Downregulation of Escherichia coli yfiD expression by FNR occupying a site at −93.5 involves the AR1-containing face of FNR

Downregulation of Escherichia coli yfiD expressionby FNR occupying a site at ¹93.5 involves theAR1-containing face of FNR

Jeffrey Green, * Mandy L. Baldwin and JoanneRichardsonDepartment of Molecular Biology and Biotechnology,University of Sheffield, Western Bank, Sheffield S10 2TN,UK.

Summary

The promoter of the FNR-activated yfiD gene of Escheri-chia coli has an unusual architecture because it con-tains two FNR sites, an arrangement usually associatedwith FNR-mediated repression. Investigation of yfiDpromoter derivatives with altered FNR sites revealedthat occupation of the far upstream FNR site (FNR II)downregulated expression, despite the presence ofa FNR dimer activating expression from the promoterproximal site (FNR I). Transcript mapping by primerextension, and mutagenesis of potential ¹10 ele-ments, indicated that yfiD expression is driven froma single FNR-dependent promoter with FNR sites at¹40.5 (FNR I) and ¹93.5 (FNR II). However, yfiD mRNAis processed in stationary-phase cultures indepen-dently of rne, rpoS , ihfA and fis to yield transcriptslacking 12 and 21 bases from their respective 5 8 ends.Single amino acid substitutions (G74 →C, F92→S,A95→P, R184→P, P188→A or L193 →P) in the surfaceof FNR that contains activating region 1 (AR1 contactsthe a-subunit of RNA polymerase to promote tran-scription activation) reduced the inhibitory effect ofFNR at FNR II, indicating that this region of the proteinmay have a role in repression as well as activation.The FNR variant F92 →S was notable because, althoughit activated transcription of yfiD (two FNR sites), it wasunable to activate transcription from model Class Iand II promoters, which contain only a single FNR site.

Introduction

The FNR protein of Escherichia coli is an oxygen-respon-sive member of the structurally related CRP/FNR family oftranscription regulators (Guest et al., 1996). FNR senses

anaerobiosis through the acquisition of an oxygen-labile[4Fe–4S]2þ cluster that promotes dimerization of the pro-tein and enhances site-specific DNA binding (Khoroshi-lova et al., 1995; Green et al., 1996a; Lazazzera et al.,1996). A number of FNR homologues have been identifiedand are characterized by the presence of four essentialcysteine residues that act as ligands for the [4Fe–4S]2þ

cluster, and the amino acid sequence E–SR in the DNA-binding helix, which confers specificity for the FNR ope-rator sequence TTGAT----ATCAA (Guest et al., 1996).Expression of a heterologous fnr gene (the hlyX gene ofActinobacillus pleuropneumoniae) confers a haemolyticphenotype upon E. coli K-12 (Lian et al., 1989; Green etal., 1992). The primary structure of HlyX is 73% identicalto that of FNR (MacInnes et al., 1990). Like FNR, HlyXsenses and responds to oxygen through the assembly/disassembly of a [4Fe–4S]2þ cluster and they recognizethe same DNA target (Green and Baldwin, 1997a). Studieswith FNR–HlyX hybrid proteins indicated that elements ofboth N- and C-terminal regions of HlyX are required forhaemolysin production in E. coli (Green et al., 1992). Morerecently, it has been shown that HlyX is a better activatorof Class I promoters than FNR (FNR site is situated at¹61 or beyond) and that an improved activating region 1(AR1) contact is, at least in part, responsible for the dis-tinct but overlapping FNR and HlyX modulons (Greenand Baldwin, 1997a).

The production of at least five polypeptides was enhancedwhen E. coli strains expressing hlyX in place of fnr weregrown anaerobically (Green and Baldwin, 1997a). Amongthese was the yfiD gene product (YfiD), a protein (Mr

14 300) of unknown function that is 77% identical to theC-terminal region of pyruvate formate-lyase. Genes poten-tially encoding YfiD proteins have been identified in Serratiasp., Serratia liquefaciens, Haemophilus influenzae and bac-teriophages T4 and T5.

Analysis of the DNA upstream of the yfiD coding regionrevealed an unusual architecture for an FNR-activatedpromoter (Fig. 1) with two FNR sites positioned at ¹61.5and ¹114.5 relative to the transcription start for HlyX-mediated expression (Green and Baldwin, 1997a). Mul-tiple FNR sites are usually associated with FNR-mediatedrepression (Green and Guest, 1994; Guest et al., 1996;Meng et al., 1997). Footprinting analysis indicated thatboth FNR and HlyX interacted with yfiD promoter DNA in

Molecular Microbiology (1998) 29(4), 1113–1123

Q 1998 Blackwell Science Ltd

Received 19 October, 1997; revised 1 June, 1998; accepted 5 June,1998. *For correspondence. E-mail [email protected]; Tel.(0114) 222 4403; Fax (0114) 272 8697.

the same manner. Therefore, the enhanced expression ofyfiD in hlyX- compared with fnr-expressing cultures wasnot due to preferential occupation of either FNR site byeither regulator. It is now apparent that anaerobic yfiDexpression is driven from a single FNR (HlyX)-dependentpromoter with FNR sites at ¹40.5 (FNR I) and ¹93.5 (FNRII) but, the yfiD transcript is processed in stationary phasesuch that the FNR sites appear to be positioned at ¹61.5and ¹114.5. Activation of yfiD expression by both FNRand HlyX is shown to be mainly mediated by the regulatorbound at the promoter proximal FNR site (FNR I). FNRoccupation of the distal FNR site (FNR II) downregulatesFNR-mediated activation of yfiD expression, whereasHlyX bound at this site is neutral/activating for yfiD expres-sion. The inhibitory effect of FNR at FNR II involves theAR1-containing surface of FNR, and subtle differencesbetween the AR1-containing faces of FNR and HlyX may

account for the differential regulation of yfiD expressionby these two regulators.

Results

FNR occupation of the upstream FNR site of the yfiDpromoter is inhibitory

The yfiD gene has unusual promoter architecture (Fig. 1A)for an FNR-activated gene because the presence of mul-tiple FNR sites is usually associated with FNR-mediatedrepression (Guest et al., 1996). Therefore, the roles of thetwo FNR sites present in the yfiD promoter have been inves-tigated in vivo and in vitro using a set of yfiD promoterswith specific substitutions within the FNR sites, designedto impair FNR (HlyX) recognition (Fig. 1B): þþpyfiD (wild-type); þ¹pyfiD (altered FNR I); ¹þpyfiD (altered FNR II);

Q 1998 Blackwell Science Ltd, Molecular Microbiology, 29, 1113–1123

Fig. 1. Nucleotide sequence of the yfiDpromoter region.A. The two FNR binding sites (boxed); thetranscript start point (large arrowed base, þ1,t1) and the functional ¹10 element (P1,overlined, consensus bases underlined); twoother apparent transcript start points (t2 andt3, small arrows) and their associatedpotential ¹10 elements (lower case,consensus bases underlined); the ribosomebinding site (rbs) and initiating methionine(Met) are indicated.B. The nucleotide sequences of wild-type (þ)and impaired (¹, or [þ /¹]) FNR-sites of thenormal and altered yfiD promoters arecompared. Bases substituted are shown inbold lower case letters; the core motifs of thetwo FNR-sites are highlighted in bold:þþpyfiD (wild-type); þ¹pyfiD (substitution ofthe key GC base pair in each FNR I coremotif); ¹þpyfiD (substitution of the key GCbase pair in each FNR II core motif);[þ /¹]þpyfiD (substitution of the key GC basepair of the promoter proximal FNR II coremotif only).C. The nucleotide sequences of wild-type andimpaired ¹10 elements of the unaltered andmutated yfiD promoters are compared. Thereplacements directed in each of the potential¹10 elements are indicated in lower case.

1114 J. Green, M. L. Baldwin and J. Richardson

and [þ/¹]þpyfiD (altered promoter proximal FNR II coremotif).

In accord with previous observations, yfiD (wild-typepromoter, þþpyfiD) expression was anaerobically induced13-fold relative to the aerobic level in exponential culturesexpressing FNR. However, a further 1.7-fold induction wasobserved for stationary- compared with exponential-phasecultures. Anaerobic HlyX-driven expression from þþpyfiDwas approximately fourfold higher than that observedwith equivalent FNR expressing cultures in both exponen-tial and stationary phases (Table 1). After replacement ofthe key GC bases pairs in each core motif (TTGAT----ATCAA) of the FNR I site (Fig. 1) with AT base pairs(þ¹pyfiD) the anaerobic induction was reduced to twofold(cf. aerobic cultures) when either FNR, or HlyX, or neitherregulator was expressed, indicating that FNR I is essentialfor FNR (HlyX)-mediated anaerobic activation (Table 1).Replacement of the equivalent bases in FNR II (¹þpyfiD)reduced HlyX-driven expression to 90% (exponential cul-tures) and 65% (stationary-phase cultures) of that observedfor the corresponding þþpyfiD, cultures. In contrast, FNR-driven expression from ¹þpyfiD was increased relative toþþpyfiD by 5.8-fold for exponential-phase cultures and3.1-fold for stationary-phase cultures (Table 1). Theseobservations indicate that occupation of FNR II by FNR,but not by HlyX, downregulates yfiD expression. Themutations introduced into the yfiD promoter do not createa site for an unknown anaerobic regulator capable of acti-vating expression from ¹þpyfiD because, in the absenceof FNR, yfiD expression remained low. Interestingly, replace-ment of the GC base pair in the downstream (AAaAA)motif of FNR II while the symmetrical upstream position(TTGAT) was unaltered was sufficient to increase FNR-driven anaerobic expression and decrease HlyX-drivenexpression relative to þþpyfiD (Table 1).

DNAse I footprinting analyses of the FNR- and HlyX–þþpyfiD (wild type) and [þ/¹]þpyfiD (FNR II, TTGAT----AAaAA) complexes were used to establish whether replac-ing the key GC base pair in the FNR site core motif hadhad the desired effect of compromising FNR and HlyX

binding. For þþpyfiD, FNR I was fully occupied whenFNR or HlyX were added to a final concentration of 5 nM(not shown) whereas FNR II became saturated when theconcentration of either regulator was $10 nM. Both FNR


Table 1. Anaerobic activation of yfiDexpression. b-Galactosidase activity (Miller units)

þþpyfiD þ¹pyfiD ¹þpyfiD [þ /¹]þpyfiD

Regulator E S E S E S E S

FNR 910 1520 140 140 5300 4700 5220 5820HlyX 3720 5190 180 180 3400 3450 2810 3540No regulator 68 51 230 280 110 480 120 270

b-Galactosidase activities (Miller units) expressed from wild-type and altered yfiD ::lac reporterplasmids in JRG1728 (Dlac Dfnr ) strains expressing either FNR, HlyX or neither regulator.Anaerobic cultures were assayed during both exponential (E) and stationary (S) phases ofthe growth cycle. The values quoted are representative of measurements obtained from dupli-cate assays of three independent cultures.

Fig. 2. DNAse I footprints of FNR or HlyX at þþpyfiD (wild-type)and [þ /¹]þpyfiD (defective FNR II).A. þþpyfiD (lanes 1–4) and [þ /¹]þ pyfiD (lanes 6–9). HlyX wasadded as indicated: lanes 1 and 6, no protein; lanes 2 and 7,10 nM; lanes 3 and 8, 40 nM; lanes 4 and 9, 80 nM; lanes 5 and 10,Maxam and Gilbert G tracks.B. þþpyfiD (lanes 1 and 2) and [þ /¹]þpyfiD (lanes 3 and 4). FNRwas added as indicated: lanes 1 and 3, no protein; lanes 2 and 4,80 nM. The position of the two FNR sites (FNR boxes I and II) andhypersensitive bases (arrowed) are indicated.

Regulation of yfiD expression 1115

and HlyX failed to recognize the altered FNR II site of[þ/¹]þpyfiD even when added to a final concentrationof 80 nM (Fig. 2). Therefore, the replacement of the keyGC base pair from just one of the core motifs of FNR IIwas sufficient to disrupt FNR binding.

The yfiD transcript is processed in a growth phase-dependent manner

The data presented above and that reported previously(Green and Baldwin, 1997a) indicate that HlyX is a betteractivator of yfiD expression than FNR, and that expressionincreases in stationary-phase cultures. It has been estab-lished that HlyX prefers Class I (FNR site at ¹61 or beyond),whereas FNR prefers Class II (FNR site close to ¹40) pro-moters, and that in stationary-phase hlyX-expressing cul-tures, yfiD transcription initiates 61.5 bp downstream ofFNR I (Green and Baldwin, 1997a). Therefore, a plausibleexplanation for the differences in FNR- and HlyX-mediatedregulation of yfiD expression is that the two regulatorsserve different promoters whose activity is influenced bythe growth phase of the culture.

Primer extension was used to monitor FNR-dependentyfiD transcripts in exponential and stationary-phase, anae-robic cultures of E. coli MC4100 and fnr, rpoS, ihfA andfis strains (Fig. 3A). The fnr strain, JRG1728, failed to pro-duce a detectable yfiD transcript in both exponential (notshown) and stationary-phase cultures, indicating that allyfiD expression is FNR dependent. For all the other strains,in exponential-phase cultures, two yfiD transcripts weredetected that centre FNR I at ¹40.5 (t1) or ¹52.5 (t2).

However, stationary-phase cultures lacked t1, retainedt2 and acquired the previously detected t3 (Green andBaldwin, 1997a), which centres FNR I at ¹61.5. No othertranscripts specifically associated with stationary-phasecultures were noted. A similar pattern of transcripts wasobserved in cultures expressing hlyX. Thus, it appearedthat the yfiD transcript start point was growth phase depen-dent. The pattern of transcripts in a rpoS mutant was thesame as that observed for the parental strain, and thus thestationary-phase appearance of t3 is not dependent onthe stationary-phase sigma factor sS. Similarly t3 produc-tion was not dependent on IHF (integration host factor, astationary-phase-induced transcription factor and chromo-some organizer) because stationary-phase cultures ofSJP3, an ihfA strain, produced t2 and t3. Neither wasthe pattern of FNR-dependent transcripts altered in a fisstrain that lacked the early exponential-phase-inducedfactor for inversion stimulation (Fis), another histone-like,growth phase-regulated transcription factor (Fig. 3A).

The pattern of transcripts [þ/¹]þpyfiD (Fig. 1B) in cul-tures expressing either FNR or HlyX was the same asthat from þþpyfiD, indicating that the absence of a regula-tor at FNR II does not affect the production of all three yfiDtranscripts (Fig. 3B).

All three yfiD transcripts were associated with potential¹10 elements (Fig. 1A and C). Therefore, the possibilitythat FNR and HlyX facilitate the formation of different tern-ary complexes at yfiD was investigated by incubating pre-formed FNR:þþpyfiD or HlyX:þþpyfiD complexes withRNA polymerase. The DNAse I footprints indicated thatsimilar ternary complexes were formed (Fig. 4). However,


Fig. 3. Location of the transcript start point for yfiD in a variety of genetic backgrounds. Primer extension analyses were used to define the 58ends of yfiD transcripts. The sizes of the primer extended molecules were determined by comparison with a Maxam and Gilbert G track ofyfiD DNA (lane G).A. RNA extracted from exponential-phase cultures of MC4100, wild-type (lane 1); stationary-phase cultures of MC4100 (lane 2); exponentialRH90, rpoS (lane 3); stationary-phase RH90 (lane 4); exponential RJ1802, fis (lane 5); stationary RJ1802 (lane 6); stationary SJP3, ihfA(lane 7); stationary JRG1728, fnr (lane 8); and stationary HAK117, rne (lane 9). Exponential-phase cultures were harvested after 4–6 h ofanaerobic growth (A600 0.5–0.7), stationary-phase cultures were collected after 24 h. The HAK117 strain was grown at 308C before incubatingat 428C for 15 min to effect the rne mutation.B. Transcripts detected in anaerobically grown exponential (lanes 1 and 3) and stationary (lanes 2 and 4) phase cultures of JRG1728containing: [þ /¹]þpyfiD and FNR (lanes 1 and 2) or HlyX (lanes 2 and 4). FNR was expressed from pGS330; HlyX from pGS415; and[þ /¹]þpyfiD as pGS1052.C. Effect of mutating three predicted ¹10 elements in the yfiD promoter region. Transcripts detected in exponential (lanes 1–4) and stationary(lanes 5–8) phase cultures of DH5a harbouring: pGS1155 (wild-type, lanes 1 and 5); pGS1154 (P1 knock-out, lanes 2 and 6); pGS1156(P2 knock-out, lanes 3 and 7); or pGS1157 (P3 knock-out, lanes 4 and 8).


differences in the position of a hypersensitive band (¹18for FNR, ¹14 for HlyX) adjacent to FNR I may reflect differ-ences in the interaction between RNA polymerase and theregulators. The region of FNR- or HlyX-mediated RNApolymerase protection extended as far as þ51. In general,

RNA polymerase protects promoter DNA from about ¹60to þ20. The extent of protection observed implies that theregulators may allow RNA polymerase to occupy two ormore positions at yfiD. Equivalent footprinting reactionswith [þ/¹]þpyfiD (which has an FNR II site that is notrecognized by FNR or HlyX, Fig. 2) indicated that theabsence of a functional FNR II site did not improve orimpair RNA polymerase binding to the respective FNR orHlyX binary complexes (not shown).

To establish whether the three yfiD transcripts wereproduced from discrete promoters, the base sequencesof the ¹10 elements were altered to impair RNA polymer-ase recognition (Fig. 1C). Transcript mapping indicatedthat the ¹10 element of promoter 1 (P1) associated witht1 was essential for the production of all three transcripts,whereas compromising the other potential ¹10 elementshad no effect on the pattern of transcripts produced (Fig.3C). Furthermore, transcription reactions in vitro, usingeither purified FNR or HlyX with s70-saturated RNA poly-merase, revealed that both regulators produced t1, butt2 and t3 were not detected (not shown), suggesting thatt2 and t3 may result from mRNA processing.

Therefore, the yfiD transcript initiates 41.5 bp down-stream of FNR I and the previously detected (stationaryphase) transcript, t3, placing FNR I at ¹61.5, is a pro-cessed form of t1. The E. coli rne strain, NAK117, wasunimpaired in the ability to process t1, indicating that theproduction of yfiD transcripts t2 and t3 from t1 is RNAseE independent (Fig. 3b).

Both N- and C-terminal elements of the AR1 surface ofFNR are required for downregulation of yfiD expression

The experiments described above indicate that FNR andHlyX serve the same yfiD promoter, and that HlyX makesa positive contribution to yfiD expression when bound atFNR II, whereas FNR acts negatively when bound at thissite. These observations suggested that the previouslyconstructed HlyX–FNR and FNR–HlyX hybrids (Greenet al., 1992) could be used to delimit the inhibitory com-ponent of FNR to either the N- or the C- terminal regionof the protein. Plasmids encoding the hybrids HlyX–FNR(pGS412) and FNR–HlyX (pGS413) were introduced intoJRG1728 pGS1000 (þþpyfiD). The series was completedwith the addition of equivalent FNR (pGS408) and HlyX(pGS409) expression plasmids (Green et al., 1992). Anae-robic yfiD expression driven by FNR, HlyX, or the hybridregulators was monitored by estimating b-galactosidaseactivity (Table 2). The results indicate that both N-terminal(M1 to E190) and C-terminal (F191 to A250) elementsof FNR are involved in downregulating yfiD expressionbecause both hybrids were better activators than FNR,but neither was as good as HlyX.

In an attempt to define the contribution of specific amino


Fig. 4. DNAse I footprints of the FNR- and HlyX-generated RNApolymerase: þþpyfiD ternary complexes. Lane 1, no addition; lane2, FNR (3.3 nM) plus RNA polymerase (20 nM); lane 3, FNR(33 nM) plus RNA polymerase (20 nM); lane 4, HlyX (3.3 nM) plusRNA polymerase; lane 5, HlyX (33 nM) plus RNA polymerase(20 nM); lane 6, RNA polymerase (20 nM). Lane 7 is a calibratingMaxam and Gilbert G track. The position of the two FNR sites(FNR boxes I and II), hypersensitive bases (arrowed) and theextent of RNA polymerase protection (solid line) are indicated.


acid residues to the inhibitory effect of FNR on yfiD expres-sion, a library of randomly mutated fnr genes in pBR322 wascreated by error-prone PCR. Approximately 3000 coloniesof JRG1728 pGS1000 transformed with the fnr mutantlibrary were screened for HlyX-like regulation of yfiD expres-sion. Four plasmids were recovered that encoded FNRproteins with single amino acid substitutions (G74→C,F92→S, A95→P, or L193→P). All the FNR variants dis-played enhanced anaerobic activation of yfiD expression,indicating that their ability to activate transcription has notbeen compromised but their ability to downregulate yfiDexpression from FNR II is impaired (Table 3). All the sub-stitutions recovered were located in the face of FNR thatcontains activating region 1 (AR1), a surface-exposedregion of FNR that has a role in transcription activationby making direct contacts with the a-subunit of RNA

polymerase (Fig. 5; Bell and Busby, 1994; Green andBaldwin, 1997a,b; Williams et al., 1997; Wing et al., 1995).Therefore, other previously identified FNR AR1 variants(S73→F, R184→P and P188→A) were tested for theirability to downregulate yfiD expression from FNR II. Thetwo substitutions in the b9–b10 region (Fig. 5) of FNRallowed increased expression of yfiD, indicating that thesereplacements also reduced the inhibitory effect of FNRat FNR II (Table 3). However, the inhibitory effect of theS73→F variant at FNR II was greater than that of FNR


Table 2. Anaerobic activation of yfiD expression by FNR, HlyX andhybrid proteins.

Regulator

b-Galactosidaseactivity(Miller units)

FNR 770FNR–HlyX 1260HlyX–FNR 1450HlyX 5670

b-Galactosidase activities expressed from a wild-type yfiD::lac reporterplasmid (pGS1000) in JRG1728 (Dlac Dfnr ) strains expressing eitherFNR, HlyX or hybrid regulators. The values quoted are representativeof measurements obtained from duplicate assays of three indepen-dent cultures.

Table 3. Anaerobic activation of yfiD expression by FNR variants.

b-Galactosidase activity (Miller units)

FNR variant þþpyfiD FFpmelR FF-71.5pmelR

FNR 950 7850 1600S73→F 570 2650 160G74→C 5300 5000 650F92→S 5300 290 290A95→P 2200 7700 4100R184→P 1650 1030 1070P188→A 4200 4200 2680L193→P 4600 7600 1770

The effect of amino acid substitutions on anaerobic activation of FNR-dependent promoters. Promoter activity was estimated by measuringb-galactosidase activity after anaerobic growth (16 h at 378C) ofJRG1728 (Dfnr ) carrying the indicated pRW50 derivatives encodingthe lac operon under the control of either the unaltered yfiD pro-moter (þþpyfiD ), the Class II FFpmelR promoter, or the Class IFF-71.5pmelR promoter. The values quoted are representative ofmeasurements obtained from duplicate assays of three independentcultures.

Fig. 5. Amino acid substitutions in the face ofFNR containing AR1 increase anaerobic yfiDexpression. Predicted structure of an FNRmonomer based on the known structure ofCRP illustrating the positions of amino acidsubstitutions that increase anaerobic yfiDexpression in E. coli. The DNA binding,helix–turn–helix, motif (aE–aF); the 85-loopthat forms AR3; the extent of AR1; and theessential cysteine ligands of the [4Fe–4S]cluster.


as evidenced by the very low anaerobic expression of yfiD(Table 3).

The FNR variants that failed to downregulate yfiDexpression could be classified in to two groups when testedagainst a model Class I (FF-71.5pmelR) promoter (Table 3).The proteins with replacements at S73, G74, F92 and R184were poorer activators than FNR, whereas the A95, P188and L193 variants were better. This indicates that the AR1surface of FNR can be impaired or improved by specificsubstitutions. Furthermore, most of the substitutions hadlittle effect on expression from the Class II (FFpmelR) pro-moter, indicating that the AR3 surface of these proteinsremains functional. However, the F92→S and P184→Pvariants were defective in activating expression fromFFpmelR but were effective at þþpyfiD. This suggeststhat single dimers of these variants cannot operate atClass II promoters, but in combination with an upstreamdimer they are able to activate transcription.

Discussion

Investigation of the regulation of yfiD expression by FNRand HlyX has revealed that the yfiD transcript is processedin a growth phase-dependent manner and that occupationof an upstream (¹93.5) FNR site by FNR, but not by HlyX,downregulates yfiD expression despite the presence ofan FNR dimer at the conventional activating position of¹40.5.

The effect of growth phase on the yfiD transcriptionstart

In previous work, it was reported that HlyX is a better acti-vator of yfiD expression than FNR, and that both regula-tors bind to two FNR sites in the yfiD promoter region(Green and Baldwin, 1997a). Transcript mapping usingRNA isolated from HlyX-expressing stationary-phase cul-tures indicated that the FNR sites were 61.5 (FNR I) and114.5 (FNR II) bp upstream of the transcript start (Greenand Baldwin, 1997a). It was also shown that HlyX is abetter activator than FNR of model Class I promoters (regu-lator site at, or upstream, ¹61). Therefore, it was reasonedthat HlyX preferentially activated yfiD expression becausethe FNR sites are situated at ¹61 and beyond in the yfiDpromoter rather than the more usual ¹41 favoured byFNR (Green and Baldwin, 1997a). The data presentedhere indicate that this is not the case. Transcript mappingrevealed that the yfiD transcript start apparently changesin a growth cycle-dependent manner. However, mutationof three potential ¹10 elements indicated that only onepromoter is present upstream of the yfiD coding regionand that this promoter has FNR sites centred at ¹40.5and ¹93.5. The transcripts placing the FNR sites either at¹61.5 and ¹114.5, or at ¹52.5 and ¹105.5, arise from

stationary-phase degradation of the yfiD message. Thesestationary-phase processing events occur independentlyof rpoS, fis or ihfA. Furthermore, studies with a rne mutantindicated that RNAse E did not contribute to yfiD mRNAprocessing. Therefore, how and why the yfiD message isprocessed remains unknown. The processing only resultsin the removal of either 12 or 21 bases from the yfiD mes-sage and is unlikely to involve RNAse III, which is known tocleave mRNA within stem–loop or hairpin structures (Court,1993), as there are no strongly predicted features of thistype in the relevant region of yfiD. Also, RNAse III proces-sing has not been shown to be stationary phase specific.The presence of the processed yfiD transcript, t3, instationary phase could contribute to the increase in b-galactosidase activity observed in such cultures. It mayrepresent a more stable form of the yfiD message, allow-ing more YfiD (b-galactosidase) protein to be generated instationary phase without the requirement for changes intranscription regulation.

The role of FNR II in the control of yfiD expression

It is clear that enhanced yfiD expression in HlyX-expres-sing cultures is not due to the superior ability of HlyX (com-pared with FNR) to activate transcription from Class Ipromoters but rather that HlyX occupation of FNR II hasa neutral/positive effect on yfiD expression, whereas FNRhas a negative effect at this site.

The studies with altered FNR and FNR–HlyX hybridproteins indicate that a large region of the FNR face con-taining AR1 (Fig. 5) is involved in the downregulation ofyfiD expression. Three FNR variants (A95→P, R184→P,P188→A) found to enhance anaerobic yfiD expressioncontained a direct replacement of the amino acid foundin FNR by that in the equivalent position in HlyX. This indi-cates that the differences in the AR1-containing faces ofthe two regulators may be sufficient to account for theirdistinct transcriptional properties. It may be that the AR1face of HlyX is better adapted to activate Class I promoters,whereas that of FNR is configured to optimize the anti-inhibition contact at Class II promoters. This latter arrange-ment may be more compatible with the inhibitory contactsformed at promoters with multiple FNR sites, such as yfiD.

Several observations indicate that although a large por-tion of the AR1 surface is involved in FNR II mediateddownregulation, the protein–protein interactions that areinvolved are specific and easily perturbed. For example,the variants S73→F and G74→C have substitutions ofadjacent amino acids, yet have opposite effects uponyfiD expression. Also, some FNR variants that permitelevated yfiD expression improve, whereas other impair,activation of a model Class I promoter. The nature of theFNR interactions responsible for the downregulation ofyfiD activation remains unknown, but FNR–FNR or



FNR–polymerase interactions, or a combination of both,may be involved. It has been proposed that contactsbetween two FNR dimers are important in the anaerobicactivation of pfl expression (Sawers, 1993). The obser-vations reported here raise the possibility that FNR canact as an ‘active’ repressor.

Studies with model CRP-dependent promoters with afixed CRP site at ¹41, and an additional site positionedat different upstream locations indicated that, dependingupon the position of the upstream site, expression couldbe increased or reduced compared with a promoter carry-ing the downstream site alone (Savery et al., 1996). Thus,the relative positions of tandem regulator binding sites canhave profound effects on promoter activity. Such contexteffects are evident in comparing the ansB and yfiD pro-moters of E. coli. Although, the architecture of the yfiD pro-moter is related to that of ansB and some derivatives(Scott et al., 1995) in so far as both promoters possessan FNR binding site centred at ¹40.5 and another upstreamregulator site, their response to FNR is very different. TheansB promoter has an FNR site centred at ¹40.5 and aCRP site at ¹90.5 (yfiD has FNR sites at ¹40.5 and¹93.5) but FNR is unable to activate ansB expressionwhen the upstream CRP site is inactivated (Scott et al.,1995). This is unusual as most FNR-activated promotershave an FNR site centred near ¹41.5 (i.e. they are ClassII promoters). Clearly, the context of the promoter has arole in determining whether an FNR site is functional ornot. For example, the FNR variants F92→S and R184→Pwere poor activators of the model Class II promoterFFpmelR but were able to activate yfiD expression fromFNR I. This suggests that for these variants, the geometryof the transcription complexes are such that two FNRdimers are necessary for transcription activation. Perhapsthe DNA sequence of the ansB promoter itself imposesequivalent restraints on the transcription complex suchthat an FNR dimer at ¹40.5 is ineffective and two regula-tors are required for activation. However, the observationsmade here indicate that, unlike ansB, all the FNR-mediatedactivation of yfiD expression arises from FNR bound at thedownstream (FNR I, ¹41.5) site.

An ansB derivative (FF-FFansB) in which the CRP site(¹90.5) was replaced by an FNR site was approximatelythree times more active than the wild-type promoter in invivo tests (Scott et al., 1995), indicating that the combi-nation of FNR at ¹40.5 and ¹90.5 is productive at ansB.In contrast, occupation of the upstream FNR site (FNRII, ¹93.5) of the yfiD promoter by FNR inhibits activation.Thus, in an appropriate context FNR can activate tran-scription when positioned at ¹41 (FFpmelR), and addi-tional upstream FNR sites can produce inhibitory (yfiD þ

FNR), neutral/positive (yfiD þ FNR variants or HlyX) oractivating (FF-FFansB þ FNR) interactions. The potentialfor switching between activation and repression of

transcription merely by altering the position of an upstreamFNR site suggests that FNR repressible promoters, suchas that of the ndh gene (Meng et al., 1997), may haveevolved through duplication and shuffling of the positionsof FNR sites. By this mechanism, promoter regions thatdisplay the full range of FNR regulation, from synergisticactivation to full repression, could be generated.

In conclusion, the yfiD promoter joins the ndh (Meng etal., 1997) and fdnGHI (Guest et al., 1996) promoters as anFNR-regulated promoter with an inhibitory upstream FNRsite. The inhibitory action of FNR bound at the mostupstream site appears to be mediated through protein–protein contacts involving the face of FNR that includesAR1.

Experimental procedures

Bacterial strains and plasmids

Relevant details of the E. coli strains and plasmids used aregiven in Table 4. Plasmids used to test the effects of the anae-robic expression of fnr, hlyX and fnr mutants on yfiD promoteractivity were the ptac85 derivatives: pGS330, FNR (Green etal., 1991); pGS415, HlyX (Green et al., 1992); pGS1056,FNR-R184→P; and pGS1057, FNR-P188→A (Green andBaldwin, 1997b). Other plasmids encoding FNR variantswere pBR322 derivatives isolated after screening of a mutantfnr library (generated by error-prone PCR; Bell and Busby,1994) for enhanced yfiD expression. Corresponding plasmidsencoding FNR (pFNR) and the archetypal AR1 mutant FNR-S73→F (pS73→F) have been described previously (Belland Busby, 1994).

The yfiD::lac operon fusion reporter plasmid pGS1000 wasformed by ligating the PCR amplified yfiD promoter region(¹220 to þ82) into EcoRI–BamHI-digested pRW50. Deri-vatives of pGS1000 carrying specific mutations in the FNRsites or ¹10 elements were generated using the AlteredSites II System (Promega) yielding: pGS1052 ([þ /¹]þpyfiD);pGS1066 (þ¹pyfiD); pGS1067 (¹þpyfiD), pGS1154 (P1–10knock-out); pGS1156 (P2–10 knock-out); and pGS1157(P3–10 knock-out). The previously constructed pUC18 deri-vatives, pGS408, 409, 412 and 413, which express FNR,HlyX, a HlyX–FNR hybrid and an FNR–HlyX hybrid, respec-tively (Green et al., 1992), were transformed into JRG1728pGS1000 to investigate the roles of the N- and C-terminalelements of FNR on yfiD expression.

Cultures were grown in the presence of appropriate anti-biotics either, aerobically in L broth with vigorous shaking, oranaerobically in L broth supplemented with 0.4% glucose toeither mid-exponential, or stationary phase in sealed bottlesat 378C. b-Galactosidase activity was determined accordingto Miller (1972). Western blotting of the soluble fractions ofcell extracts obtained from stationary-phase cultures was asdescribed by Spiro and Guest (1987) and indicated thatexpression of FNR, HlyX, FNR–HlyX hybrids and the FNRvariants were similar, except S73→F and F92→S, whichwere present at <20% of the level observed with FNR. TheEcoRI–BamHI yfiD promoter fragments of pGS1000 andpGS1052 were transferred to pUC118 to create pGS1036



and pGS1052a for sequencing and as source of promoterDNA for footprinting.

DNAse I footprinting

DNAse I footprinting was carried out essentially as previouslydescribed (Green et al., 1991), except that the reactions wereperformed anaerobically and contained (in a total volume of10 ml): yfiD promoter DNA (10–100 ng), end-labelled at theBamHI site (top strand) of the EcoRI–BamHI fragment ofpGS1036 or pGS1052a respectively; HlyX or FNR (0–80nM);2 ml of 5× binding buffer (0.1 M Tris-HCl pH 8.0, 0.05 M MgCl2,50mM dithiothreitol and 25% glycerol). Where indicated, RNApolymerase (Pharmacia) was added. The mixtures were incu-bated for 5 min at 258C followed by digestion with DNAse I(1 ml of 1 U ml¹1 for 10–30 s at 258C). Reactions were stoppedby the addition of 200 ml of 0.3 M sodium acetate containing10mM EDTA followed by phenol–chloroform extraction. TheDNA was ethanol precipitated and resuspended in 10 ml ofloading buffer (40% v/v formamide, 5 M urea, 5 mM NaOH,1 mM EDTA, 0.03% w/v bromophenol blue and 0.03% w/vxylene cyanol) for electrophoretic fractionation on polyacryl-amide-urea gels and autoradiographic analysis. Maxam andGilbert G tracks were used to provide a calibration.

Purification and reconstitution of FNR and HlyX proteinswere as described previously (Green and Baldwin, 1997a).

Transcript mapping

The transcription start point of the yfiD promoter was deter-mined by RNA extraction and primer extension. Total RNAwas prepared from: MC4100; JRG1728 (fnr ); JRG2269(hlyX þ); JRG3350 (fnr þ); RH90 (rpoS); SJP3 (ihfA); RJ1802(fis); and JRG1728 transformed with plasmids encoding eitherFNR, HlyX in combination with pGS1000 or pGS1052, afteranaerobic growth as described (Aiba et al., 1981). For primerextension the method of Gerischer et al. (1992) was used with10 pmol of primer S377 (GTAATCTGGATCCCTGTAATCA-TG, yfiD co-ordinates 7652–7675) <100 mg RNA and 50 UAMV reverse transcriptase (Nbl). After ethanol precipitation,the cDNA was fractionated on urea-polyacrylamide gels andanalysed by autoradiography. The gels were calibrated usingMaxam and Gilbert G tracks of yfiD DNA.

Other methods

Site-specific substitutions in the yfiD promoter region, to


Table 4. E. coli strains and plasmids.

Strain or plasmid Relevant characteristics Source or reference

DH5a D(argF-lac)U169(f80DlacZ ) recA Sambrook et al. (1989)MC1000 D(lacIPOZYA)X74 galU galK rpsL D(ara-leu ) Silhavy et al. (1984)JRG1728 MC1000 D(tyrR-fnr-rac-trg )17 zdd-230::Tn9 Spiro and Guest (1987)RH90 D(argF-lac)U169 rpoS359:Tn10 R. Hennge-Aronisa

SJP3 ihfAD82tet R Schroder et al. (1993)RJ1802 fis :767 Johnson et al. (1988)HAK117 rne ts, rne strain at 428C O. Meleforsb

ptac85 IPTG-inducible expression vector Marsh (1985)pGS330 ptac85 derivative encoding FNR, ApR Green et al. (1991)pGS415 ptac85 derivative encoding HlyX, ApR Green et al. (1992)pGS1056 ptac85 derivative encoding FNR-R184P, ApR Green and Baldwin (1997b)pGS1057 ptac85 derivative encoding FNR-P188 A, ApR Green and Baldwin (1997b)pBR322 vector for the mutant fnr library Sambrook et al. (1989)pFNR pBR322 derivative encoding FNR, ApR Bell and Busby (1994)pS73F pBR322 derivative encoding FNR-S73→F, ApR Bell and Busby (1994)pGS408 pUC18 derivative encoding FNR, ApR Green et al. (1992)pGS409 pUC18 derivative encoding HlyX, ApR Green et al. (1992)pGS412 pUC18 derivative encoding HlyX-FNR hybrid, ApR Green et al. (1992)pGS413 pUC18 derivative encoding FNR HlyX hybrid, ApR Green et al. (1992)pRW50 a low copy, ColE1-compatible, broad host range lac reporter vector, TetR Lodge et al. (1990)pRW2a/FF FFpmelR ::lac operon fusion in low copy, with a consensus FNR site at ¹41.5, TetR Lodge et al. (1990)pRW50/FF–71.5 FF-71.5 pmelR::lac operon fusion in low copy, with a consensus FNR site at ¹71.5 and an

improved ¹35 element, TetRWing et al. (1995)

pGS1000 pRW50 derivative, yfiD ::lac operon fusion, þþpyfiD, wild-type, TetR This workpGS1052 pRW50 derivative, yfiD ::lac operon fusion, [þ /¹]þpyfiD, impaired promoter proximal core

motif in FNR II, TetRThis work

pGS1066 pRW50 derivative, yfiD ::lac operon fusion, þ¹pyfiD, impaired FNR I, TetR This workpGS1067 pRW50 derivative, yfiD ::lac operon fusion, ¹þpyfiD, impaired FNR II, TetR This workpGS1155 pALTER-1(Promega) derivative containing þþpyfiD, TetR This workpGS1154 pALTER-1 derivative containing þþpyfiD P1–10 element knock-out, ApR This workpGS1156 pALTER-1 derivative containing þþpyfiD P2–10 element knock-out, ApR This workpGS1157 pALTER-1 derivative containing þþpyfiD P3–10 element knock-out, ApR This workpGS1036 pUC118 derivative containing þþpyfiD, ApR This workpGS1052a pUC118 derivative containing [þ /¹]þpyfiD, ApR This work

a. University of Konstanz, Germany.b. Karolinska Institute, Sweden.


produce yfiD derivatives with altered FNR sites, were intro-duced using the Altered Sites II System (Promega) with theappropriate mutagenic oligonucleotides. An fnr mutant library(Bell and Busby, 1994) was generated as previously describedand screened in JRG1728 pGS1000. The presence of thedesired substitutions was confirmed by automated DNA sequ-encing. In vitro transcription was as previously described(Green et al., 1996b), except ndh DNA was replaced by yfiD(EcoRI–BamHI fragment from pGS1036) and Nbp wasreplaced by FNR or HlyX. Gels were calibrated with a Maxamand Gilbert G track of yfiD DNA.

Acknowledgements

We would like to thank: J. R. Guest, J. I. MacInnes and L.Cunningham for their helpful suggestions; S. J. W. Busbyfor many useful discussions and the gift of some of the plas-mids used; R. P. Gunsalus, O. Melefors and R. Johnson fordonating bacterial strains; A. J. G. Moir for DNA sequencing.We are indebted to Jackie Earl for contributions made duringan undergraduate research project. This work was supportedby the BBSRC and the Royal Society.

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Downregulation of Escherichia coli yfiD expression by FNR occupying a site at −93.5 involves the AR1-containing face of FNR