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Journal of Bacteriology, August 2006, p. 5775-5782, Vol. 188, No. 16
0021-9193/06/$08.00+0     doi:10.1128/JB.00276-06
Copyright © 2006, American Society for Microbiology. All Rights Reserved.

DksA Is Required for Growth Phase-Dependent Regulation, Growth Rate-Dependent Control, and Stringent Control of fis Expression in Escherichia coli

Prabhat Mallik,1 Brian J. Paul,2,{dagger} Steven T. Rutherford,2 Richard L. Gourse,2 and Robert Osuna1*

Department of Biological Sciences, University at Albany, 1400 Washington Avenue, Albany, New York 12222,1 Department of Bacteriology, University of Wisconsin, 420 Henry Mall, Madison, Wisconsin 537062

Received 21 February 2006/ Accepted 31 May 2006


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ABSTRACT
 
DksA is a critical transcription factor in Escherichia coli that binds to RNA polymerase and potentiates control of rRNA promoters and certain amino acid promoters. Given the kinetic similarities between rRNA promoters and the fis promoter (Pfis), we investigated the possibility that DksA might also control transcription from Pfis. We show that the absence of dksA extends transcription from Pfis well into the late logarithmic and stationary growth phases, demonstrating the importance of DksA for growth phase-dependent regulation of fis. We also show that transcription from Pfis increases with steady-state growth rate and that dksA is absolutely required for this regulation. In addition, both DksA and ppGpp are required for inhibition of Pfis promoter activity following amino acid starvation, and these factors act directly and synergistically to negatively control Pfis transcription in vitro. DksA decreases the half-life of the intrinsically short-lived fis promoter-RNA polymerase complex and increases its sensitivity to the concentration of CTP, the predominant initiating nucleotide triphosphate for this promoter. This work extends our understanding of the multiple factors controlling fis expression and demonstrates the generality of the DksA requirement for regulation of kinetically similar promoters.


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INTRODUCTION
 
Fis is the most abundant nucleoid-associated protein during logarithmic growth phase in Escherichia coli growing in rich medium (2). Besides stimulating specialized site-specific DNA inversion events (hence its name: factor for inversion stimulation) and {lambda} phage DNA recombination (17), Fis acts as a transcription factor to stimulate rRNA and various tRNA promoters (35, 48). In addition, a growing number of genes are reported to be regulated positively or negatively by Fis (13, 15, 21, 22, 24, 29, 61, 63), including several genes that play roles in pathogenesis in various bacterial species (16, 20, 52, 60). In cases where positive control by Fis has been examined in detail (e.g., at the rrnB P1 and proP promoters), activation requires a direct interaction between Fis and the RNA polymerase (RNAP) {alpha} subunit C-terminal domain (1, 30).

Regulation by Fis results from large changes in its intracellular levels, which are triggered by changes in the nutritional environment or the growth phase (3, 36, 37, 55). A dramatic burst in both fis mRNA and protein levels is observed when cells in stationary phase are outgrown in rich medium. fis mRNA and protein levels peak during early logarithmic growth phase, decrease soon thereafter, and become nearly undetectable as cells enter the stationary phase, an expression pattern referred to as growth phase-dependent regulation (GPDR). GPDR is controlled by changes in fis transcription initiation and not by changes in the decay rates of the fis mRNA (47). Additionally, it was reported recently that translational control of fis expression is exerted by BipA, a ribosome-associated protein (40).

A single promoter (Pfis) is responsible for transcribing the fis operon in E. coli (28). Pfis is negatively autoregulated by Fis binding at two sites centered at –44 and +25 relative to the transcription start site (3, 37, 47) and positively controlled by integration host factor (IHF) binding at a single site centered at –94 (47). Pfis is also negatively controlled during the stringent response by ppGpp (28, 37, 57). However, GPDR of Pfis is relatively normal in strains lacking ppGpp (3). Both the stringent response and GPDR require only the core promoter region from about –38 to +5, the binding site for RNAP holoenzyme (37, 47), and these regulatory properties are strictly conserved in other bacterial species (8, 28, 39). Additionally, because maximal Fis levels increase with the quality of the growth medium (3, 36), it has been suggested that Pfis activity might increase with steady-state growth rate, and this in turn might contribute to the growth rate-dependent control of some Fis-activated promoters (6, 35, 46). However, growth rate-dependent control of Pfis itself has not been demonstrated directly.

Pfis is among a small number of E. coli promoters that initiate transcription predominantly with CTP (23, 27), a feature that is strongly conserved in Pfis in other bacteria (28, 59). Mutations in the transcription initiation region that caused a switch in CTP to ATP or GTP as the predominant initiating nucleoside triphosphate (iNTP) profoundly altered GPDR of fis (57). As in the case of the rrnB P1 and P2 promoters (18, 33, 43), complexes formed by the Pfis promoter with RNAP are unusually short-lived, hypersensitive to salts, and strongly dependent on high concentrations of the iNTP for maximal transcription (58).

Recently, it was found that the small RNAP-associated protein DksA is a critical component of the transcription initiation complex that is required for negative regulation of rRNA promoters (41, 44) and positive regulation of several amino acid promoters in vitro and in vivo (42). DksA destabilizes intrinsically unstable rRNA promoter complexes, enhances their sensitivity to ppGpp and the iNTP concentration, and is essential for their growth rate-dependent control, growth phase-dependent control, and stringent control (41).

Considering the kinetic and regulatory similarities between rRNA promoters and Pfis, we investigated the possibility that DksA might also target Pfis for transcriptional regulation. Here we demonstrate that DksA greatly affects growth phase-dependent control, growth rate-dependent control, and stringent control of Pfis. DksA acts on the Pfis promoter directly in vitro, decreasing the lifetime of its complex with RNAP, enhancing its iNTP sensitivity, and, together with ppGpp, negatively regulating fis transcription. These results expand our understanding of fis regulation and demonstrate the generality of the role of DksA in facilitating regulation of promoters sharing similar kinetic characteristics.


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MATERIALS AND METHODS
 
Chemicals, enzymes, and growth media. Chemicals were purchased from Sigma-Aldrich, Fisher Scientific, Life Technologies Inc. (Gibco BRL), Pharmacia, or VWR Scientific. Nucleotides and radioisotopes were from Amersham Biosciences Corp. or Tri-Link BioTechnologies. Oligonucleotides were synthesized at the Center for Comparative Functional Genomics, State University of New York at Albany. Enzymes were from New England BioLabs, Inc., Promega Corp., or Roche Molecular Biochemicals. RNA polymerase (E{sigma}70) purified by standard procedures (10) was a gift from R. Landick (University of Wisconsin—Madison) or purchased from Epicentre (Madison, WI). N-terminally hexahistidine-tagged DksA was purified by affinity chromatography and functioned indistinguishably from native DksA in vivo and in vitro (41).

Bacterial culture media were from Difco Laboratories. Cultures were grown at 31°C in Luria-Bertani (LB) medium or M9 minimal medium (50) supplemented with 0.4% carbon source (glucose or glycerol), 0.4% Casamino Acids, or 40 µg/ml methionine, aspartic acid, and threonine, as indicated for each experiment. To select for drug resistance, 100 µg of ampicillin per ml or 12 µg of tetracycline per ml was added to the growth medium as appropriate for each strain.

Strains and plasmids. Relevant strains used in this work are listed in Table 1. RO1250 was made by P1 transduction of the dksA::tet mutation from RLG7062 (41) into VH1000 following procedures described previously (31). Transductants were selected on LB agar containing tetracycline, and the presence of the dksA::tet construct was verified by PCR using the oligonucleotides 5'-dGCTATCCGGAAAAGCATCTGC and 5'-dCTGTGGTAAACGTGATGGAAC, which anneal at 54°C within regions upstream and downstream of dksA, respectively, to give distinct DNA fragments for the dksA::tet mutation and the wild-type gene. PCR was conducted using Taq polymerase (Roche Molecular Biochemicals), as described by the manufacturer. Strains (RO1261 and RO1265) carrying prophage-containing promoter-lacZ fusions (Pfis DNA from –373 to +83 with respect to the transcription start site) were made by infection of wild-type (WT) or dksA mutant strains with phage from previously existing lysogens or by P1 transduction (with the same result). This DNA region contains a single promoter (Pfis) responsible for transcribing the fis operon (3, 28, 47). pRO362 is a pKK223-3-based plasmid that contains the Pfis region from –166 to +83 cloned within EcoRI and BamHI restriction sites. This replaces the tac promoter in pKK223-3 and positions the Pfis start site about 340 bp upstream of the rrnB T1 rho-independent terminator (28).


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  		TABLE 1. Strains used in this work

RNA extraction and primer extension assays. Primer extension assays were conducted to examine effects of dksA on Pfis GPDR in RO1275 and RO1276. The relative fis mRNA levels measured at 0 min of growth were from total RNA prepared from cultures grown in LB medium for 18 h. Subsequent measurements were from cultures diluted in LB to an optical density at 600 nm (OD600) of 0.06 and grown at 31°C with shaking. At intervals, cells were harvested for total RNA preparation using the hot acid-phenol method of extraction (11). Primer extension reactions were performed as described previously (57, 59) using 10 µg total cellular RNA and 2 pmol of 32P-end-labeled oRO109 oligonucleotide (5'-dGCTGATATTGTCCGATG), which anneals to the fis mRNA region from +54 to +38, relative to the transcription initiation site at +1C. A second oligonucleotide oRO133 (5'-dGGTGAGCAAAAACAGGAAGG) anneals to the ß-lactamase (bla) promoter region from +76 to +57 on pBR322 present in these strains and was used as a control. The resulting products were separated on 8 M urea-8% polyacrylamide gels, and the relative signal intensities were quantified by phosphorimaging. The relative intensities measured for the Pfis transcripts were adjusted by those of the bla transcripts in each data set to correct for loading errors and were then normalized to the amount of cells (based on OD600 readings) that yielded the RNA signals in each reaction. The proximity of the primer-annealing site to the fis promoter allows the primer extension assay to accurately measure changes in transcription initiation.

Starvation induction. Saturated cultures of RO1275, RO1276, and RO1279 were diluted in LB to an OD600 of 0.06 and grown at 31°C with shaking for 30 min to induce fis expression. At this time half the culture was transferred to another flask containing sufficient serine hydroxamate (SH) to generate a final concentration of 1 mg/ml and allowed to continue shaking at 31°C. The nontreated (control) culture received an equivalent volume of sterile distilled water and was allowed to continue shaking at 31°C. At various times after addition of SH or water (see Fig. 3), a sample from each culture was harvested and used to prepare total cellular RNA. Primer extension reactions were performed with 10 µg total RNA and oligonucleotides oRO109 and oRO133 as described above.


Figure 3
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  		FIG. 3. Effect of dksA on stringent control of Pfis. (A) Primer extension assays of fis mRNA under starved and nonstarved conditions. At the indicated times after SH addition, samples of the SH-treated and untreated (control) cell cultures were harvested and used to prepare total RNA. Primer extension reactions were performed to detect both the fis and bla mRNA signals. The two Pfis transcript signals correspond to those initiating at +1C and –2G; two prominent transcript signals were also detected for the bla transcript. Strains used in this experiment were RO1275 (WT for dksA), RO1276 ({Delta}dksA), and RO1279 ({Delta}relA {Delta}spoT). Duplicate reactions similar to those represented in panel A for (B) dksA WT (WT), (C) {Delta}dksA, and (D) {Delta}relA {Delta}spoT strains were quantified by phosphorimaging and averaged and are shown relative to the values at time zero in each set, which were assigned a value of 1.0. Error bars indicate standard deviations. Open circles, relative fis transcript levels in the control cultures (-SH); filled circles, relative fis transcript levels in the serine hydroxamate-treated cultures (+SH).

ß-Galactosidase assays. For determining the effect of dksA on growth phase-dependent regulation, saturated cultures of RO1261 and RO1265 were diluted in LB medium to an OD600 of 0.06 and grown at 31°C. Culture samples were removed at various times during growth for ß-galactosidase assays, which were performed as described elsewhere (31). For determining the effect of dksA on growth rate-dependent control of Pfis, the same strains were diluted in the experimentally specified growth medium and allowed to grow at 31°C. Culture samples were removed during early logarithmic growth phase, when fis expression is high (OD600 from 0.08 to 0.15, depending on the growth medium) and assayed for ß-galactosidase activity. Results are given as averages from three independent assays.

In vitro transcription. Multiple round in vitro transcription assays were performed using supercoiled plasmid template pRO362 containing Pfis with the promoter endpoints –168 and +83 with respect to the transcription start site (28). Reactants (0.5 nM plasmid and specified concentrations of ppGpp and DksA) were incubated at 30°C for 10 min in 40 mM Tris · HCl (pH 7.9), 150 mM KCl, 10 mM NaCl, 5% glycerol, 10 mM MgCl2, 1 mM dithiothreitol (DTT), 0.1 µg/ml bovine serum albumin (BSA), 200 µM ATP, CTP and GTP, 10 µM UTP, and [{alpha}-32P]UTP (2.5 µCi). Transcription was initiated by addition of 5 nM RNAP and terminated after 10 min by addition of an equal volume of formamide loading buffer, and the products were electrophoresed on 7 M urea-6% polyacrylamide gels and visualized and quantified by phosphorimaging.

CTP concentration dependence of transcription. To evaluate the CTP dependence on transcription, multiple-round in vitro transcription assays were performed using buffer conditions similar to those described above, except that 200 mM KCl, 40 µM ATP and GTP, 4 µM UTP, 2.5 µCi [{alpha}-32P]UTP, and various concentrations of CTP (see Fig. 6) were used. Reactions were initiated by addition of RNAP and allowed to proceed for 30 min at 22°C, and the products were analyzed as described above. As a control, ATP dependence was similarly examined but with the NTP concentrations adjusted to 40 µM GTP and CTP, 4 µM UTP, 2.5 µCi [{alpha}-32P]UTP, and the concentrations of ATP indicated in Fig. 6. To evaluate the effect of DksA on the CTP dependence, multiple-round in vitro transcription assays were performed in the absence or presence of 6 µM DksA.


Figure 6
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  		FIG. 6. Effect of DksA on promoter sensitivity to CTP. Multiple-round in vitro transcription assays were performed with supercoiled pRO362 in transcription buffer containing 200 mM KCl and various concentrations of ATP ({circ}) or CTP (•, {triangledown}), in the absence ({circ}, •) or presence ({triangledown}) of 6 µM DksA, as described in Materials and Methods. fis transcripts were electrophoretically separated and quantified by phosphorimaging and are shown relative to the maximal levels obtained at the highest NTP concentrations used.

Promoter complex half-life assays. Complex lifetime was determined using a transcription-based assay essentially as described previously (5). pRO362 (0.5 nM) and RNAP (5 nM) were incubated in the absence or presence of 2 µM DksA for 10 min at 30°C in 40 mM Tris · HCl (pH 7.9), 100 mM KCl, 10 mM NaCl, 5% glycerol, 10 mM MgCl2, 1 mM DTT, and 0.1 µg/µl BSA. At time zero, heparin at a final concentration of 10 µg/ml was added as a competitor, and at different times 10-µl aliquots were added to tubes containing 1.25 µl NTPs (final concentrations, 200 µM ATP, CTP, and GTP, 10 µM UTP, and 2.5 µCi [{alpha}-32P]UTP). Reactions were stopped after 10 min, and the products were analyzed as described above. We note that at 175 mM KCl, the half-life of the competitor-resistant complex was too short (<15 s) to quantify (58).


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RESULTS
 
DksA alters growth phase-dependent regulation of fis. We used primer extension assays to measure the relative levels of chromosomally derived fis transcripts in strains with and without dksA (Fig. 1A, B, and C). As reported previously (58), fis mRNA levels in strains grown in LB medium were maximal during early logarithmic phase (15 to 60 min after dilution of stationary-phase cells), decreased during mid-log phase, and then became undetectable as cells entered stationary phase. In the {Delta}dksA mutant, fis mRNA levels increased during early log phase, reaching peak levels that were about 1.5-fold higher than in the dksA wild-type strain (WT). These levels then decreased more slowly during mid-log and stationary phases, exceeding those in the wild-type strain even 4 h after entry into stationary phase. Similar results were observed when Pfis was present on a multicopy plasmid in a {Delta}dksA strain (not shown). In contrast, the ß-lactamase (bla) transcript showed minimal variation with growth phase and was unaffected by dksA. Thus, dksA is required for inhibition of fis transcription in mid-log and late log growth and in stationary phase.


Figure 1
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  		FIG. 1. Effect of dksA on growth phase-dependent regulation of Pfis. (A) Schematic representation of the fis operon, consisting of two genes (dusB and fis) that are transcribed by a single promoter (Pfis). The approximate annealing region of the oligonucleotide oRO109 used in the primer extension assays is represented with an arrow. Beneath is the sequence of the minimal Pfis promoter. The operationally defined –10 and –35 promoter sequences (57) are boxed, and the major and minor transcription start sites are indicated with a large and small arrow, respectively. (B) Effect of DksA on GPDR of Pfis. Primer extension assays were performed to detect Pfis transcripts synthesized from the chromosome using total RNA obtained from RO1275 (WT) or RO1276 ({Delta}dksA) at various times of outgrowth from sta- tionary phase in LB medium. The signals corresponding to the two fis mRNA start sites (+1C and –2G) and for the bla mRNA produced in these strains are shown with arrows. (C) Effect of dksA on the fis mRNA expression pattern. Primer extension results similar to those shown in panel B were quantified by phosphorimaging, normalized to the amount of cells used (as determined by OD600 readings) in each reaction, and plotted relative to the maximum value in RO1275, which was assigned a value of 100. The results from two experiments were averaged, with standard deviations being within 30% or less of the values. Relative fis mRNA levels are shown for RO1275 (dksA+) ({circ}) and RO1276 (dksA) (•); growth curves based on OD600 measurements are shown for dksA+ ({triangleup}) and dksA ({blacktriangleup}) strains. (D) Effect of dksA on ß-galactosidase activity from a Pfis-lacZ fusion during growth in LB medium. Saturated cultures of RO1261 (dksA+) ({circ}, {triangleup}) and RO1265 (dksA) (•, {blacktriangleup}) were diluted to an OD600 of 0.06 in LB and grown at 31°C. ß-Galactosidase assays ({circ}, •) were performed at the indicated times during growth. Results are averages from three independent cultures; standard deviations were within 14% of the average values. Growth curves for both strains ({triangleup}, {blacktriangleup}) are shown.

We confirmed that dksA alters GPDR of the fis promoter by comparing expression from a chromosomal Pfis-lacZ fusion in WT versus {Delta}dksA strains (Fig. 1D). ß-Galactosidase activity peaked during early logarithmic growth in the WT strain and then decreased during mid-logarithmic and late logarithmic growth. Consistent with the primer extension results described above, Pfis activity was higher in the {Delta}dksA than in the WT strain during all phases of growth, and this increase was most prominent during late log phase and in stationary phase. The enzymatic activity observed in the WT strain during late log and stationary phases is likely attributable to ß-galactosidase that accumulated earlier in growth, since ß-galactosidase is stable and Pfis-lacZ mRNA hybrid transcripts were not detected in late log or stationary phase (37) (data not shown). These results indicate that DksA acts negatively on Pfis and is required for normal GPDR of this promoter.

DksA is required for growth rate-dependent regulation of Pfis. To determine if Pfis transcription is controlled by the growth rate, we measured Pfis activity using promoter-lacZ fusions in media of varying nutritional quality during steady-state growth, when fis is maximally expressed (Fig. 2). ß-Galactosidase activity increased >4-fold (255 to 1,230 units), with an ~2-fold increase in growth rate (0.8 to 1.5 doublings/h), demonstrating that Pfis transcription is subject to growth rate-dependent control. In contrast, Pfis activity was higher and changed little or not at all with growth rate in the {Delta}dksA mutant (Fig. 2A). There was a 5.5-fold difference in Pfis activity in the two strains grown in M9 glucose medium supplemented with glucose, methionine, aspartic acid, and threonine and a 1.6-fold difference in LB medium (Fig. 2B). These results demonstrate that DksA is essential for limiting Pfis promoter activity, especially at low steady-state growth rates.


Figure 2
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  		FIG. 2. Effect of dksA on growth rate-dependent control of Pfis. (A) Transcription activity from Pfis was monitored by ß-galactosidase assays in strains RO1261 (WT for dksA; open symbols) and RO1265 ({Delta}dksA; filled symbols) grown in different media at 31°C to generate different growth rates. Growth media used were ({square}, {blacksquare}) M9 salts, 0.4% glucose, and 40 µg/ml each of methionine, aspartic acid, and threonine, ({triangleup}, {blacktriangleup}) M9 salts, 0.4% glycerol, and 0.4% Casamino Acids, ({circ}, •) M9 salts, 0.4% glucose, and 0.4% Casamino Acids, and ({diamond}, {blacklozenge}) LB. Results are averages of three independent cultures, with standard deviations indicated by error bars. (B) The results from panel A are displayed in a bar graph to compare the effects of dksA on Pfis transcription in each growth medium used. Open bars, RO1261; filled bars, RO1265.

DksA greatly amplifies stringent control of Pfis. To determine if DksA affected stringent control of Pfis in vivo, we compared relative transcript levels from Pfis in a WT, {Delta}dksA, and {Delta}relA {Delta}spoT strain that is unable to synthesize ppGpp (62), before and after starvation for serine (Fig. 3). fis transcription decreased ~10-fold by 15 min after starvation (induced by addition of serine hydroxamate) in the WT strain. In contrast, fis transcription decreased <2-fold in the {Delta}dksA and not at all in the {Delta}relA {Delta}spoT strain. As expected, there was no significant effect of starvation on transcripts from the bla promoter, confirming that the effects of DksA and ppGpp are promoter specific. Taken together, our results indicate that although ppGpp may be able to inhibit fis expression slightly in the absence of DksA (41), both DksA and ppGpp are required for normal stringent control of Pfis.

DksA directly inhibits transcription from Pfis, amplifies inhibition by ppGpp, and decreases the lifetime of the Pfis complex with RNAP. To determine whether the effects of ppGpp and DksA observed on Pfis in vivo were direct, transcription from the promoter was analyzed in vitro in the presence or absence of purified DksA and/or ppGpp (Fig. 4). Whereas either DksA or ppGpp alone reduced Pfis activity ~2-fold, the two factors together reduced transcription ~10-fold. Thus, as observed for rRNA promoters (41), DksA and ppGpp inhibit Pfis directly and synergistically.


Figure 4
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  		FIG. 4. Effect of ppGpp and DksA on Pfis transcription in vitro. Duplicate reactions of multiple round in vitro transcription assays were performed with pRO362 in the absence or presence of 4 µM purified DksA and 200 µM ppGpp, as indicated. Transcripts from Pfis and the RNA-1 promoter (derived from the plasmid) are indicated. The Pfis signals from two independent reactions were averaged and are shown as a fraction of the Pfis activity in the absence of DksA and ppGpp.

It was previously shown that the Pfis complex with RNAP is very short-lived, too short to measured accurately in buffers containing relatively high salt concentrations; e.g., the half-life of the complex was <15 s in a buffer containing 175 mM KCl (58). We took advantage of the fact that the complex is longer-lived at lower salt concentrations to measure effects of DksA on the half-life of the Pfis complex with RNAP. Figure 5 demonstrates that DksA further decreases the lifetime of the complex directly, ~3-fold (from ~14 min to ~4.6 min) in a buffer containing 100 mM KCl. These results are consistent with the model that DksA inhibits transcription, in part, by further destabilizing intrinsically unstable promoter complexes.


Figure 5
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  		FIG. 5. Effect of DksA on the stability of RNAP complexes with Pfis. Pfis complexes with RNAP were preformed with supercoiled pRO362 in the presence ({triangledown}) or absence (•) of 2 µM DksA in transcription buffer containing 100 mM KCl as described in Materials and Methods. The complexes were challenged with heparin and assayed for single-round transcription at various times thereafter. Electrophoretically separated transcripts were quantified by phosphorimaging and are shown relative to the amount present prior to the heparin addition.

DksA increases the sensitivity of Pfis to CTP. Previous studies indicated that high concentrations of CTP stabilize the short-lived Pfis complex with RNAP to increase transcription >20-fold (58), suggesting that transcription from Pfis is highly sensitive to the concentration of CTP. To verify the Pfis dependence on high CTP concentrations, we performed multiple-round transcription from Pfis with increasing concentrations of CTP or ATP while the remaining NTP concentrations were kept constant (Fig. 6). We found that half-maximal Pfis promoter activity required ~280 µM CTP and maximal transcription required ~900 µM CTP. In contrast, half-maximal promoter activity required only ~5 µM ATP and maximal activity required only ~100 µM ATP. Thus, Pfis transcription in vitro is highly sensitive to the concentration of the iNTP, CTP, but not to that of ATP.

To determine if DksA affected the sensitivity of Pfis to the iNTP, we performed transcription in the presence of 6 µM DksA with various concentrations of CTP while keeping the other three NTP concentrations constant. The results show that DksA further increased the relative KNTP for CTP by about 185 µM (from ~280 µM to ~465 µM) and caused the maximal transcription activity to require >1,500 µM CTP (Fig. 6). We emphasize that the absolute KNTP values are dependent on the solution conditions, and it is not valid to compare the apparent KNTP values obtained under different conditions. Nevertheless, our results demonstrate that not only does DksA amplify the sensitivity of Pfis to ppGpp, but also it increases the concentration of the initiating NTP required for transcription.


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DISCUSSION
 
In a {Delta}dksA strain, we found that the fis mRNA levels are higher than in a WT strain, persisting through mid-logarithmic and late logarithmic growth and several hours into stationary phase and that this results from an increase in Pfis promoter activity. Steady-state Pfis activity increases with growth rate, and this is entirely dependent on dksA. Stringent control of fis is nearly abolished in a {Delta}dksA strain. Furthermore, we show that DksA acts directly on Pfis promoter complexes in vitro, reducing the lifetime of the competitor-resistant complex with RNAP. DksA elevates the concentration of the iNTP (CTP) required for efficient transcription from Pfis and strongly amplifies the inhibitory effect of ppGpp on Pfis. Our results are consistent with the model that DksA inhibits Pfis activity, in part, by reducing the half-life of Pfis promoter complexes. In conjunction with changes in the concentrations of ppGpp and CTP, DksA constrains fis expression primarily to early log phase at high growth rates, and it inhibits expression at low growth rates or following amino acid starvation. We conclude that DksA is crucial for regulation of fis expression in E. coli.

Blastn and Blastx searches indicate that fis homologues are present throughout the {gamma} and ß subdivisions of proteobacteria, which include the Enterobacteriales, Pasteurellaceae, Pseudomonadaceae, Vibrionaceae, Xanthomonadaceae, Burkholderiaceae, and Neisseriaceae, among others (not shown). In every one of these organisms, a dksA homologue is also evident. Additionally, fis core promoter sequences and transcription initiation of Pfis with CTP, as well as GPDR and stringent control of fis, are strongly conserved among enteric bacteria (3, 28, 37, 39). Therefore, we suggest that DksA-dependent control of fis expression is likely to be a feature conserved in these bacteria as well.

The effects of DksA on Pfis transcription are strikingly similar to those observed on rrnB P1 (41). This can be attributed to the overall similarities in the kinetic properties of these promoters. The parallel regulation of these promoters is consistent with the role of Fis in stimulating rRNA promoter activity (9, 48), and this is apparently accomplished by linking their synthesis rates to the same regulatory molecules: DksA, ppGpp, and NTPs.

DksA does not bind to DNA but instead binds directly to RNAP to mediate its effect (41). The structural similarities among DksA (44, 56) and the transcription elongation factors GreA and GreB (26, 38, 53, 54) suggested a model whereby the coiled coil of DksA inserts deep into the RNAP secondary channel with its tip approaching the active site (44). There are strong correlations between the effects of promoter mutations on the lifetimes of rrnB P1 promoter complexes (18, 33) and Pfis promoter complexes (P. Mallik and R. Osuna, unpublished results), the sensitivity of these complexes to small molecule regulators, and their control in vivo, suggesting that a short-lived complex with RNAP is a prerequisite for regulation by DksA. However, the precise mechanism(s) by which DksA and ppGpp ultimately affect the kinetics of promoter complexes remains to be determined.

Relative DksA levels change only slightly in different phases of growth and with changes in steady-state growth rate (41; S. T. Rutherford and R. L. Gourse, unpublished results). Thus, rapid changes in the intracellular concentrations of ppGpp and iNTPs specify when rRNA promoter regulation occurs and which of these small molecules is responsible (34). The rapid increase in ppGpp levels that occurs during the stringent response (12) effectively inhibits fis expression. The role of DksA in amplifying negative control by ppGpp likely explains the DksA requirement for stringent control of Pfis. In contrast, CTP pools rapidly increase during outgrowth from stationary phase (33), fluctuate during logarithmic growth, and substantially decrease as cells enter the stationary phase, all in a pattern that qualitatively correlates with the pattern of fis expression (58). We suggest that the DksA requirement for limiting fis expression to the logarithmic growth phase may derive from its role in decreasing the lifetime of Pfis complexes and increasing the sensitivity to the CTP concentration (58).

Since ppGpp functions negatively and its concentrations increase during outgrowth from stationary phase, ppGpp cannot be responsible for the increase in fis expression during this time (34). In contrast, there is a transient increase in ppGpp levels during entry into stationary phase (34) as well as a decrease in CTP levels (34, 58). Thus, it is possible that the changes in both ppGpp and CTP levels contribute to the shutdown of fis expression at this time. However, since normal GPDR of fis was observed in a {Delta}relA {Delta}spoT strain (3), apparently other mechanisms can compensate for the role of ppGpp in this process.

Although ppGpp concentrations correlate inversely with control of rRNA and fis promoter activities, whereas NTP pools remain relatively unchanged at different steady-state growth rates (43, 45, 49, 51, 64), growth rate-dependent regulation of rrnB P1 and P2 is maintained in {Delta}relA and {Delta}relA {Delta}spoT strains (5, 7, 19, 32). DksA, however, is essential for growth rate-dependent regulation of both rRNA and fis expression. Thus, other factors are apparently able to compensate for the loss of ppGpp and confer DksA-dependent regulation on rRNA promoters (and possibly on Pfis) when the cell is provided with enough time to adjust its macromolecular synthesis rates.

In addition to the mechanisms that control fis transcription, it has been reported that there is also control of fis translation by a mechanism requiring BipA (40). Levels of BipA vary with the growth phase and with the nutritional quality of the growth medium in a manner that correlates with variations in Fis levels. Thus, control of Fis synthesis may also involve BipA, directly or indirectly. Contributions from multiple mechanisms is a common feature for regulation of genes associated with synthesis of the translation machinery (12, 14, 25, 43).

DksA has emerged as an essential component of three mechanisms that involve negative regulation of fis and stable RNA promoters: stringent, growth phase-dependent, and growth rate-dependent control. Furthermore, its direct effects are not limited to negative control of promoters sharing similar kinetic properties; in conjunction with ppGpp, DksA also plays a role in direct positive control of several amino acid promoters (42). DksA thus has global effects in regulating gene expression, some of which are direct and some of which are indirect (resulting from its direct effects on stable RNA expression) (4, 65). Since Fis acts as both an activator and a repressor of numerous genes, it can be expected that some of the indirect effects of DksA on global gene expression will be mediated through its effects on fis expression.

. . . . . .


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ACKNOWLEDGMENTS
 
We thank members of the Osuna and Gourse laboratories for helpful comments.

This work was funded in part by National Institutes of Health grants GM52051 (to R.O.) and GM37048 (to R.L.G.).


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FOOTNOTES
 
* Corresponding author. Mailing address: Department of Biological Sciences, University at Albany, 1400 Washington Avenue, Albany, NY 12222. Fax: (518) 442-4767. Phone: (518) 591-8827. E-mail: osuna{at}albany.edu. Back

{dagger} Present address: Cell Biology and Metabolism Branch, NICHD, NIH, Bldg. 18T, Rm. 101, 18 Library Dr., MSC 5430, Bethesda, MD 20892. Back


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Journal of Bacteriology, August 2006, p. 5775-5782, Vol. 188, No. 16
0021-9193/06/$08.00+0     doi:10.1128/JB.00276-06
Copyright © 2006, American Society for Microbiology. All Rights Reserved.



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