase during exponential growth. A large body of statistical and genetic evidence has identified the D consensus promoter as two hexamers centered at about Ϫ10 and Ϫ35 nucleotides upstream relative to the start site of transcription (19,20,66). The ability of certain rpoD mutants to specifically suppress mutations at the Ϫ10 and Ϫ35 sites of the E. coli lac and P22 ant promoters strongly suggests that promoter recognition is determined by direct interactions between certain amino acids of regions 2.4 and 4.2 of the D protein and nucleotides in the conserved Ϫ10 and Ϫ35 promoter hexamers (15,52,59).Studies of promoters used by secondary sigmas in a variety of bacteria, including E. coli, Bacillus subtilis, and Pseudomonas aeruginosa, have also identified two regions of conserved sequence believed to function as promoter recognition elements (10, 21, 67). The homology between S and D in the regions thought to determine promoter specificity is sufficient to predict that S holoenzyme will interact with promoter DNA in a manner resembling that of D holoenzyme. Specifically, one would suppose that S promoters would consist of two conserved sequence elements.It has been demonstrated through in vitro assays that transcription by S holoenzyme is determined by recognition of nucleotides downstream from position Ϫ17 of rpoS-dependent promoters (56). We have investigated the in vivo requirements for transcription by E S . We ...

σ S -Dependent Gene Expression at the Onset of Stationary Phase in Escherichia coli : Function of σ S -Dependent Genes and Identification of Their Promoter Sequences

“…4). It has been proposed that DNA bending upstream of the promoter region as well as motifs rich in C/G in the Ϫ35 region would favor S selectivity (45,98). Although our results do not allow us to confirm this hypothesis, we did find fairly high occurrence of GC or CG dinucleotides in the Ϫ35 area (Fig.…”

“…At some rpoS-dependent promoters, such as osmE (12), disruption of the Ϫ35 sequence (TTGAAA) has a negative effect on S -mediated transcription. However, data on the importance of a Ϫ35 sequence for E S are controversial, and very few known S -dependent promoters possess a Ϫ35 sequence similar to that recognized by E 70 (12,72,87,98). Among the newly identified promoters, only three (pfkB, ytfK, and yggE) have a discernible Ϫ35 element with four of six matches to the 70 consensus sequence, possibly suggesting that E S -specific Ϫ35 sequences might strongly diverge from the E 70 consensus (Fig.…”

A comprehensive library of DNA-binding site matrices for 55 proteins applied to the complete Escherichia coli K-12 genome 1 1Edited by R. Ebright

“…Five different RpoD matrices were built based on the promoter compilation reported by Lisser & Margalit (1993), corresponding to the 15-19 nucleotide spacing classes of E. coli RpoD promoters. Two different RpoH and RpoS matrices were constructed, representing two promoter spacing classes for each (Gross, 1996;Wise et al, 1996).…”

Sequence and properties of pentaerythritol tetranitrate reductase from Enterobacter cloacae PB2

“…A putative ribosome-binding site and transcription termination sequence were detected. No obvious 70 -like promoter sequence was present, but three regions between a putative upstream termination sequence and the ribosome-binding site have significant homology to Escherichia coli S -dependent promoters (21). The deduced amino acid sequence of PETN reductase was compared to sequences in protein and nucleic acid databases using the BLAST program of the GCG package (6).…”