Promoter selectivity of Escherichia coli RNA polymerase E sigma 70 and E sigma 38 holoenzymes. Effect of DNA supercoiling

Hyperglycemia and the O-GlcNAc transferase in rat aortic smooth muscle cells: elevated expression and altered patterns of O-GlcNAcylation

Hyperglycemia leads to vascular disease specific to diabetes mellitus. This pathology, which results from abnormal proliferation of smooth muscle cells in arterial walls, may lead to cataract, renal failure, and atherosclerosis. The hexosamine biosynthetic pathway is exquisitely responsive to glucose concentration and plays an important role in glucose-induced insulin resistance. UDP-GlcNAc: polypeptide O-N-acetylglucosaminyltransferase (O-GlcNAc transferase; OGTase) catalyzes the O-linked attachment of single GlcNAc moieties to serine and threonine residues on many cytosolic or nuclear proteins. Polyclonal antibody against OGTase was used to examine the expression of OGTase in rat aorta and aortic smooth muscle (RASM) cells. OGTase enzymatic activity and expression at the mRNA and protein levels were determined in RASM cells cultured at normal (5 mM) and at high (20 mM) glucose concentrations. OGTase mRNA and protein are expressed in both endothelial cells and smooth muscle cells in the aorta of normal rats. In both cell types, the nucleus is intensely stained, while the cytoplasm stains diffusely. Immunoelectron microscopy shows that OGTase is localized to euchromatin and around the myofilaments of smooth muscle cells. In RASM cells grown in 5 mM glucose, OGTase is also located mainly in the nucleus. Hyperglycemic RASM cells also display a relative increase in OGTase's p78 subunit and an overall increase protein and activity for OGTase. Biochemical analyses show that hyperglycemia qualitatively and quantitatively alters the glycosylation or expression of many O-GlcNAc-modified proteins in the nucleus. These results suggest that the abnormal O-GlcNAc modification of intracellular proteins may be involved in glucose toxicity to vascular tissues.

What makes an Escherichia coli promoter sigma(S) dependent? Role of the -13/-14 nucleotide promoter positions and region 2.5 of sigma(S)

The sigmaS and sigma70 subunits of Escherichia coli RNA polymerase recognize very similar promoter sequences. Therefore, many promoters can be activated by both holoenzymes in vitro. The same promoters, however, often exhibit distinct sigma factor selectivity in vivo. It has been shown that high salt conditions, reduced negative supercoiling and the formation of complex nucleoprotein structures in a promoter region can contribute to or even generate sigmaS selectivity. Here, we characterize the first positively acting sigmaS-selective feature in the promoter sequence itself. Using the sigmaS-dependent csiD promoter as a model system, we demonstrate that C and T at the -13 and -14 positions, respectively, result in strongest expression. We provide allele-specific suppression data indicating that these nucleotides are contacted by K173 in region 2.5 of sigmaS. In contrast, sigma70, which features a glutamate at the corresponding position (E458), as well as the sigmaS(K173E) variant, exhibit a preference for a G(-13). C(-13) is highly conserved in sigmaS-dependent promoters, and additional data with the osmY promoter demonstrate that the K173/C(-13) interaction is of general importance. In conclusion, our data demonstrate an important role for region 2.5 in sigmaS in transcription initiation. Moreover, we propose a consensus sequence for a sigmaS-selective promoter and discuss its emergence and functional properties from an evolutionary point of view.

Escherichia coli and Salmonella 2000: the view from here

Five years after the publication of the second edition of the reference book Escherichia coli and Salmonella: Cellular and Molecular Biology, and on the eve of launching a successor venture, the editors and colleagues examine where we stand in our quest for an understanding of these organisms. The main areas selected for this brief inquiry are genomics, evolution, molecular multifunctionality, functional backups, regulation of gene expression, cell biology, sensing of the environment, and ecology.

The effects of DNA supercoiling on the expression of operons of the ilv regulon of Escherichia coli suggest a physiological rationale for divergently transcribed operons

Transcriptional activities of closely spaced divergent promoters are affected by the accumulation of local negative superhelicity in the region between transcribing RNA polymerase molecules (transcriptional coupling). The effect of this transcription-induced DNA supercoiling on these promoters depends on their intrinsic properties. As the global superhelical density of the chromosome is controlled by the energy charge of the cell, which is affected by environmental stresses and transitions from one growth state to another, the transcriptional coupling that occurs between divergently transcribed promoters is likely to serve a physiological purpose. Here, we suggest that transcriptional coupling between the divergent promoters of the ilvYC operon of Escherichia coli serves to co-ordinate the expression of this operon with other operons of the ilv regulon during metabolic adjustments associated with growth state transitions. As DNA supercoiling-dependent transcriptional coupling between the promoters of other divergently transcribed operons is investigated, additional global gene regulatory mechanisms and physiological roles are sure to emerge.

Functional modulation of Escherichia coli RNA polymerase

The promoter recognition specificity of Escherichia coli RNA polymerase is modulated by replacement of the sigma subunit in the first step and by interaction with transcription factors in the second step. The overall differentiated state of approximately 2000 molecules of the RNA polymerase in a single cell can be estimated after measurement of both the intracellular concentrations and the RNA polymerase-binding affinities for all seven species of the sigma subunit and 100-150 transcription factors. The anticipated impact from this line of systematic approach is that the prediction of the expression hierarchy of approximately 4000 genes on the E. coli genome can be estimated.

Roles of the glutathione- and thioredoxin-dependent reduction systems in the Escherichia coli and saccharomyces cerevisiae responses to oxidative stress

The glutathione- and thioredoxin-dependent reduction systems are responsible for maintaining the reduced environment of the Escherichia coli and Saccharomyces cerevisiae cytosol. Here we examine the roles of these two cellular reduction systems in the bacterial and yeast defenses against oxidative stress. The transcription of a subset of the genes encoding glutathione biosynthetic enzymes, glutathione reductases, glutaredoxins, thioredoxins, and thioredoxin reductases, as well as glutathione- and thioredoxin-dependent peroxidases is clearly induced by oxidative stress in both organisms. However, only some strains carrying mutations in single genes are hypersensitive to oxidants. This is due, in part, to the redundant effects of the gene products and the overlap between the two reduction systems. The construction of strains carrying mutations in multiple genes is helping to elucidate the different roles of glutathione and thioredoxin, and studies with such strains have recently revealed that these two reduction systems modulate the activities of the E. coli OxyR and SoxR and the S. cerevisiae Yap1p transcriptional regulators of the adaptive responses to oxidative stress.

DNA supercoiling and transcription in Escherichia coli: The FIS connection

The nucleoid-associated protein FIS modulates the topology of DNA in a growth-phase dependent manner functioning homeostatically to counteract excessive levels of negative superhelicity. We propose that this is achieved by at least two mechanisms: the physical constraint of low levels of negative superhelicity by FIS binding to DNA and by a reduction in the expression and effectiveness of DNA gyrase. In addition, high levels of expression of the fis gene do themselves require a high negative superhelical density. On DNA substrates containing phased high affinity binding sites, as exemplified by the upstream activating sequence of the tyrT promoter, FIS forms tightly bent DNA structures, or microloops, that are necessary for the optimal expression of the promoter. We suggest that these microloops compensate in part for the FIS-induced lowering of the superhelical density.

Effects of combination of different -10 hexamers and downstream sequences on stationary-phase-specific sigma factor sigma(S)-dependent transcription in Pseudomonas putida

The main sigma factor activating gene expression, necessary in stationary phase and under stress conditions, is sigma(S). In contrast to other minor sigma factors, RNA polymerase holoenzyme containing sigma(S) (Esigma(S)) recognizes a number of promoters which are also recognized by that containing sigma(70) (Esigma(70)). We have previously shown that transposon Tn4652 can activate silent genes in starving Pseudomonas putida cells by creating fusion promoters during transposition. The sequence of the fusion promoters is similar to the sigma(70)-specific promoter consensus. The -10 hexameric sequence and the sequence downstream from the -10 element differ among these promoters. We found that transcription from the fusion promoters is stationary phase specific. Based on in vivo experiments carried out with wild-type and rpoS-deficient mutant P. putida, the effect of sigma(S) on transcription from the fusion promoters was established only in some of these promoters. The importance of the sequence of the -10 hexamer has been pointed out in several published papers, but there is no information about whether the sequences downstream from the -10 element can affect sigma(S)-dependent transcription. Combination of the -10 hexameric sequences and downstream sequences of different fusion promoters revealed that sigma(S)-specific transcription from these promoters is not determined by the -10 hexameric sequence only. The results obtained in this study indicate that the sequence of the -10 element influences sigma(S)-specific transcription in concert with the sequence downstream from the -10 box.

A novel NO-responding regulator controls the reduction of nitric oxide in Ralstonia eutropha

Ralstonia eutropha H16 mediates the reduction of nitric oxide (NO) to nitrous oxide (N2O) with two isofunctional single component membrane-bound NO reductases (NorB1 and NorB2). This reaction is integrated into the denitrification pathway that involves the successive reduction of nitrate to dinitrogen. The norB1 gene is co-transcribed with norA1 from a sigma54 (RpoN)-dependent promoter, located upstream of norA1. With the aid of norA1'-lacZ transcriptional fusions and the generation of regulatory mutants, it was shown that norB1 gene transcription requires a functional rpoN gene and the regulator NorR, a novel member of the NtrC family of response regulators. The regulator gene maps adjacent to norAB, is divergently transcribed and present in two copies on the megaplasmid pHG1 (norR1) and the chromosome (norR2). Transcription activation by NorR responds to the availability of NO. A nitrite reductase-deficient mutant that is incapable of producing NO endogenously, showed a 70% decrease of norA1 expression. Addition of the NO-donating agent sodium nitroprusside caused induction of norA1'-lacZ transcription. Truncation of the N-terminal receiver domain of NorR1 interrupted the NO signal transduction and led to a constitutive expression of norA1'-lacZ. The results indicate that NorR controls the reductive conversion of NO in R. eutropha. This reaction is not strictly co-ordinated on the regulatory level with the other nitrogen oxide-reducing steps of the denitrification chain that are independent of NorR.

Competition among seven Escherichia coli sigma subunits: relative binding affinities to the core RNA polymerase

Seven different species of the RNA polymerase sigma subunit exist in Escherichia coli, each binding to a single species of the core enzyme and thereby directing transcription of a specific set of genes. To test the sigma competition model in the global regulation of gene transcription, all seven E.coli sigma subunits have been purified and compared for their binding affinities to the same core RNA polymerase (E). In the presence of a fixed amount of sigma(70), the principal sigma for growth-related genes, the level of Esigma(70) holoenzyme formation increased linearly with the increase in core enzyme level, giving an apparent K:(d) for the core enzyme of 0.26 nM. Mixed reconstitution experiments in the presence of a fixed amount of core enzyme and increasing amounts of an equimolar mixture of all seven sigma subunits indicated that sigma(70) is strongest in terms of core enzyme binding, followed by sigma(N), sigma(F), sigma(E)/sigma(FecI), sigma(H) and sigma(S) in decreasing order. The orders of core binding affinity between sigma(70) and sigma(N) and between sigma(70) and sigma(H) were confirmed by measuring the replacement of one core-associated sigma by another sigma subunit. Taken together with the intracellular sigma levels, we tried to estimate the number of each holoenzyme form in growing E. coli cells.

Conservation of sigma-core RNA polymerase proximity relationships between the enhancer-independent and enhancer-dependent sigma classes

Two distinct classes of RNA polymerase sigma factors (sigma) exist in bacteria and are largely unrelated in primary amino acid sequence and their modes of transcription activation. Using tethered iron chelate (Fe-BABE) derivatives of the enhancer-dependent sigma(54), we mapped several sites of proximity to the beta and beta' subunits of the core RNA polymerase. Remarkably, most sites localized to those previously identified as close to the enhancer-independent sigma(70) and sigma(38). This indicates a common use of sets of sequences in core for interacting with the two sigma classes. Some sites chosen in sigma(54) for modification with Fe-BABE were positions, which when mutated, deregulate the sigma(54)-holoenzyme and allow activator-independent initiation and holoenzyme isomerization. We infer that these sites in sigma(54) may be involved in interactions with the core that contribute to maintenance of alternative states of the holoenzyme needed for either the stable closed promoter complex conformation or the isomerized holoenzyme conformation associated with the open promoter complex. One site of sigma(54) proximity to the core is apparently not evident with sigma(70), and may represent a specialized interaction.

sigma factor selectivity of Escherichia coli RNA polymerase: role for CRP, IHF and lrp transcription factors

osmY is a stationary phase-induced and osmotically regulated gene in Escherichia coli that requires the stationary phase RNA polymerase (Esigma(S)) for in vivo expression. We show here that the major RNA polymerase, Esigma(70), also transcribes osmY in vitro and, depending on genetic background, even in vivo. The cAMP receptor protein (CRP) bound to cAMP, the leucine-responsive regulatory protein (Lrp) and the integration host factor (IHF) inhibit transcription initiation at the osmY promoter. The binding site for CRP is centred at -12.5 from the transcription start site, whereas Lrp covers the whole promoter region. The site for IHF maps in the -90 region. By mobility shift assay, permanganate reactivity and in vitro transcription experiments, we show that repression is much stronger with Esigma(70) than with Esigma(S) holoenzyme. We conclude that CRP, Lrp and IHF inhibit open complex formation more efficiently with Esigma(70) than with Esigma(S). This different ability of the two holoenzymes to interact productively with promoters once assembled in complex nucleoprotein structures may be a crucial factor in generating sigma(S) selectivity in vivo.

6S RNA regulates E. coli RNA polymerase activity

The E. coli 6S RNA was discovered more than three decades ago, yet its function has remained elusive. Here, we demonstrate that 6S RNA associates with RNA polymerase in a highly specific and efficient manner. UV crosslinking experiments revealed that 6S RNA directly contacts the sigma70 and beta/beta' subunits of RNA polymerase. 6S RNA accumulates as cells reach the stationary phase of growth and mediates growth phase-specific changes in RNA polymerase. Stable association between sigma70 and core RNA polymerase in extracts is only observed in the presence of 6S RNA. We show 6S RNA represses expression from a sigma70-dependent promoter during stationary phase. Our results suggest that the interaction of 6S RNA with RNA polymerase modulates sigma70-holoenzyme activity.

RpoS-dependent promoters require guanosine tetraphosphate for induction even in the presence of high levels of sigma(s)

RpoS-dependent promoters require ppGpp for induction in the stationary phase. This has been thought to be a simple consequence of final sigma(S) itself requiring ppGpp for its production. By using four model promoters requiring final sigma(S) for normal induction in the stationary phase, we demonstrate that final sigma(S)-dependent promoters require ppGpp even in the presence of high levels of final sigma(S) produced ectopically. Similar to final sigma(70)-dependent promoters under positive control by ppGpp, the requirement of final sigma(S)-dependent promoters for this alarmone is bypassed by specific "stringent" mutations in the beta-subunit of RNA polymerase. The results suggest that stationary phase induction of both final sigma(S)- and final sigma(70)-dependent genes requires the stringent control modulon and that stringency confers dual control on the RpoS regulon by affecting promoter activity and the levels of the required final sigma-factor.

Negative regulation of the bolA1p of Escherichia coli K-12 by the transcription factor OmpR for osmolarity response genes

To test whether OmpR is involved in regulation of the bolA1p, we investigated possible effects of ompR mutation on transcription from bolA1p. In vivo, bolA1p was found to be repressed by OmpR. Furthermore in vitro, the phospho-OmpR was found to bind to the OmpR binding region of bolA1p and repress the transcription by Esigma(S) or Esigma(D). These results suggest that the phosphorylated form of OmpR is a negative regulator for the transcription of the bolA1p promoter.

The response regulator RssB, a recognition factor for sigmaS proteolysis in Escherichia coli, can act like an anti-sigmaS factor

sigmaS (RpoS) is the master regulator of the general stress response in Escherichia coli. Several stresses increase cellular sigmaS levels by inhibiting proteolysis of sigmaS, which under non-stress conditions is a highly unstable protein. For this ClpXP-dependent degradation, the response regulator RssB acts as a recognition factor, with RssB affinity for sigmaS being modulated by phosphorylation. Here, we demonstrate that RssB can also act like an anti-sigma factor for sigmaS in vivo, i.e. RssB can inhibit the expression of sigmaS-dependent genes in the presence of high sigmaS levels. This becomes apparent when (i) the cellular RssB/sigmaS ratio is at least somewhat elevated and (ii) proteolysis is reduced (for example in stationary phase) or eliminated (for example in a clpP mutant). Two modes of inhibition of sigmaS by RssB can be distinguished. The 'catalytic' mode is observed in stationary phase cells with a substoichiometric RssB/sigmaS ratio, requires ClpP and therefore probably corresponds to sequestering of sigmaS to Clp protease (even though sigmaS is not degraded). The 'stoichiometric' mode occurs in clpP mutant cells upon overproduction of RssB to levels that are equal to those of sigmaS, and therefore probably involves binary complex formation between RssB and sigmaS. We also show that, under standard laboratory conditions, the cellular level of RssB is more than 20-fold lower than that of sigmaS and is not significantly controlled by stresses that upregulate sigmaS. We therefore propose that antisigma factor activity of RssB may play a role under not yet identified growth conditions (which may result in RssB induction), or that RssB is a former antisigma factor that during evolution was recruited to serve as a recognition factor for proteolysis.

Involvement of differential efficiency of transcription by esigmas and esigma70 RNA polymerase holoenzymes in growth phase regulation of the Escherichia coli osmE promoter

Transcription of the gene osmE of Escherichia coli is inducible by elevated osmotic pressure and during the decelerating phase of growth. osmE expression is directed by a single promoter, osmEp. Decelerating phase induction of osmEp is dependent on the sigmas (RpoS) factor, whereas its osmotic induction is independent of sigmas. Purified Esigmas and Esigma70 were both able to transcribe osmEp in vitro on supercoiled templates. In the presence of rpoD800, a mutation resulting in a thermosensitive sigma70 factor, a shift to non-permissive temperature abolished induction of osmEp after an osmotic shock during exponential phase, but did not affect the decelerating phase induction. Point mutations affecting osmEp activity were isolated. Down-promoter mutations decreased transcription in both the presence and the absence of sigmas, indicating that the two forms of RNA polymerase holoenzyme recognize very similar sequence determinants on the osmE promoter. Three up-promoter mutations brought osmEp closer to the consensus of Esigma70-dependent promoters. The two variant promoters exhibiting the highest efficiency became essentially independent of sigmas in vivo. Our data suggest that Esigmas transcribes wild-type osmEp with a higher efficiency than Esigma70. A model in which an intrinsic differential recognition contributes to growth phase-dependent regulation is proposed. Generalization of this model to other sigmas-dependent promoters is discussed.

Transcriptional coupling between the divergent promoters of a prototypic LysR-type regulatory system, the ilvYC operon of Escherichia coli

The twin-domain model [Liu, L. F. & Wang, J. C. (1987) Proc. Natl. Acad. Sci. USA 84, 7024-7027] suggests that closely spaced, divergent, superhelically sensitive promoters can affect the transcriptional activity of one another by transcriptionally induced negative DNA supercoiling generated in the divergent promoter region. This gene arrangement is observed for many LysR-type-regulated operons in bacteria. We have examined the effects of divergent transcription in the prototypic LysR-type system, the ilvYC operon of Escherichia coli. Double-reporter constructs with the lacZ gene under transcriptional control of the ilvC promoter and the galK gene under control of the divergent ilvY promoter were used to demonstrate that a down-promoter mutation in the ilvY promoter severely decreases in vivo transcription from the ilvC promoter. However, a down-promoter mutation in the ilvC promoter only slightly affects transcription from the ilvY promoter. In vitro transcription assays with DNA topoisomers showed that transcription from the ilvC promoter increases over the entire range of physiological superhelical densities, whereas transcription initiation from the ilvY promoter exhibits a broad optimum at a midphysiological superhelical density. Evidence that this promoter coupling is DNA supercoiling-dependent is provided by the observation that a novobiocin-induced decrease in global negative superhelicity results in an increase in ilvY promoter activity and a decrease in ilvC promoter activity predicted by the in vitro data. We suggest that this transcriptional coupling is important for coordinating basal level expression of the ilvYC operon with the nutritional and environmental conditions of cell growth.

Mechanisms for redox control of gene expression

This review discusses various mechanisms that regulatory proteins use to control gene expression in response to alterations in redox. The transcription factor SoxR contains stable [2Fe-2S] centers that promote transcription activation when oxidized. FNR contains [4Fe-4S] centers that disassemble under oxidizing conditions, which affects DNA-binding activity. FixL is a histidine sensor kinase that utilizes heme as a cofactor to bind oxygen, which affects its autophosphorylation activity. NifL is a flavoprotein that contains FAD as a redox responsive cofactor. Under oxidizing conditions, NifL binds and inactivates NifA, the transcriptional activator of the nitrogen fixation genes. OxyR is a transcription factor that responds to redox by breaking or forming disulfide bonds that affect its DNA-binding activity. The ability of the histidine sensor kinase ArcB to promote phosphorylation of the response regulator ArcA is affected by multiple factors such as anaerobic metabolites and the redox state of the membrane. The global regulator of anaerobic gene expression in alpha-purple proteobacteria, RegB, appears to directly monitor respiratory activity of cytochrome oxidase. The aerobic repressor of photopigment synthesis, CrtJ, seems to contain a redox responsive cysteine. Finally, oxygen-sensitive rhizobial NifA proteins presumably bind a metal cofactor that senses redox. The functional variability of these regulatory proteins demonstrates that prokaryotes apply many different mechanisms to sense and respond to alterations in redox.

Growth phase-dependent variation in protein composition of the Escherichia coli nucleoid

The genome DNA of Escherichia coli is associated with about 10 DNA-binding structural proteins, altogether forming the nucleoid. The nucleoid proteins play some functional roles, besides their structural roles, in the global regulation of such essential DNA functions as replication, recombination, and transcription. Using a quantitative Western blot method, we have performed for the first time a systematic determination of the intracellular concentrations of 12 species of the nucleoid protein in E. coli W3110, including CbpA (curved DNA-binding protein A), CbpB (curved DNA-binding protein B, also known as Rob [right origin binding protein]), DnaA (DNA-binding protein A), Dps (DNA-binding protein from starved cells), Fis (factor for inversion stimulation), Hfq (host factor for phage Q(beta)), H-NS (histone-like nucleoid structuring protein), HU (heat-unstable nucleoid protein), IciA (inhibitor of chromosome initiation A), IHF (integration host factor), Lrp (leucine-responsive regulatory protein), and StpA (suppressor of td mutant phenotype A). Intracellular protein levels reach a maximum at the growing phase for nine proteins, CbpB (Rob), DnaA, Fis, Hfq, H-NS, HU, IciA, Lrp, and StpA, which may play regulatory roles in DNA replication and/or transcription of the growth-related genes. In descending order, the level of accumulation, calculated in monomers, in growing E. coli cells is Fis, Hfq, HU, StpA, H-NS, IHF*, CbpB (Rob), Dps*, Lrp, DnaA, IciA, and CbpA* (stars represent the stationary-phase proteins). The order of abundance, in descending order, in the early stationary phase is Dps*, IHF*, HU, Hfq, H-NS, StpA, CbpB (Rob), DnaA, Lrp, IciA, CbpA, and Fis, while that in the late stationary phase is Dps*, IHF*, Hfq, HU, CbpA*, StpA, H-NS, CbpB (Rob), DnaA, Lrp, IciA, and Fis. Thus, the major protein components of the nucleoid change from Fis and HU in the growing phase to Dps in the stationary phase. The curved DNA-binding protein, CbpA, appears only in the late stationary phase. These changes in the composition of nucleoid-associated proteins in the stationary phase are accompanied by compaction of the genome DNA and silencing of the genome functions.

Transcriptional organization and in vivo role of the Escherichia coli rsd gene, encoding the regulator of RNA polymerase sigma D

The regulator of sigma D (Rsd) was identified as an RNA polymerase sigma70-associated protein in stationary-phase Escherichia coli with the inhibitory activity of sigma70-dependent transcription in vitro (M. Jishage and A. Ishihama, Proc. Natl. Acad. Sci. USA 95:4953-4958, 1998). Primer extension analysis of rsd mRNA indicated the presence of two promoters, sigmaS-dependent P1 and sigma70-dependent P2 with the gearbox sequence. To get insight into the in vivo role of Rsd, the expression of a reporter gene fused to either the sigma70- or sigmaS-dependent promoter was analyzed in the absence of Rsd or the presence of overexpressed Rsd. In the rsd null mutant, the sigma70- and sigmaS-dependent gene expression was increased or decreased, respectively. On the other hand, the sigma70- or sigmaS-dependent transcription was reduced or enhanced, respectively, after overexpression of Rsd. The repression of the sigmaS-dependent transcription in the rsd mutant is overcome by increased production of the sigmaS subunit. Together these observations support the prediction that Rsd is involved in replacement of the RNA polymerase sigma subunit from sigma70 to sigmaS during the transition from exponential growth to the stationary phase.

Sequences in sigmaN determining holoenzyme formation and properties

Sigma subunits of bacterial RNA polymerases are closely involved in many steps of promoter-specific transcription initiation. Holoenzyme formed with the specialised minor sigma-N (sigmaN) protein binds rare promoters in a transcriptionally inactive state and functions in enhancer-dependent transcription. Using competition and dissociation assays, we show that sigmaN-holoenzyme has a stability comparable to the major sigma70-holoenzyme. Purified partial sequences of sigmaN were prepared and assayed for retention of core RNA polymerase binding activity. Two discrete fragments of sigmaN which both bind the core but with significantly different affinities were identified, demonstrating that the sigmaN interface with core RNA polymerase is extensive. The low affinity segment of sigmaN included region I sequences, an amino terminal domain which mediates activator responsiveness and formation of open promoter complexes. The higher affinity site lies within a 95 residue fragment of region III. We propose that the core to region I contact mediates properties of the sigmaN-holoenzyme important for enhancer responsiveness. Heparin is shown to dissociate sigmaN and core, indicating that disruption of the holoenzyme is involved in the heparin sensitivity of the sigmaN closed complex.

Interplay of global regulators and cell physiology in the general stress response of Escherichia coli

Under various stress conditions, two sigma subunits of RNA polymerase, sigmaS and sigma70, coexist in Escherichia coli cells. In contrast to sigma70, sigmaS is subject to intricate regulation and coordinates an emergency reaction to stress as well as long term stress adaptation. In vivo, the two sigma factors clearly control different genes. Yet, they are structurally and functionally very similar and basically recognize the same promoter sequences. Recent data suggest that sigma factor specificity at stress-activated promoters is affected by the interplay of the two RNA polymeraseholoenzymes with additional regulatory factors, such as H-NS, Lrp, CRP, IHF or Fis, that differentially affect transcription initiation by sigmaS or sigma70 in a promoter-specific manner.

Role of the alternative sigma factor sigmaS in expression of the AlkS regulator of the Pseudomonas oleovorans alkane degradation pathway

The AlkS protein activates transcription from the PalkB promoter, allowing the expression of a number of genes required for the assimilation of alkanes in Pseudomonas oleovorans. We have identified the promoter from which the alkS gene is transcribed, PalkS, and analyzed its expression under different conditions and genetic backgrounds. Transcription from PalkS was very low during the exponential phase of growth and increased considerably when cells reached the stationary phase. The PalkS -10 region was similar to the consensus described for promoters recognized by Escherichia coli RNA polymerase bound to the alternative sigma factor sigmaS, which directs the expression of many stationary-phase genes. Reporter strains containing PalkS-lacZ transcriptional fusions showed that PalkS promoter is very weakly expressed in a Pseudomonas putida strain bearing an inactivated allele of the gene coding for sigmaS, rpoS. When PalkS was transferred to E. coli, transcription started at the same site and expression was higher in stationary phase only if sigmaS-RNA polymerase was present. The low levels of AlkS protein generated in the absence of sigmaS were enough to support a partial induction of the PalkB promoter. The -10 and -35 regions of PalkS promoter also show some similarity to the consensus recognized by sigmaD-RNA polymerase, the primary form of RNA polymerase. We propose that in exponential phase PalkS is probably recognized both by sigmaD-RNA polymerase (inefficiently) and by sigmaS-RNA polymerase (present at low levels), leading to low-level expression of the alkS gene. sigmaS-RNA polymerase would be responsible for the high level of activity of PalkS observed in stationary phase.

Modulation of the nucleoid, the transcription apparatus, and the translation machinery in bacteria for stationary phase survival

Upon sensing an impending saturation level of their population density, Escherichia coli cells enter into the stationary phase. We have identified structural and functional modulations of the nucleoid, the transcription apparatus and the translation machinery occurring during the transition from exponential growth to stationary phase. The major DNA-binding proteins, Fis, HU and Hfq, in the exponential-phase nucleoid are replaced by a single stationary-phase protein Dps, thereby compacting the nucleoid and ultimately leading to silencing of the DNA functions. The transcription apparatus is modified by replacing the major promoter recognition subunit, sigma70, with sigmaS. A stationary-phase protein, Rsd (Regulator of Sigma D), with the binding activity of sigma70 is involved in the efficient replacement of sigma and/or the storage of unused sigma70. Changes in cytoplasmic composition also differentially influence the activity of Esigma70 and EsigmaS holoenzymes. Together, these effects may result in the preferential transcription of stationary-phase specific genes. The translation machinery is also modulated in stationary phase, by the formation of translationally incompetent 100S ribosomes. A small stationary-phase protein, RMF (Ribosome Modulation Factor), is involved in the dimerization of 70S ribosome monomers.

NMR spectroscopic studies of the hydrogenosomal [2Fe-2S] ferredoxin from Trichomonas vaginalis: hyperfine-shifted 1H resonances

The hyperfine-shifted 1H NMR resonances of oxidized and reduced Trichomonas vaginalis ferredoxin, a functionally unique [2Fe-2S] ferredoxin, have been studied. The oxidized protein spectrum displayed a pattern of six broad upfield-shifted resonances between 13 and 40 ppm with chemical shifts distinct from those of other [2Fe-2S] ferredoxins. All hyperfine 1H resonances of the oxidized ferredoxin displayed anti-Curie temperature dependences. Reduced T. vaginalis ferredoxin displayed hyperfine resonances both upfield and downfield of the diamagnetic region. These resonances showed Curie temperature dependences. Overall the hyperfine-shifted NMR spectrum of T. vaginalis ferredoxin, along with other spectroscopic properties, suggested different structural properties for the active center of oxidized hydrogenosomal ferredoxins from those of other [2Fe-2S] ferredoxins.

Bacterial gene products in response to near-ultraviolet radiation

Our research has focused on bacterial gene products that protect cells from damage by near-ultraviolet radiation (near-UV) including gene products involved in the subsequent recovery process. Protective gene products include such anti-oxidants as catalases, superoxide dismutases and glutathione reductase. Near-UV damage recovery products include exonuclease III and DNA-glycosylases. Perhaps more critical than the products of structural genes are certain regulatory gene products that are triggered upon excess near-UV oxidation and lead to synthesis of entire batteries of anti-oxidant enzymes, DNA repair enzymes, and DNA-integrity proteins. Our recent experiments have focused on RpoS and its interaction with OxyR, two proteins that regulate the synthesis of molecules that protect cells from near-UV and other oxidative stresses.

The ftsQ1p gearbox promoter of Escherichia coli is a major sigma S-dependent promoter in the ddlB-ftsA region

The most potent promoters in the ddlB-ftsA region of the dcw cluster have been analysed for sigmaS-dependent transcription. Only the gearbox promoter ftsQ1p was found to be transcribed in vitro by RNA polymerase holoenzyme coupled to sigmaS (EsigmaS). This dependency on sigmaS was also found in vivo when single-copy fusions to a reporter gene were analysed in rpoS and rpoS+ backgrounds. Although ftsQ1p can be transcribed by RNA polymerase containing either sigmaD or sigmaS, there is a preference for EsigmaS when the assay conditions include potassium glutamate and supercoiled templates, a property shared with the bolA1p gearbox promoter. The rest of the promoters assayed, ftsQ2p and ftsZ2p3p4p, similarly to the control bolA2p promoter, were preferentially transcribed by EsigmaD, the housekeeper polymerase. The ftsQ1p and the bolA1p promoters also share the presence of AT-rich sequences upstream of the - 35 region and the requirement for an intact wild-type alpha-subunit for a proficient transcription, allowing their joint classification as gearboxes.

Negative regulation by RpoS: a case of sigma factor competition

A mutation in the Escherichia coli gene encoding the stationary phase-inducible sigma factor (sigmaS, RpoS) not only abolishes transcription of some genes in stationary phase, but also causes superinduction of other stationary phase-induced genes. We have examined this phenomenon of repression by sigmaS using as a model system the divergently transcribed stationary phase-inducible genes, uspA and uspB. uspA is transcribed by sigma70-programmed RNA polymerase and is superinduced in an rpoS mutant, while uspB induction is sigmaS dependent. The data suggest that the superinduction of uspA is caused by an increased amount of sigma70 bound to RNA polymerase in the absence of the competing sigmaS. Increasing the ability of sigma70 to compete against sigmaS by overproducing sigma70 mimics the effect of an rpoS mutation by causing superinduction of sigma70-dependent stationary phase-inducible genes (uspA and fadD), silencing of sigmaS-dependent genes (uspB, bolAp1 and fadL) and inhibiting the development of sigmaS-dependent phenotypes, such as hydrogen peroxide resistance in stationary phase. In addition, overproduction of sigmaS markedly reduced stationary phase expression of a sigma70-dependent promoter. Thus, we conclude that sigma factors compete for a limiting amount of RNA polymerase during stationary phase. The implications of this competition in the passive control of promoter activity is discussed.

Mapping the promoter DNA sites proximal to conserved regions of sigma 70 in an Escherichia coli RNA polymerase-lacUV5 open promoter complex

Base-specific interactions between promoter DNA and Escherichia coli RNA polymerase are regulated by a sigma (sigma) protein during transcription initiation. To map spatial relations between evolutionarily conserved regions of the primary sigma (sigma 70) and each DNA strand along the lacUV5 promoter in the transcriptionally active "open" complex, we have used a cysteine-tethered cutting reagent to cleave DNA strands. The chemical nuclease FeBABE [iron (S)-1-(p-bromoacetamidobenzyl)ethylenediaminetetraacetate] was conjugated to single-cysteine mutants of sigma 70 at sites 132C, 376C, 396C, 422C, 496C, 517C, or 581C. After formation of open promoter complexes between lacUV5 DNA and RNA polymerase holoenzymes carrying conjugated sigma 70 subunits, we observed promoter DNA cleavage spanning at least 60 bases, between positions -48 and +12. The results show that sigma 70 region 2.1, otherwise implicated in core enzyme binding, is proximal to the nontemplate strand of lacUV5 DNA between the -10 promoter element and positions as far downstream of the transcription start site as +12. Conserved region 3.2 of sigma 70 is proximal to the template strand near the +1 transcription start site, and region 3.1 is positioned between the lacUV5-10 and -35 promoter elements. We propose a model for the orientation of sigma 70 and DNA in the open complex.

Mapping the sigma70 subunit contact sites on Escherichia coli RNA polymerase with a sigma70-conjugated chemical protease

The core enzyme of Escherichia coli RNA polymerase acquires essential promoter recognition and transcription initiation activities by binding one of several sigma subunits. To characterize the proximity between sigma70, the major sigma for transcription of the growth-related genes, and the core enzyme subunits (alpha2 beta beta'), we analyzed the protein-cutting patterns produced by a set of covalently tethered FeEDTA probes [FeBABE: Fe (S)-1-(p-bromoacetamidobenzyl)EDTA]. The probes were positioned in or near conserved regions of sigma70 by using seven mutants, each carrying a single cysteine residue at position 132, 376, 396, 422, 496, 517, or 581. Each FeBABE-conjugated sigma70 was bound to the core enzyme, which led to cleavage of nearby sites on the beta and beta' subunits (but not alpha). Unlike the results of random cleavage [Greiner, D. P., Hughes, K. A., Gunasekera, A. H. & Meares, C. F. (1996) Proc. Natl. Acad. Sci. USA 93, 71-75], the cut sites from different probe-modified sigma70 proteins are clustered in distinct regions of the subunits. On the beta subunit, cleavage is observed in two regions, one between residues 383 and 554, including the conserved C and Rif regions; and the other between 854 and 1022, including conserved region G, regions of ppGpp sensitivity, and one of the segments forming the catalytic center of RNA polymerase. On the beta' subunit, the cleavage was identified within the sequence 228-461, including beta' conserved regions C and D (which comprise part of the catalytic center).

A stationary phase protein in Escherichia coli with binding activity to the major sigma subunit of RNA polymerase

Switching of the transcription pattern in Escherichia coli during the growth transition from exponential to stationary phase is accompanied by the replacement of the RNA polymerase-associated sigma70 subunit (sigmaD) with sigma38 (sigmaS). A fraction of the sigma70 subunit in stationary phase cell extracts was found to exist as a complex with a novel protein, designated Rsd (Regulator of sigma D). The intracellular level of Rsd starts to increase during the transition from growing to stationary phase. The rsd gene was identified at 90 min on the E. coli chromosome. Overexpressed and purified Rsd protein formed complexes in vitro with sigma70 but not with other sigma subunits, sigmaN, sigmaS, sigmaH, sigmaF, and sigmaE. Analysis of proteolytic fragments of sigma70 indicated that Rsd binds at or downstream of region 4, the promoter -35 recognition domain. The isolated Rsd inhibited transcription in vitro to various extents depending on the promoters used. We propose that Rsd is a stationary phase E. coli protein with regulatory activity of the sigma70 function.

Two types of differentially photo-regulated nuclear genes that encode sigma factors for chloroplast RNA polymerase in the red alga Cyanidium caldarium strain RK-1

A nuclear gene, sigA, that encodes a sigma factor for chloroplast RNA polymerase has previously been identified and characterized in the primitive red alga Cyanidium caldarium strain RK-1. Southern hybridization analysis indicated the presence of two additional sigma factor genes, which have now been cloned and shown to encode virtually identical proteins that are homologous to eubacterial sigma factors. These genes, which are also present in the nuclear genome, have therefore been named sigB and sigC. The substantial sequence similarity of sigB and sigC to sigA of the same strain as well as to cyanobacterial principal sigma factors and other chloroplast sigma factors strongly suggests that the nuclear genome of C. caldarium contains three genes that encode two types of chloroplast sigma factors. Each of the three recombinant Sig proteins showed sigma factor activity in vitro when combined with the Escherichia coli RNA polymerase core enzyme. Northern blot analysis revealed that, whereas the overall abundance of sigA transcripts was not affected by light, the amount of sigB and sigC mRNAs was greater in the light than in the dark. Thus, multiple sigma factors appear to contribute to light-regulated gene expression in the chloroplast.

Trehalose is not relevant for in vivo activity of sigmaS-containing RNA polymerase in Escherichia coli

The sigmaS- and sigma70-associated forms of RNA polymerase core enzyme (E) of Escherichia coli have very similar promoter recognition specificities in vitro. Nevertheless, the in vivo expression of many stress response genes is strongly dependent on sigmaS. Based on in vitro assays, it has recently been proposed that the disaccharide trehalose specifically stimulates the formation and activity of EsigmaS and thereby contributes to promoter selectivity (S. Kusano and A. Ishihama, J. Bacteriol. 179:3649-3654, 1997). However, we demonstrate here that a trehalose-free otsA mutant exhibits growth phase-related and osmotic induction of various sigmaS-dependent genes which is indistinguishable from that of an otherwise isogenic wild-type strain and that stationary-phase cells do not accumulate trehalose (even though the trehalose-synthesizing enzymes are induced). We conclude that in vivo trehalose does not play a role in the expression of sigmaS-dependent genes and therefore also not in sigma factor selectivity at the promoters of these genes.

Molecular analysis of the regulation of csiD, a carbon starvation-inducible gene in Escherichia coli that is exclusively dependent on sigma s and requires activation by cAMP-CRP

The general stress-induced sigma subunit sigma s of Escherichia coli RNA polymerase is closely related to the vegetative sigma factor sigma 70. In view of their very similar promoter specificity in vitro, it is unclear how sigma factor selectivity in the expression of sigma s-dependent genes is generated in vivo. The csiD gene is such a strongly sigma s-dependent gene. In contrast to sigma s, which is induced in response to many different stresses, csiD, whose expression is driven from a single promoter, is induced by carbon starvation only. To our knowledge, the csiD promoter is the first characterized promoter which is not only exclusively dependent on sigma s-containing RNA polymerase (E sigma s), but also requires an activator, cAMP-CRP. In addition, leucine-responsive regulatory protein (Lrp) acts as a positive modulator of csiD expression. Also in vitro, E sigma s is more efficient than E sigma 70 in csiD promoter binding, open complex formation and run-off transcription, which might be due to the poor match of the csiD -35 region to the sigma 70 consensus and to transcription by E sigma s being less dependent on contacts in this region. By DNase I protection experiments, a cAMP-CRP binding site centered at -68.5 nucleotides upstream of the csiD transcriptional start site was identified. While cAMP-CRP stimulates E sigma 70 binding, it does not promote open complex formation by E sigma 70, but does so in conjunction with E sigma s. With linear templates, cAMP-CRP significantly stimulates E sigma s-mediated in vitro transcription, whereas transcription by E sigma 70 is negligible and hardly stimulated by cAMP-CRP. These findings may reflect different or less stringent positional requirements for an activator site for E sigma s than for E sigma 70, and indicate that cAMP-CRP contributes to sigma factor selectivity at the csiD promoter. In vitro transcription experiments with super-coiled templates, however, revealed significant cAMP-CRP-stimulated transcription also by E sigma 70. Yet, under these conditions, H-NS was found to restore E sigma s specificity by strongly interfering with cAMP-CRP/E sigma 70-dependent transcription. Lrp strongly and cooperatively binds to multiple sites located between positions -14 and -102 (in a way that suggests DNA wrapping around multiple Lrp molecules) and moderately stimulates in vitro transcription, especially with E sigma s. In summary, we conclude that the csiD promoter has an intrinsic preference for E sigma s, but that also protein factors such as cAMP-CRP, Lrp and probably H-NS as well as DNA conformation contribute to its strong E sigma s selectivity. Furthermore, this strong E sigma s preference in combination with a requirement for high concentrations of the essential activator cAMP-CRP ensures csiD expression under conditions of carbon starvation, but not other stress conditions.

Role of DNA supercoiling and rpoS sigma factor in the osmotic and growth phase-dependent induction of the gene osmE of Escherichia coli K12

Transcription of the gene osmE of Escherichia coli is osmotically inducible and regulated by the growth phase. In a medium of low osmotic pressure, expression of osmE is induced at the onset of stationary phase. At elevated osmotic pressure, a biphasic induction pattern is observed. The first step occurs during exponential phase, and this is followed by a strong induction at the onset of stationary phase. Both steps appear to result from stimulation of transcription at the same promoter, osmEp. In the absence of sigma s, the stationary phase sigma factor encoded by rpoS, osmEp stationary phase induction is abolished, while the osmotic effect is still observed. Mutations that compensate for the absence of sigma s mapped to the gene topA. The effect of such mutation and of novobiocin, an inhibitor of DNA gyrase, suggest that changes in DNA supercoiling are involved in the osmotic induction of osmEp. In addition, modulation of the supercoiling level of a reporter plasmid was observed during growth in rich media. The kinetics of osmEp transcription are discussed in light of the variations of DNA supercoiling.

Adaptation of gene expression in stationary phase bacteria

In nature, bacteria can survive for long periods in non-growing stationary states. Some species of bacteria survive by forming spores but non-spore-forming bacteria, including Escherichia coli, survive in the stationary phase. Gross changes in morphology and physiology occur in the stationary-phase bacteria and concomitantly a state of increased resistance against various stresses is established. The stationary-phase adaptation of E. coli has only recently begun to be investigated at the molecular level.

Activation of RpoS-dependent proP P2 transcription by the Fis protein in vitro

The proP gene, encoding a transporter of the osmoprotecting compounds proline and glycine betaine, is expressed from two promoters. Transcription of the P2 promoter occurs at a transient period in late exponential phase and is dependent upon Fis and the RpoS (sigma38) sigma factor. Here we characterize Fis-mediated activation of the P2 promoter in vitro. We find that this promoter displays unusually high specificity for sigma38. Fis strongly activates P2 when bound to site I centered at -41 within the promoter region. There is a complex relationship involving DNA supercoiling and potassium glutamate concentration on Fis activation, but most efficient transcription occurs under high salt conditions when the superhelical density is above -0.03. The major stimulatory effect of DNA supercoiling occurs between superhelical densities of 0 to -0.02 suggesting that, while supercoiling is mechanistically important, it may not be a physiologically relevant controlling factor. However, the stimulation of transcription by high potassium glutamate concentrations may contribute to the osmotic inducibility of the P2 promoter. We show that Fis and E sigma38 bind cooperatively on supercoiled DNA to form a stable complex at P2 that involves promoter melting. Fis also binds to a second site within the proP regulatory region. While binding to this site appears to play no role in Fis activation of the P2 promoter, it functions as a repressor of transcription initiating from the P1 promoter by either sigma70 or sigma38.

Promoter selectivity of Escherichia coli RNA polymerase sigmaF holoenzyme involved in transcription of flagellar and chemotaxis genes

The rpoF gene of Escherichia coli codes for the RNA polymerase sigmaF (or sigma28) subunit, which is involved in transcription of the flagellar and chemotaxis genes. Both sigmaF and sigma70 (the major sigma subunit in growing cells) were overexpressed, purified to homogeneity, and compared with respect to activity and specificity. The affinity of sigmaF to core RNA polymerase (E) is higher than that of sigma70, as measured by gel filtration high-pressure liquid chromatography. In an in vitro transcription system, the holoenzyme (E sigmaF) containing sigmaF selectively transcribed the flagellar and chemotaxis genes, all of which could not be transcribed by E sigma70. This strict promoter recognition property of sigmaF is similar to those of other stress response minor sigma subunits but different from those of the principal sigma subunits, sigma70 and sigma38. sigma70-dependent transcription in vitro is inhibited at high concentrations of all salts tested, showing maximum activity at 50 mM. In contrast, sigmaF-dependent transcription was maximum at 50 mM KCI and then decreased to negligible level at 300 mM; in the cases of potassium acetate and potassium glutamate, maximum transcription was between 200 and 300 mM. DNase I foot printing of the fliC and fliD promoters indicated that sigmaF alone is unable to bind DNA, but E sigmaF specifically recognizes -10 and -35 regions of the sigmaF-dependent promoters with rather long upstream protection. Alteration of the promoter structure after binding of E sigmaF was suggested.

Stimulatory effect of trehalose on formation and activity of Escherichia coli RNA polymerase E sigma38 holoenzyme

The intracellular concentration of trehalose increases in the stationary-phase cells of Escherichia coli. The effects of trehalose on transcription in vitro by E. coli RNA polymerase were compared for two holoenzymes, E sigma70 and E sigma38, which were reconstituted from purified core enzyme and either sigma70 (the major sigma at the exponential growth phase) or sigma38 (the essential sigma at the stationary growth phase), respectively. The optimum trehalose concentration giving maximum transcription by E sigma38 was higher than that by E sigma70. Transcription activation by trehalose was attributed to both increased formation of E sigma38 holoenzyme and increased transcription initiation by E sigma38 from sigma38-dependent promoters. The activation of E sigma38 by trehalose was additive with the transcription enhancement by decreased superhelicity of template DNA prepared from stationary-phase cells. We thus propose that the selective activation of transcription by E sigma38 holoenzyme takes place in the presence of specific conditions and factors present under stress conditions.

Identification and analysis of the rpoS-dependent promoter of katE, encoding catalase HPII in Escherichia coli

The rpoS gene of Escherichia coli encodes an alternative sigma factor of RNA polymerase sigma38 (or sigma(s)) that is required for transcription of katE encoding catalase HPII. The transcription start site of the single katE transcript identified by ribonuclease protection has been determined by primer extension analysis to be either 53 or 54 bp (depending on the strain used) upstream of the open reading frame. A series of promoter fragments were constructed and fused to lacZ to confirm the start site location. A - 10 sequence similar to that found in other sigma70- and sigma38-dependent E. coli promoters was identified 8 or 7 bp upstream of the start site but a sigma70-dependent -35 sequence was not evident.