Nucleotide sequence of katF of Escherichia coli suggests KatF protein is a novel sigma transcription factor

Stationary phase expression of a novel Escherichia coli outer membrane lipoprotein and its relationship with mammalian apolipoprotein D. Implications for the origin of lipocalins

We report a novel outer membrane lipoprotein of Escherichia coli. DNA sequencing between ampC and sugE at the 94.5 min region of the E. coli chromosome revealed an open reading frame specifying 177 amino acid residues. Primer extension analysis demonstrated that the promoter is activated at the transition between exponential and stationary growth phases under control of the rpoS sigma factor gene, and this was confirmed in vivo by monitoring expression of beta-galactosidase activity from a lacZ translational fusion. The amino acid sequence exhibited 31% identity with human apolipoprotein D (apoD), which is a component of plasma high density lipoprotein and belongs to the eukaryotic family of lipocalins. The bacterial lipocalin (Blc) contained a short deletion of 7 amino acid residues corresponding to a hydrophobic surface loop that is thought to facilitate the physical interaction between apoD and high density lipoprotein. However, Blc exhibited a typical prokaryotic lipoprotein signal peptide at its amino terminus. Overexpression, membrane fractionation, and metabolic labeling with [3H]palmitate demonstrated that Blc is indeed a globomycin-sensitive outer membrane lipoprotein. Blc represents the first bacterial member of the family of lipocalins and may serve a starvation response function in E. coli.

Fis activates the RpoS-dependent stationary-phase expression of proP in Escherichia coli

Fis is a general nucleoid-associated protein in Escherichia coli whose expression is highly regulated with respect to growth conditions. A random collection of transposon-induced lac fusions was screened for those which give increased expression in the presence of Fis in order to isolate a ProP-LacZ protein fusion. We find that proP, which encodes a low-affinity transporter of the important osmoprotectants proline and glycine betaine, is transcribed from two promoters. proP1 is transiently induced upon subculture and is upregulated by increases in medium osmolarity. As cells enter stationary phase, a second promoter, proP2, is strongly induced. This promoter can also be induced by high medium osmolarity in exponential phase. The activity of proP2 depends on Fis and the stationary-phase sigma factor sigmas. In the presence of Fis, proP2 expression is increased over 50-fold, as judged by the LacZ activity of cells carrying the proP-lacZ fusion as well as by direct RNA analysis, making this the most strongly activated promoter by Fis that has been described. Two Fis binding sites centered at positions -41 (site I) and -81 (site II) with respect to the transcription initiation site of P2 have been defined by DNase I footprinting. Mutations in site I largely abolish stationary-phase activation, while mutations at site II have a minor effect, suggesting that direct binding of Fis to site I is important for Fis-mediated activation of this promoter. In addition to Fis and sigmas, sequences located over 108 bp upstream of the proP2 transcription initiation site are required for efficient expression.

Regulation of hydroperoxidase (catalase) expression in Escherichia coli

As part of its adaptive response to oxidative stress, Escherichia coli produces two inducible hydroperoxidases called HPI and HPII. Upon exposure to sublethal levels of hydrogen peroxide, HPI expression is induced at the transcriptional level by OxyR, a member of the LysR family of autoregulators. OxyR, functioning as both a sensor and transducer, contains a critical redox-sensitive Cys residue that is oxidized by hydrogen peroxide. This is thought to induce a conformational change in the tertiary structure of the OxyR tetramer altering its DNA-binding specificity and resulting in an increase in the transcription of katG and several other OxyR-dependent genes. In contrast, synthesis of the HPII enzyme is not induced by hydrogen peroxide. Expression of both HPI and HPII is growth phase-dependent levels of HPI and HPII are 10-fold higher in stationary phase than exponential phase cultures. These growth phase-dependent increases are largely dependent on RpoS, a stationary phase specific sigma factor that is itself subject to complex transcriptional and post-transcriptional controls. Several metabolic signals have been proposed to activate the RpoS regulon including hyperosmolarity, weak acids, homoserine lactone and UDP-glucose. Since both HPI and HPII are members of the RpoS regulon, elucidation of the mechanism of regulation of RpoS should contribute to our general understanding of hydroperoxidase regulation.

Central regulatory role for the RpoS sigma factor in expression of Salmonella dublin plasmid virulence genes

The plasmid virulence genes spvABCD of Salmonella spp. are regulated by SpvR and the stationary-phase sigma factor RpoS. The transcription of spv genes is induced during the post-exponential phase of bacterial growth in vitro. We sought to investigate the relationship between growth phase and RpoS in spv regulation. rpoS insertion mutations were constructed in S. dublin Lane and plasmid-cured LD842 strains, and the mutants were found to be attenuated for virulence and deficient in spv gene expression. We utilized the plasmid pBAD::rpoS to express rpoS independent of the growth phase under the control of the arabinose-inducible araBAD promoter. SpvA expression was induced within 2 h after the addition of 0.1% arabinose, even when bacteria were actively growing. This suggested that the level of RpoS, instead of the growth phase itself, controls induction of the spv genes. However, RpoS did not activate transcription of spvA in the absence of SpvR protein. Using a constitutive tet promoter to express spvR, we found that the spvA gene can be partially expressed in the rpoS mutant, suggesting that RpoS is required for SpvR synthesis. We confirmed that spvR is poorly expressed in the absence of RpoS. With an intact rpoS gene, spvR expression is not dependent on an intact spvR gene but is enhanced by spvR supplied in trans. We propose a model for Salmonella spv gene regulation in which both RpoS and SpvR are required for maximal expression at the spvR and spvA promoters.

Role of RpoS in survival of Yersinia enterocolitica to a variety of environmental stresses

rpoS, a gene that encodes an alternative sigma factor (also known as katF), is critical for the ability of Yersinia enterocolitica grown at 37 degrees C, but not at 26 degrees C, to survive diverse environmental insults such as high temperature, hydrogen peroxide, osmolarity, and low pH. However, a Y. enterocolitica rpoS mutant was not affected in expression of inv or ail, invasion of tissue culture cells, or virulence in mice.

Mutational analysis of the role of the first helix of region 4.2 of the sigma 70 subunit of Escherichia coli RNA polymerase in transcriptional activation by activator protein PhoB

Transcription of the genes belonging to the phosphate (pho) regulon in Escherichia coli requires the specific activator protein PhoB, in addition to RNA polymerase containing the major sigma factor, sigma 70, which is encoded by rpoD. We previously isolated two mutant sigma 70s (D570G and E575K) that were specifically defective in transcribing the pho genes. The mutated sites were located near and within the first helix of the helix-turn-helix (HTH) motif or region 4.2 of sigma 70. To study further the role of the first helix of the HTH motif of sigma 70 in transcriptional activation by PhoB, we made a series of rpoD mutations that alter the motif and purified the mutant sigma 70 proteins. RNA polymerases containing the mutant sigma 70s Y571A, T572L, V576T, K578E and F580V showed reduced in vitro transcription from the pstS promoter, a representative pho promoter, in the presence of PhoB, whereas RNA polymerase containing another mutant sigma 70 (E574K) showed enhanced transcription from the promoter. Transcription from the activator-independent tac promoter and the pBR-P4 promoter, which is independent of PhoB and requires cAMP-CRP (cAMP receptor protein) for transcription, was affected at most only marginally by these sigma 70 mutations. These results provide further evidence that the first helix plays an important role in the specific interaction between RNA polymerase and PhoB protein bound to the pho promoters in transcriptional activation.

aldB, an RpoS-dependent gene in Escherichia coli encoding an aldehyde dehydrogenase that is repressed by Fis and activated by Crp

Escherichia coli aldB was identified as a gene that is negatively regulated by Fis but positively regulated by RpoS. The complete DNA sequence determined in this study indicates that aldB encodes a 56.3-kDa protein which shares a high degree of homology with an acetaldehyde dehydrogenase encoded by acoD of Alcaligenes eutrophus and an aldehyde dehydrogenase encoded by aldA of Vibrio cholerae and significant homology with a group of other aldehyde dehydrogenases from prokaryotes and eukaryotes. Expression of aldB is maximally induced during the transition from exponential phase to stationary phase. Its message levels are elevated three- to fourfold by a fis mutation and abolished by an rpoS mutation. In addition, the expression of an aldB-lacZ fusion was decreased about 20-fold in the absence of crp. DNase I footprinting analysis showed that five Fis binding sites and one Crp binding site are located within the aldB promoter region, suggesting that Fis and Crp are acting directly to control aldB transcription. AldB expression is induced by ethanol, but in contrast to that of most of the RpoS-dependent genes, the expression of aldB is not altered by an increase in medium osmolarity.

Repair, refold, recycle: how bacteria can deal with spontaneous and environmental damage to proteins

Proteins, like DNA, are subject to various forms of damage that can render them non-functional. Conformational changes and covalent chemical alterations occur spontaneously, and the rates of these reactions can be increased by environmental stresses such as heat, oxidative agents, or changes in pH or osmotic conditions. Although affected proteins can be replaced by de novo biosynthesis, cells--especially those subjected to stress or nutrient limitation--have developed mechanisms which can either restore damaged polypeptides to an active state or remove them. Such mechanisms can spare the biosynthetic capacity of the cell and ensure that the presence of non-functional molecules does not disrupt cell physiology. Three major mechanisms, which operate in bacteria as well as eukaryotic organisms, have been described. First, chaperones not only assist in proper de novo folding of proteins but also provide an important means of restoring activity to conformationally damaged proteins. Second, enzymatic 'repair' systems exist to directly reverse certain forms of protein damage, including proline isomerization, methionine oxidation and the formation of isoaspartyl residues. Finally, proteolysis provides a 'last-resort' means of dealing with abnormal proteins which cannot be repaired. Protein maintenance and repair may be of special importance for bacteria preparing to survive extended periods in stationary phase: both constitutive and induced mechanisms are utilized to permit survival despite greatly reduced protein synthesis.

The rpoS gene from Yersinia enterocolitica and its influence on expression of virulence factors

The chromosome of Yersinia enterocolitica encodes a heat-stable enterotoxin called Yst and a surface antigen called Myf, which closely resembles enterotoxin-associated fimbriae. Both factors could act in conjunction to produce diarrhea. Production of the enterotoxin is regulated by temperature, osmolarity, and pH and occurs only when bacteria reach the stationary phase. Myf production is regulated by temperature and pH and, as we show in this work, also occurs after the exponential growth phase. In an attempt to understand the late-phase expression of yst and myf, we cloned, sequenced, and mutagenized the gene encoding RpoS, an alternative sigma factor of the RNA polymerase involved in expression of stationary-phase genes in other enterobacteria. An intact rpoS gene was necessary for full expression of yst in the stationary phase but not for the expression of myf and of pYV-encoded virulence determinants.

Promoter determinants for Escherichia coli RNA polymerase holoenzyme containing sigma 38 (the rpoS gene product)

Sequence determinants responsible for promoter recognition by RNA polymerase holoenzyme containing sigma 38, the rpoS gene product, were analyzed. In a previous study [Tanaka et al. (1993) Proc. Natl. Acad. Sci. USA, 90, 3511-3515], Escherichia coli promoters were classified into three groups: promoters recognized only by RNA polymerase holoenzyme containing sigma 70 (E sigma 70); promoters recognized preferentially by that containing sigma 38 (E sigma 38); promoters recognized by both E sigma 70 and E sigma 38. As representatives of each group of promoter, we chose the alaS, fic and lacUV5 promoters. Making use of a restriction enzyme site inserted between the -10 and -35 hexamer sequences, promoters were divided into the upstream (UE) and downstream (DE) elements. These UEs and DEs were combined in all possible combinations and used for in vitro transcription reactions. Promoters containing DE from the fic or lacUV5 promoter were found to be recognized by E sigma 38, while those containing DE from the alaS promoter were not. Moreover, fic DE alone functioned as an efficient promoter for E sigma 38. Thus we conclude that the discrimination signal resides within the DE sequence. To test the activator response of E sigma 38, in vitro transcription reactions were also performed with the gal and lac promoters. For both CRP-responsive P1 promoters, E sigma 38 was found to be activated by the CRP-cAMP complex.

Selectivity of the Escherichia coli RNA polymerase E sigma 38 for overlapping promoters and ability to support CRP activation

A series of gal promoter mutants has been used to compare the in vitro selectivities of the two forms of Escherichia coli RNA polymerase, E sigma 38 and E sigma 70. In the absence of the CRP-cAMP complex, E sigma 38 shows a strong preference for the ga/P1 promoter, whereas E sigma 70 preferentially initiates transcription from the ga/P2 promoter. E sigma 38 selectivity is not affected by the nature and position of the upstream sequences or by the phasing between synthetic upstream curved sequences and the -10 regions. In fact, all effects of mutations in the extended -10 region can be accounted for without evoking strong new sequence preferences for E sigma 38. Finally, both E sigma 38 and E sigma 70 initiate transcription from the ga/P1 promoter in the presence of CRP-cAMP complex and support direct cAMP-CRP activation at several CRP-dependent promoters.

Identification of genes negatively regulated by Fis: Fis and RpoS comodulate growth-phase-dependent gene expression in Escherichia coli

Fis is a nucleoid-associated protein in Escherichia coli that has been shown to regulate recombination, replication, and transcription reactions. It is expressed in a transient manner under batch culturing conditions such that high levels are present during early exponential phase and low levels are present during late exponential phase and stationary phase. We have screened a random collection of transposon-induced lac fusions for those which give decreased expression in the presence of Fis. Thirteen different Fis-repressed genes were identified, including glnQ (glutamine high-affinity transport), mglA (methyl-galactoside transport), xylF (D-xylose-binding protein), sdhA (succinate dehydrogenase flavoprotein subunit), and a newly identified aldehyde dehydrogenase, aldB. The LacZ expression patterns revealed that many of the fusions were maximally expressed at different stages of growth, including early log phase, mid- to late log phase, and stationary phase. The expression of some of the late-exponential- and stationary-phase genes was dependent on the RpoS sigma factor, whereas that of others was affected negatively by RpoS. We conclude that Fis negatively regulates a diverse set of genes and that RpoS can function to both activate and inhibit the expression of specific genes.

Escherichia coli peptide methionine sulfoxide reductase gene: regulation of expression and role in protecting against oxidative damage

The Escherichia coli peptide methionine sulfoxide reductase gene (msrA) encodes a single-subunit polypeptide of 212 amino acid residues (M. A. Rahman, H. Nelson, H. Weissbach, and N. Brot, J. Biol. Chem. 267:15549-15551, 1992). RNA blot analysis showed that the gene is transcribed into an mRNA of about 850 nucleotides. The promoter region was characterized, and the transcription initiation site was identified by primer extension. The synthesis of the MsrA protein increased about threefold in a growth-phase-dependent fashion. In an attempt to define the in vivo role of msrA, a chromosomal disruption was constructed. This mutant was more sensitive to oxidative stress, suggesting that oxidation of methionine in proteins plays an important role in oxidative damage.

Low pH adaptation and the acid tolerance response of Salmonella typhimurium

Salmonella typhimurium periodically confronts acid environments during its life. These situations arise in chemically compromised ponds, soil, degradative cellular organelles, host digestive systems, and may even result from byproducts of their own metabolism. The levels of acid that are encountered range from mild to extreme. As a neutralophile, S. typhimurium prefers to grown in pH environments above pH 5.5. They can survive down to pH 4 for extended periods of time. However, the limits of endurance can be stretched if the organisms are first adapted to a moderate acid pH before exposing them to acidity below pH 4.0. This adaptation, called the acid-tolerance response (ATR), includes several log phase and stationary phase systems. Some of these systems are dependent on an alternate sigma factor for RNA polymerase called sigma s, whereas other systems are sigma s-independent. A key to the ATR is the synthesis of a series of acid shock inducible proteins (ASPs), 51 for log phase ATR and 15 for stationary phase ATR. Some of these ASPs require sigma s for their synthesis; others require the participation of the ferric uptake regulator protein Fur. Effective acid tolerance involves RecA-independent DNA repair systems, iron, and facets of fatty acid metabolism. Aspects of medium composition and carbon metabolism are also known to influence the nature of acid tolerance in this organism. In addition to aiding survival in the natural non-host environment, aspects of acid tolerance are also tied to virulence, as evidenced by the involvement of the mouse virulence locus mviA and the fact that acid-sensitive strains of S. typhimurium exhibit reduced virulence. This review summarizes these aspects of acid adaptation and includes a discussion of acid-regulated gene expression.

Cloning, analysis and expression of an rpoS homologue gene from Pseudomonas aeruginosa PAO1

A homologue of the rpoS gene of Escherichia coli was cloned from Pseudomonas aeruginosa PAO1 by hybridization with an oligodeoxyribonucleotide probe designed from an amino-acid stretch conserved among the principal sigma factors of eubacteria. Two open reading frames, the pcm gene and the orf-297 of unknown function, were found in the upstream region of rpoS, and in the same order as in E. coli. The rpoS gene of P. aeruginosa was expressed in E. coli and complemented the catalase deficiency of the rpoS mutant of E. coli. The RpoS protein of P. aeruginosa was identified by Western blot analysis in both P. aeruginosa (Pa) and the transformed E. coli. Levels of RpoS of Pa increased drastically at the onset of the stationary growth phase.

Induction of the Escherichia coli aidB gene under oxygen-limiting conditions requires a functional rpoS (katF) gene

The Escherichia coli aidB gene is regulated by two different mechanisms, an ada-dependent pathway triggered by methyl damage to DNA and an ada-independent pathway triggered when cells are grown without aeration. In this report we describe our search for mutations affecting the ada-independent aidB induction pathway. The mutant strain identified carries two mutations affecting aidB expression. These mutations are named abrB (aidB regulator) and abrD. The abrB mutation is presently poorly characterized because of instability of the phenotype it imparts. The second mutation, abrD1, reduces the expression of aidB observed when aeration is ceased and oxygen becomes limiting. Genetic and phenotypic analysis of the abrD1 mutation demonstrates that it is an allele of rpoS. Thus, aidB is a member of the family of genes that are transcribed by a sigma S-directed RNA polymerase holoenzyme. Examination of aidB expression in an rpoS insertion mutant strain indicates that both rpoS13::Tn10 and abrD1 mutations reduce aidB expression under oxygen-limiting conditions that prevail in unaerated cultures, reduce aidB induction by acetate at a low pH, but have little or no effect on the ada-dependent alkylation induction of aidB.

Analysis of the dual regulatory mechanisms controlling expression of the vegetative catalase gene of Bacillus subtilis

The expression of a vegetative catalase gene, katA (formerly the kat-19 gene), is necessary to protect Bacillus subtilis from H2O2, presumably by removing the oxidant from the environment. Genetic analysis of katA revealed that this gene is under two distinct forms of regulation, temporal and H2O2 inducible. The results reported here demonstrate that (i) the H2O2-inducible regulation of katA gene is not a component of the SOS regulon, (ii) the regulatory genes spo0A and abrB are involved in the temporal regulation but not the H2O2-specific induction of katA gene expression, and (iii) transcription initiation for the katA gene occurs at the same site under both forms of regulation.

The Salmonella typhimurium katF (rpoS) gene: cloning, nucleotide sequence, and regulation of spvR and spvABCD virulence plasmid genes

The spv region of Salmonella virulence plasmids is essential for the development of a systemic infection in mice. Transcriptional activation of the spvABCD operon occurs during stationary growth phase and is mediated by the regulatory gene product SpvR. We have previously shown that expression of a spvRAB'-cat fusion in Escherichia coli was dependent on the katF (rpoS) locus which encodes an alternative sigma factor (sigma S). The katF gene from Salmonella typhimurium has been cloned, sequenced, and used to construct Salmonella katF mutants by allelic replacement. Using these mutants, we demonstrated by mRNA and gene fusion analyses that sigma S, in conjunction with SpvR, controls the transcription of the regulatory gene spvR. In a second series of experiments, we sought to clarify the relationship between sigma S and SpvR in the control of spvABCD transcription. It was shown that expression of a transcriptional spvAB'-lacZ fusion could be restored in E. coli and Salmonella katF mutants when spvR was expressed in trans from an exogenous promoter. Moreover, identical spvA mRNA startpoints were detected in katF+ and katF strains. These results indicate that the reduction of spvABCD transcription in katF mutants is mainly due to decreased expression of spvR. Finally, mouse inoculation studies with S. typhimurium katF mutants of both wild-type and virulence plasmid-cured strains suggest that katF contributes to Salmonella virulence via the regulation of chromosomal genes in addition to that of spv genes.

Role of rpoS in the regulation of Salmonella plasmid virulence (spv) genes

Salmonella plasmid virulence (spv) genes are organized into two transcriptional units: one formed by the spvR gene and the other by the spvA, spvB, spvC and spvD genes. Transcription of both units is activated by SpvR, a regulatory protein of the LysR family. The effect of RpoS, a stationary phase-associated sigma factor, on the expression of spv genes was studied using lacZ transcriptional fusions to spvR and spvA in wild-type and rpoS Escherichia coli backgrounds. Mutant and wild-type SpvR proteins were expressed in trans from a multicopy plasmid. The results show that the combined action of rpoS and spvR is necessary for transcription of spvA and that this combination also enhances transcription of spvR. Interestingly, spvR can also be transcribed in an alternative manner, i.e. in the absence of rpoS or spvR or both. The possible role for SpvR as a repressor of its own transcription is discussed.

Cloning and sequencing of the gene encoding the RpoS (KatF) sigma factor from Salmonella typhimurium 14028s

The gene encoding the alternative sigma factor RpoS in Salmonella typhimurium was cloned by its ability to complement acid susceptibility in rpoS mutant Escherichia coli. Sequence determination and comparison with rpoS from E. coli demonstrates a high degree of conservation, although significant differences are found within the extragenic regulatory regions.

Transcription of the principal sigma-factor genes, rpoD and rpoS, in Pseudomonas aeruginosa is controlled according to the growth phase

The rpoS gene encodes the second principal sigma factor of RNA polymerase in stationary-phase cells in Escherichia coli. We examined the transcription of Pseudomonas aeruginosa rpoS as to the growth of cells. The results of quantitative S1 nuclease mapping of rpoS and rpoD, encoding the principal sigma factor, indicated that the transcription of rpoS is induced in stationary-phase cells, whereas that of rpoD is induced in exponential-phase cells. By high-resolution S1 nuclease mapping, the 5'- and 3'-ends of rpoS mRNA were determined. The results indicated that rpoS is transcribed as a monocistronic mRNA. The sequence preceding the 5' end of rpoS mRNA showed poor homology to the consensus sequences of the previously known promoters. P. aeruginosa rpoS was not transcribed in E. coli. By in vitro transcription assaying, P. aeruginosa rpoS was shown to be transcribed by the RNA polymerase fraction containing the principal sigma (sigma 70)-RNA polymerase of P. aeruginosa.

Sigma S-dependent growth-phase induction of the csgBA promoter in Escherichia coli can be achieved in vivo by sigma 70 in the absence of the nucleoid-associated protein H-NS

The stationary-phase-specific sigma factor sigma S (RpoS/KatF) is required for Escherichia coli to induce expression of fibronectin-binding curli organelles upon reaching stationary phase. We show that the csgA gene which encodes the curlin subunit protein belongs to a dicistronic operon, csgBA. The transcriptional start site of csgBA was determined and an AT-rich up-stream activating sequence (UAS) required for transcriptional activation was identified. The pcsgBA promoter is not specific for sigma S since the same promoter sequence can be used by E sigma 70 in vivo in a strain lacking nucleoid-associated protein H-NS and sigma S. Transcription remained growth-phase induced and dependent upon the UAS in such a double mutant. Furthermore, we demonstrate that an additional operon, hdeAB, which is also dependent upon sigma S for transcription, can be transcribed by E sigma 70 in vivo in the absence of H-NS by utilizing the phdeAB promoter. Two other genes known to be under the control of sigma S for expression, bolA and katE, remained transcriptionally silent in the absence of H-NS. It is suggested that a subset of E. coli promoters can be recognized by both E sigma S and E sigma 70 in vivo but H-NS interacting with these sequences prevents formation of successful transcription-initiation complexes with E sigma 70.

RpoS is necessary for both the positive and negative regulation of starvation survival genes during phosphate, carbon, and nitrogen starvation in Salmonella typhimurium

The starvation stress response of Salmonella typhimurium encompasses the genetic and physiologic changes that occur when this bacterium is starved for an essential nutrient such as phosphate (P), carbon (C), or nitrogen (N). The responses to the limitation of each of these nutrients involve both unique and overlapping sets of proteins important for starvation survival and virulence. The role of the alternative sigma factor RpoS in the regulation of the starvation survival loci, stiA, stiB, and stiC, has been characterized. RpoS (sigma S) was found to be required for the P, C, and N starvation induction of stiA and stiC. In contrast, RpoS was found to be required for the negative regulation of stiB during P and C starvation-induced stationary phase but not during logarithmic phase. This role was independent of the relA gene (previously found to be needed for stiB induction). The role of RpoS alone and in combination with one or more sti mutations in the starvation survival of the organism was also investigated. The results clearly demonstrate that RpoS is an integral component of the complex interconnected regulatory systems involved in S. typhimurium's response to nutrient deprivation. However, differential responses of various sti genes indicate that additional signals and regulatory proteins are also involved.

An analogue of the DnaJ molecular chaperone whose expression is controlled by sigma s during the stationary phase and phosphate starvation in Escherichia coli

The Escherichia coli CbpA protein appears to be an analogue of the molecular chaperone, DnaJ, as judged from not only its structure but also its possible function. The expression of cbpA, however, was not significantly affected by up-shift of the growth temperature. Remarkably, it was found that the expression of cbpA was induced under certain growth conditions, such as the entry of cells into stationary phase, or growth in a phosphate-limited medium. Such conditional expression of cbpA was regulated at the transcriptional level in a sigma s-dependent manner. The structure of this sigma s-dependent cbpA promoter was clarified by determining its transcription start site. The cbpA promoter region was found to contain an unusual DNA structure (i.e. DNA curvature). From these results, it was suggested that, in contrast to DnaJ, CbpA may function as a molecular chaperone in an adaptive response to environmental stresses other than heat shock.

The nlpD gene is located in an operon with rpoS on the Escherichia coli chromosome and encodes a novel lipoprotein with a potential function in cell wall formation

rpoS is the structural gene for sigma s, which is a second vegetative sigma subunit of RNA polymerase in Escherichia coli and is involved in the expression of many stationary phase-induced genes. Upstream of rpoS is an open reading frame (ORF) whose function and regulation have not been studied. Strong overproduction of its gene product using the IPTG-inducible tac promoter leads to the formation of bulges at the cell septum and the cell poles, and in rapidly growing cells brings about cell lysis, indicating that the gene product has a hydrolytic function in cell wall formation or maintenance. This is corroborated by sequence homology to lysostaphin, a cell wall lytic exoenzyme synthesized by two Staphylococcus strains. Using globomycin, a specific inhibitor of signal peptidase II, we demonstrate that the product of the ORF is a novel lipoprotein (NlpD). Two transcriptional start sites for nlpD have been localized. In contrast to rpoS, nlpD is not induced during entry into stationary phase. Growth-phase-regulated transcription of rpoS is initiated at additional sites within the nlpD ORF, but the nlpD promoters contribute substantially to the basal level of rpoS expression in exponentially growing cells, indicating that nlpD and rpoS form an operon.

Sensing starvation: a homoserine lactone--dependent signaling pathway in Escherichia coli

When nutrients become limiting, many bacteria differentiate and become resistant to environmental stresses. For Escherichia coli, this process is mediated by the sigma s subunit of RNA polymerase. Expression of sigma s was induced by homoserine lactone, a metabolite synthesized from intermediates in threonine biosynthesis. Homoserine lactone-dependent synthesis of sigma s was prevented by overexpression of a newly identified protein, RspA. The function of homoserine lactone derivatives in many cell density-dependent phenomena and the similarity of RspA to a Streptomyces ambofaciens protein suggest that synthesis of homoserine lactone may be a general signal of starvation.

Analysis of the otsBA operon for osmoregulatory trehalose synthesis in Escherichia coli and homology of the OtsA and OtsB proteins to the yeast trehalose-6-phosphate synthase/phosphatase complex

The Escherichia coli otsBA operon, located at min 42, was sequenced and shown to encode a 29.1-kDa trehalose-6-phosphate phosphatase (OtsB) and a 53.6-kDa trehalose-6-phosphate synthase (OtsA). Both proteins display sequence homology with subunits of the Saccharomyces cerevisiae trehalose-6-phosphate synthase/phosphatase complex, which is made up of the subunits TPS1, TPS2 and TPS3 (TSL1). OtsA has homology to the full-length TPS1, the N-terminal part of TPS2 and an internal region of TPS3 (TSL1). OtsB has homology to the C-terminal part of TPS2, but no homology to the other subunits. Primer extension analysis showed only one transcription start point upstream from otsB and one upstream from otsA, regardless of the growth conditions tested. The start codons of the otsB and otsA genes were established by N-terminal sequence determination of the proteins. The 3' end of the otsB coding region overlaps the 5' end of the otsA coding region by 23 nucleotides. The araH gene is located directly upstream from otsBA, and otsB may be identical to pexA.

Characterization of the sigma 38-dependent expression of a core Escherichia coli starvation gene, pexB

A reverse genetics approach was used to clone a pex starvation gene that codes for an 18-kDa polypeptide, designated PexB. Single-copy pexB-lacZ operon fusions were constructed to study transcriptional regulation and the promoter region of this gene. The induction by carbon starvation or osmotic stress was transcriptional and controlled by sigma 38 but was independent of this sigma factor by the oxidative stress; presumably, it was sigma 70 mediated under the latter stress. During nitrogen starvation, the induction was controlled at the posttranscriptional level. The pexB upstream region contained 245 nucleotides within which sequences approximating the consensus for cyclic AMP receptor protein and integration host factor binding sites were discernible. Deletion of 164 bp of the upstream region, which included these consensus sequences, did not affect starvation-or osmotic stress-mediated induction of pexB but abolished its induction by oxidative stress. The same start site was used in transcription during carbon starvation, osmotic stress, or oxidative stress, suggesting that the pexB promoter can be recognized in vivo by both sigma 38 and sigma 70, depending, presumably, on the presence of appropriate transcriptional factors. The -10 and -35 regions of pexB resembled those of some but not all genes known to be controlled by sigma 38.

The cellular concentration of the sigma S subunit of RNA polymerase in Escherichia coli is controlled at the levels of transcription, translation, and protein stability

The second vegetative sigma factor sigma S (encoded by the rpoS gene) is the master regulator in a complex regulatory network that governs the expression of many stationary phase-induced and osmotically regulated genes in Escherichia coli. Using a combination of gene-fusion technology and quantitative immunoblot, pulse-labeling, and immunoprecipitation analyses, we demonstrate here that rpoS/sigma S expression is not only transcriptionally controlled, but is also extensively regulated at the levels of translation and protein stability. rpoS transcription is inversely correlated with growth rate and is negatively controlled by cAMP-CRP. In complex medium rpoS transcription is stimulated during entry into stationary phase, whereas in minimal media, it is not significantly induced. rpoS translation is stimulated during transition into stationary phase as well as by an increase in medium osmolarity. A model involving mRNA secondary structure is suggested for this novel type of post-transcriptional growth phase-dependent and osmotic regulation. Furthermore, sigma S is a highly unstable protein in exponentially growing cells (with a half-life of 1.4 min), that is stabilized at the onset of starvation. When cells are grown in minimal glucose medium, translational induction and sigma S stabilization occur in a temporal order with the former being stimulated already in late exponential phase and the latter taking place at the onset of starvation. Although sigma S does not control its own transcription, it is apparently indirectly involved in a negative feedback control that operates on the post-transcriptional level. Our analysis also indicates that at least five different signals [cAMP, a growth rate-related signal (ppGpp?), a cell density signal, an osmotic signal, and a starvation signal] are involved in the control of all these processes that regulate rpoS/sigma S expression.

Structure of the 5' upstream region and the regulation of the rpoS gene of Escherichia coli

The nucleotide sequence of the 5' upstream region of the Escherichia coli rpoS gene was determined and analyzed. At least four promoters responsible for rpoS transcription were identified, and designated P1, P2, P3 and P4, P1 being furthest from the upstream. Using lacZ fusion genes, the P2 promoter was found to be the strongest of the four. All of these promoters are regulated similarly, and their activity is enhanced 2 to 3-fold in stationary phase. P1 and P2 transcription start sites were determined by primer extension analyses. The P2 promoter region shows similarity to the consensus sigma 70-type promoter sequence, and was recognized by both E sigma 70 and E sigma 38 holoenzymes in vitro. The mRNA transcribed from the most distal promoter, P1, appears to include another open reading frame (orf-281), indicating that the two open reading frames comprise an operon. The rpoS gene product (sigma 38) was rapidly degraded after addition of chloramphenicol to cultures in the exponential, but not the stationary phase. This strongly suggests that posttranslational regulation is involved in the control of rpoS expression.

A peroxide/ascorbate-inducible catalase from Haemophilus influenzae is homologous to the Escherichia coli katE gene product

Bacterial catalases are induced by exposure to peroxide (e.g., Escherichia coli katG) or entry into stationary phase (e.g., E. coli katE). To study regulatory systems in Haemophilus influenzae, we complemented an E. coli rpoS mutant, which is unable to induce katE in stationary phase, with a plasmid library of H. influenzae Rd- chromosomal DNA. Nineteen complementing clones with a catalase-positive phenotype were obtained and characterized after screening about 10(5) transformants. All carried the same structural gene for an H. influenzae catalase. The DNA sequence of this gene, called hktE, encodes a 508-amino-acid polypeptide with strong homology to eukaryotic catalases and E. coli katE. However, hktE is regulated like E. coli katG, with catalase activity increasing 10-fold and hktE mRNA levels increasing 4-fold upon exposure to ascorbic acid, which serves to generate hydrogen peroxide. Mutations in the known global regulatory genes of H. influenzae--crp, cya, and sxy--do not affect the inducibility of hktE. The hktE gene maps to a 225-kb segment of the H. influenzae chromosome in a region encoding resistance to spectinomycin.

Induction of Escherichia coli hydroperoxidase I by acetate and other weak acids

Escherichia coli produces two independently regulated hydroperoxidases (catalases) that protect the cell from toxic concentrations of hydrogen peroxide. Hydroperoxidase I (HPI) is induced by hydrogen peroxide in an OxyR-dependent manner, while hydroperoxidase II (HPII) synthesis is regulated by an alternative sigma factor called RpoS (KatF). The activities of both hydroperoxidases increase as exponentially growing cells enter stationary phase. In this study, we examined the growth phase-dependent expression of HPI. Treatment of early-exponential-phase cells with spent culture supernatant resulted in induction of HPI synthesis. Extracellular levels of hydrogen peroxide, accumulating in the culture supernatant during late exponential phase, were found to be lower than the concentrations normally required to induce OxyR-dependent synthesis of HPI. This finding suggested that factors other than hydrogen peroxide may play a role in HPI expression. Weak acids such as acetate, which accumulate in culture supernatant and have been implicated in the regulation of HPII, caused a sixfold increase in HPI expression. Increases in HPI synthesis, mediated by weak acids and spent culture fluid supernatant, could be prevented by chloramphenicol, indicating that de novo protein synthesis is required for induction. Expression studies using a plasmid-borne lacZ transcriptional fusion to katG, the structural gene for HPI, indicated that growth phase-dependent regulation of HPI occurs primarily at the level of transcription and is dependent on RpoS. These results suggest that there may be a common regulatory mechanism of HPI and HPII expression in addition to previously described independent control mechanisms.

The delta (argF-lacZ)205(U169) deletion greatly enhances resistance to hydrogen peroxide in stationary-phase Escherichia coli

In this study, we demonstrate that a strain bearing the delta (argF-lacZ)205(U169) deletion exhibits a high level of resistance to hydrogen peroxide compared with its undeleted parent. Our initial investigation of the mechanism behind the observed differences in peroxide resistance when parent and mutant strains are compared indicates that the parent strain carries a region near argF that is responsible for the H2O2-sensitive phenotype, which we have named katC. The H2O2 resistance phenotype of the delta katC [delta (argF-lacZ)205(U169)] mutant strain can be duplicated by Tn9 insertion in a specific locus (katC5::Tn9) which maps near argF. The increased H2O2 resistance of the delta katC and katC5::Tn9 mutant strains can be seen only when cells are grown to stationary phase; exponential-phase cells are unaffected by the presence or absence of katC. This H2O2 resistance mechanism requires functional katE and katF genes, which suggests that the mechanism of H2O2 resistance may involve the activity of the stationary-phase-specific catalase HPII. Cloning, DNA sequencing, and analysis of the katC5::Tn9 insertion allele in comparison with its parent allele implicate two insertion elements, IS1B and IS30B, and suggest that their presence sensitizes parent cells to H2O2.

Starvation-induced expression of SspA and SspB: the effects of a null mutation in sspA on Escherichia coli protein synthesis and survival during growth and prolonged starvation

Maxicell labelling and two-dimensional gel electrophoresis (2-D PAGE) have identified the proteins encoded by sspA and sspB (SspA, SspB) as proteins D27.1 and A25.8, respectively, in the Escherichia coli gene-protein database. SspA expression increases with decreasing growth rate and is induced by glucose, nitrogen, phosphate or amino acid starvation. The promoter, Pssp, is similar to gearbox promoters. Inactivation of SspA (sspA::neo) blocks sspB expression. [35S]-methionine-labelled proteins synthesized during growth and during stationary phase are different in delta sspA strains compared to sspA+ strains. This difference is enhanced during extended stationary phase (24-72 h). Long-term (10 d) viability of arginine-starved isogenic strains shows that sspA+ cultures remain viable significantly longer than delta sspA mutants. 2-D PAGE of proteins expressed during exponential growth shows that expression of at least 11 proteins is altered in delta sspA strains. A functional relA gene is required for sspA to affect protein synthesis.

A gene at 59 minutes on the Escherichia coli chromosome encodes a lipoprotein with unusual amino acid repeat sequences

We report a 1.432-kb DNA sequence at 59 min on the Escherichia coli chromosome that connects the published sequences of the pcm gene for the isoaspartyl protein methyltransferase and that of the katF or rpoS (katF/rpoS) gene for a sigma factor involved in stationary-phase gene expression. Analysis of the DNA sequence reveals an open reading frame potentially encoding a polypeptide of 379 amino acids. The polypeptide sequence includes a consensus bacterial lipidation sequence present at residues 23 to 26 (Leu-Ala-Gly-Cys), four octapeptide proline- and glutamine-rich repeats of consensus sequence QQPQIQPV, and four heptapeptide threonine- and serine-rich repeats of consensus sequence PTA(S,T)TTE. The deduced amino acid sequence, especially in the C-terminal region, is similar to that of the Haemophilus somnus LppB lipoprotein outer membrane antigen (40% overall sequence identity; 77% identity in last 95 residues). The LppB lipoprotein binds Congo red dye and has been proposed to be a virulence determinant in H. somnus. Utilizing a plasmid construct with the E. coli gene under the control of a phage T7 promoter, we demonstrate the lipidation of this gene product by the incorporation of [3H]palmitic acid into a 42-kDa polypeptide. We also show that treatment of E. coli cells with globomycin, an inhibitor of the lipoprotein signal peptidase, results in the accumulation of a 46-kDa precursor. We thus designate the protein NlpD (new lipoprotein D). E. coli cells overexpressing NlpD bind Congo red dye, suggesting a common function with the H. somnus LppB protein. Disruption of the chromosomal E. coli nlpD gene by insertional mutagenesis results in decreased stationary-phase survival after 7 days.

The growth phase-dependent synthesis of cyclopropane fatty acids in Escherichia coli is the result of an RpoS(KatF)-dependent promoter plus enzyme instability

The formation of cyclopropane fatty acids (CFAs) in Escherichia coli is a post-synthetic modification of the phospholipid bilayer that occurs predominantly as cultures enter the stationary phase of growth. The mechanism of this growth phase-dependent regulation of CFA synthesis was unclear, since log-phase and stationary-phase cultures had been reported to contain similar levels of the enzyme catalysing the reaction (CFA synthase). We report that the timing of CFA synthesis can be explained by two unusual features. Fist, the gene encoding CFA synthase (cfa) was found to be transcribed from two promoters and the 5' ends of both transcripts were mapped by primer extension. One of the promoters was active only during the log-to-stationary phase transition and depended on the putative sigma factor encoded by the rpoS(katF) gene whereas the other promoter had a standard sigma 70 promoter consensus sequence and was expressed throughout the growth curve. Second, CFA synthase activity was shown to be unstable in vivo and a Cfa fusion protein was found to have a half life of < 5 min. The combination of these factors meant that, although CFA synthase was synthesized throughout the growth curve, a large increase in activity occurred during the log-to-stationary phase transition. As stationary phase progressed, the increased CFA synthase activity rapidly declined to the basal level. This transient increase in CFA synthase activity coupled with the cessation of net phospholipid synthesis in stationary phase provides an explanation for the unusual time course of CFA synthesis.

Acid and base resistance in Escherichia coli and Shigella flexneri: role of rpoS and growth pH

Escherichia coli K-12 strains and Shigella flexneri grown to stationary phase can survive several hours at pH 2 to 3, which is considerably lower than the acid limit for growth (about pH 4.5). A 1.3-kb fragment cloned from S. flexneri conferred acid resistance on acid-sensitive E. coli HB101; sequence data identified the fragment as a homolog of rpoS, the growth phase-dependent sigma factor sigma 38. The clone also conferred acid resistance on S. flexneri rpoS::Tn10 but not on Salmonella typhimurium. E. coli and S. flexneri strains containing wild-type rpoS maintained greater internal pH in the face of a low external pH than strains lacking functional rpoS, but the ability to survive at low pH did not require maintenance of a high transmembrane pH difference. Aerobic stationary-phase cultures of E. coli MC4100 and S. flexneri 3136, grown initially at an external pH range of 5 to 8, were 100% acid resistant (surviving 2 h at pH 2.5). Aerobic log-phase cultures grown at pH 5.0 were acid resistant; survival decreased 10- to 100-fold as the pH of growth was increased to pH 8.0. Extended growth in log phase also decreased acid resistance substantially. Strains containing rpoS::Tn10 showed partial acid resistance when grown at pH 5 to stationary phase; log-phase cultures showed < 0.01% acid resistance. When grown anaerobically at low pH, however, the rpoS::Tn10 strains were acid resistant. E. coli MC4100 also showed resistance at alkaline pH outside the growth range (base resistance). Significant base resistance was observed up to pH 10.2. Base resistance was diminished by rpoS::Tn10 and by the presence of Na+. Base resistance was increased by an order of magnitude for stationary-phase cultures grown in moderate base (pH 8) compared with those grown in moderate acid (pH 5). Anaerobic growth partly restored base resistance in cultures grown at pH 5 but not in those grown at pH 8. Thus, both acid resistance and base resistance show dependence on growth pH and are regulated by rpoS under certain conditions. For acid resistance, and in part for base resistance, the rpoS requirement can be overcome by anaerobic growth in moderate acid.

The Escherichia coli gapA gene is transcribed by the vegetative RNA polymerase holoenzyme E sigma 70 and by the heat shock RNA polymerase E sigma 32

Escherichia coli D-glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is produced by the gapA gene and is structurally related to eukaryotic GAPDHs. These facts led to the proposal that the gapA gene originated by a horizontal transfer of genetic information. The yields and start sites of gapA mRNAs produced in various fermentation conditions and genetic contexts were analyzed by primer extension. The transcriptional regulatory region of the gapA gene was found to contain four promoter sequences, three recognized by the vegetative RNA polymerase E sigma 70 and one recognized by the heat shock RNA polymerase E sigma 32. Transcription of gapA by E sigma 32 is activated in the logarithmic phase under conditions of starvation and of heat shock. Using a GAPDH- strain, we found that GAPDH production has a positive effect on cell growth at 43 degrees C. Thus, E. coli GAPDH displays some features of heat shock proteins. One of the gapA promoter sequences transcribed by E sigma 70 is subject to catabolic repression. Another one has growth phase-dependent efficiency. This complex area of differentially regulated promoters allows the production of large amounts of gapA transcripts in a wide variety of environmental conditions. On the basis of these data, the present view of E sigma 32 RNA polymerase function has to be enlarged, and the various hypotheses on E. coli gapA gene origin have to be reexamined.

Penicillin-binding proteins are regulated by rpoS during transitions in growth states of Escherichia coli

Attention has been recently focused on the role of the rpoS (formerly katF) gene product as a regulator during the transition from the exponential growth phase to the stationary phase as well as during nutritional starvation. It has been demonstrated that RpoS is an alternate sigma factor which would bind to promoters of genes induced at these times. It was previously noted that rpoS mutants do not undergo a transition to short rods during entry into the stationary phase. Because of their well-established role in morphogenesis, we investigated the status of the penicillin-binding proteins (PBPs) in Escherichia coli wild-type and isogenic rpoS mutants. Samples from cultures of E. coli ZK126 and ZK1000 (rpoS::kan) were taken in the midlogarithmic, early stationary, and late (24 h) stationary phases. The increase in PBP 6 seen upon entry of the wild-type strain into the stationary phase was not observed with the rpoS::kan cells, even after 24 h. There was also a marked decrease of PBP 3 in wild-type stationary-phase cells; PBP 3 has a known influence on morphogenesis. This decrease in PBP 3 was found to be markedly affected by the disruption of rpoS. Similar observations were made after prolonged starvation of the two strains for either glucose or a required amino acid. Inasmuch as PBPs are involved in peptidoglycan synthesis, we also examined two properties of peptidoglycan, autolysis and cross-linkage, that might be altered by the PBP differences. However, neither of these properties, which are known to undergo changes in the stationary phase, appeared to be influenced by the status of RpoS.

Expression and role of the universal stress protein, UspA, of Escherichia coli during growth arrest

The synthesis of the small, cytoplasmic protein UspA universal stress protein A) of Escherichia coli is induced as soon as the cell growth rate falls below the maximal growth rate supported by the medium, regardless of the condition inhibiting growth. The increase in UspA synthesis appears to be the result of induction of the monocistronic uspA gene. Induction of this gene during a heat-shock treatment is demonstrated to be the result of transcriptional activation of a sigma 70-dependent promoter which has previously been shown to be activated also during carbon starvation-induced growth arrest. Mutant cells lacking UspA grow at rates indistinguishable from the isogenic parent at different temperatures and in the presence of different growth inhibitors but are impaired in their ability to survive prolonged periods of complete growth inhibition caused by a variety of diverse stresses, including CdCl2, H2O2, DNP, CCCP exposure, and osmotic shock. Moreover, the uspA mutation results in an increased sensitivity of cells to carbon-source starvation (i.e. glucose, glycerol or succinate depletion). Also, the mutation causes a marked alteration in the timing of starvation protein expression but protein expression during steady-state growth appears to be normal. The results presented have prompted us to postulate that UspA may have a general protective function related to the growth arrest state.

Synthesis of the stationary-phase sigma factor sigma s is positively regulated by ppGpp

Strains of Escherichia coli which lack detectable guanosine 3',5'-bispyrophosphate (ppGpp) display a pleiotropic phenotype that in some respects resembles that of rpoS (katF) mutants. This led us to examine whether ppGpp is a positive regulator of sigma s synthesis. sigma s is a stationary-phase-specific sigma factor that is encoded by the rpoS gene. We found that a ppGpp-deficient strain is defective in sigma s synthesis as cells enter stationary phase in a rich medium, as judged by immunoblots. Under more-defined conditions we found that the stimulation of sigma s synthesis following glucose, phosphate, or amino acid starvation of wild-type strains is greatly reduced in a strain lacking ppGpp. The failure of ppGpp-deficient strains to synthesize sigma s in response to these starvation regimens could indicate a general defect in gene expression rather than a specific dependence of rpoS expression on ppGpp. We therefore tested the effect of artificially elevated ppGpp levels on sigma s synthesis either with mutations that impair ppGpp decay or by gratuitously inducing ppGpp synthesis with a Ptac::relA fusion. In both instances, we observed enhanced sigma s synthesis. Apparently, ppGpp can activate sigma s synthesis under conditions of nutrient sufficiency as well as during entry into stationary phase. This finding suggests that changes in ppGpp levels function both as a signal of imminent stationary phase and as a signal of perturbations in steady-state growth.

Complex transcriptional control of the sigma s-dependent stationary-phase-induced and osmotically regulated osmY (csi-5) gene suggests novel roles for Lrp, cyclic AMP (cAMP) receptor protein-cAMP complex, and integration host factor in the stationary-phase response of Escherichia coli

osmY (csi-5) is a representative of a large group of sigma s-dependent genes in Escherichia coli that exhibit both stationary-phase induction and osmotic regulation. A chromosomal transcriptional lacZ fusion (csi-5::lacZ) was used to study the regulation of osmY. We show here that in addition to sigma s, the global regulators Lrp, cyclic AMP (cAMP) receptor protein-cAMP complex (cAMP-CRP), and integration host factor (IHF) are involved in the control of osmY. All three regulators negatively modulate the expression of osmY, and they act independently from sigma s. Stationary-phase induction of osmY in minimal medium can be explained by stimulation by sigma s combined with a relief of Lrp repression. Stationary-phase induction of osmY in rich medium is mediated by the combined action of sigma s, Lrp, cAMP-CRP, and IHF, with the latter three proteins acting as transition state regulators. The transcriptional start site of osmY was determined and revealed an mRNA with an unusual long nontranslated leader of 244 nucleotides. The regulatory region is characterized by a sigma 70-like -10 promoter region and contains potential binding sites for Lrp, CRP, and IHF. Whereas sigma s, Lrp, CRP, and IHF are clearly involved in stationary-phase induction, none of these regulators is essential for osmotic regulation of osmY.

Stationary phase-specific expression of the fic gene in Escherichia coli K-12 is controlled by the rpoS gene product (sigma 38)

The fic gene, near pabA located at 75 min of the Escherichia coli chromosome, was previously identified as the regulatory factor of cell division. In this paper we have examined how fic gene expression is controlled during the growth cycle using a fic-lacZ protein fusion plasmid (pFL1). Its expression was induced at stationary phase while it was nearly abolished in rpoSmutants. Using a RNase protection assay, fic transcript at stationary phase was detected in rpoS+ strains, but not in the rpoS mutants. Furthermore, primer extension analysis indicated that the fic transcript controlled by RpoS initiates at a G located 185 bp upstream from ATG of the fic coding region. Compared with the sigma 70 recognition sequence, the -10 region of fic promoter resembled the Pribnow box, but no homologous sequence was observed at the -35 region. These results were consistent with the characteristic sequence profile of fic promoter recognized specifically by RpoS in vitro, which is the only example of the type III promoter so far detected in vitro and in vivo.

Early and late responses of TOL promoters to pathway inducers: identification of postexponential promoters in Pseudomonas putida with lacZ-tet bicistronic reporters

Transcriptional lacZ fusions to the Pu and Pm promoters of the TOL (toluene degradation) plasmid inserted in monocopy in the chromosome of Pseudomonas putida showed a very different responsiveness to their respective aromatic effectors regarding growth phase. While a substantial XylS-dependent activation of Pm-lacZ was detected nearly instantly after m-toluate addition, XylR- and xylene-mediated induction of the sigma 54 promoter Pu became significant only after cells slowed down exponential growth and entered stationary phase. When Pu and Pm were fused to lacZ-tet reporters (i.e., promoterless lacZ genes coupled to a tet gene which confers resistance to tetracycline when cotranscribed with the leading gene) instead of lacZ alone, the resulting colonies displayed a distinct phenotype consisting of hyperfluorescence on agar plates after being sprayed with 4-methylumbelliferyl-beta-D-galactoside, simultaneously with being either sensitive (Pu) or resistant (Pm) to tetracycline. To examine whether the same phenotype could be scored in strains carrying transcriptional fusions of the lacZ-tet cassettes to other genes or promoters whose expression is silenced during growth and activated in stationary phase, we constructed mini-Tn5 lacZ-tet transposons for random genetic probing of promoters preferentially active at advanced stages of growth. Chromosomal insertions of this mobile element were selected by means of the constitutive resistance to kanamycin which is also specified by the transposon. A number of kanamycin-resistant colonies which are hyperfluorescent with 4-methylumbelliferyl-beta-D-galactosidase but sensitive to tetracycline and which reached full induction only at postexponential growth stages were obtained.

In vitro functional characterization of overproduced Escherichia coli katF/rpoS gene product

The katF/rpoS gene product (sigma s), a central regulator of stationary-phase gene expression in Escherichia coli, has been purified from an overproducing strain. sigma s was used as an immunogen for the production of monoclonal antibodies. Previous sequence analysis of sigma s strongly indicated homology to the sigma factor family. We show biochemically in this paper that sigma s is a sigma factor. This protein can bind to core RNA polymerase (E), and this binding can be competed effectively by the major E. coli transcription initiation factor, sigma 70. Immunopurified sigma s holoenzyme (E sigma s) transcribes the promoters of the bolAp1 gene and the xthA gene. Interestingly, both promoters can also be transcribed by sigma 70 holoenzyme (E sigma 70).

Sigma s-dependent promoters in Escherichia coli are located in DNA regions with intrinsic curvature

Expression of a number of genes during stationary phase in Escherichia coli is controlled by the alternative sigma factor sigma s (KatF). Promoters recognized by sigma s do not present a well-defined consensus sequence in their -10 and -35 regions. By polyacrylamide gel electrophoresis of DNA fragments performed at different temperatures, and by computer prediction analyses, we have found that sigma s-regulated promoters are located in regions where DNA shows intrinsic curvatures. This feature does not appear in a stationary-phase-induced promoter which is not controlled by sigma s. We propose that DNA bending may help in recognition and/or binding of sigma s to stationary-phase-induced promoters.