Molecular Microbiology (2005)

56

(2), 492–508 doi:10.1111/j.1365-2958.2005.04553.x

© 2005 Blackwell Publishing Ltd

Blackwell Science, LtdOxford, UKMMIMolecular Microbiology0950-382XBlackwell Publishing Ltd, 2005

? 2005

56

2492508

Original Article

Co-regulation by SlyA and PhoP/PhoQ in S. TyphimuriumW. W. Navarre

et al.

Accepted 24 December, 2004. *For correspondence. E-mailslibby@u.washington.edu; Tel. (

+

1) 206 616 4941; Fax (

+

1) 206616 1575.

†

Present address: Department of Laboratory Medicine,University of Washington, Seattle, WA 98195-7110, USA.

Co-regulation of

Salmonella enterica

genes required for virulence and resistance to antimicrobial peptides by SlyA and PhoP/PhoQ

William Wiley Navarre,

1

Thomas A. Halsey,

2

Don Walthers,

3

Jonathan Frye,

4

Michael McClelland,

4

Jennifer L. Potter,

2

Linda J. Kenney,

3

John S. Gunn,

5

Ferric C. Fang

1

and Stephen J. Libby

1,2

*

1

Departments of Microbiology and Laboratory Medicine, University of Washington, Seattle, WA 98195, USA.

2

Department of Microbiology, North Carolina State University, Raleigh, NC 27695, USA.

3

University of Illinois at Chicago, Chicago, IL 60612, USA.

4

Sidney Kimmel Cancer Center, San Diego, CA 92121, USA.

5

Department of Molecular Virology, Immunology, and Medical Genetics; Department of Medicine, Division of Infectious Diseases; and The Center for Microbial Interface Biology, The Ohio State University, Columbus, OH 43210, USA.

Summary

Analysis of the transcriptome of

slyA

mutant

Salmo-nella enterica

serovar Typhimurium revealed thatmany SlyA-dependent genes, including

pagC

,

pagD

,

ugtL

,

mig-14

,

virK

,

phoN

,

pgtE

,

pipB2

,

sopD2

,

pagJ

and

pagK

, are also controlled by the PhoP/PhoQregulatory system. Many SlyA- and PhoP/PhoQ-co-regulated genes have functions associated with thebacterial envelope, and some have been directlyimplicated in virulence and resistance to antimicro-bial peptides. Purified His-tagged SlyA binds to the

pagC

and

mig-14

promoters in regions homologousto a previously proposed ‘SlyA-box’. The

pagC

pro-moter lacks a consensus PhoP binding site and doesnot bind PhoP

in vitro

, suggesting that the effect ofPhoP on

pagC

transcription is indirect. Stimulation of

pagC

expression by PhoP requires SlyA. Levels ofSlyA protein and mRNA are not significantly changedunder low-magnesium PhoP-inducing conditions inwhich

pagC

expression is profoundly elevated, how-ever, indicating that the PhoP/PhoQ system does not

activate

pagC

expression by altering SlyA proteinconcentration. Models are proposed in which PhoPmay control SlyA activity via a soluble ligand or SlyAmay function as an anti-repressor to allow PhoP acti-vation. The absence of almost all SlyA-activatedgenes from the

Escherichia coli

K12 genome sug-gests that the functional linkage between the SlyAand PhoP/PhoQ regulatory systems arose as

Salmo-nella

evolved its distinctive pathogenic lifestyle.

Introduction

Salmonella enterica

serovar Typhimurium (

S.

Typhimu-rium) encodes multiple regulatory systems that are criticalfor intramacrophage survival and pathogenicity. ThePhoP/PhoQ two-component regulatory system controlsthe expression of more than 40 genes required for viru-lence, growth at low Mg

2

+

concentrations, and resistanceto antimicrobial peptides, bile salts and acid pH (Sonciniand Groisman, 1996; Groisman

et al

., 1997; van Velkin-burgh and Gunn, 1999; Groisman, 2001). PhoP regulatesthe expression of some genes indirectly by stimulating theactivity of other transcriptional regulators such as thePmrA/PmrB two-component regulatory system (Gunn andMiller, 1996; Kox

et al

., 2000; Wosten

et al

., 2000). ThePmrA/PmrB system directly controls the expression of aset of genes that mediate resistance to polymyxin B byadding 4-aminoarabinose to the lipid A portion oflipopolysaccharide (Gunn

et al

., 1998). A direct repeatsequence (T/G)GTTA(A/T) is present in the promoterregions of a subset of genes dependent on PhoP forexpression (Yamamoto

et al

., 2002; Lejona

et al

., 2003;Minagawa

et al

., 2003). The promoter regions of thesePhoP-dependent genes (including

phoPQ

,

mgtA

,

slyB

,

pmrD

and

pcgL

) interact directly with the PhoP protein,whereas promoter sequences from PhoP-regulated locilacking canonical PhoP binding sites (such as

pagC

,

phoN

and

mgtCB

) do not (Lejona

et al

., 2003). This suggeststhat PhoP/PhoQ may indirectly control the expression ofgenes such as

pagC

,

phoN

and

mgtCB

by altering theexpression or activity of additional transcriptional regula-tors. One such regulator has been proposed to be SlyA,a DNA-binding protein whose expression can be modu-lated by PhoP (Norte

et al

., 2003; Shi

et al

., 2004a).

Co-regulation by SlyA and PhoP/PhoQ in

S.

Typhimurium

493

© 2005 Blackwell Publishing Ltd,

Molecular Microbiology

,

56

, 492–508

SlyA appears to influence expression of a number of

Salmonella

genes, but few SlyA-dependent loci have beenidentified (Buchmeier

et al

., 1997; Spory

et al

., 2002; Sta-pleton

et al

., 2002). The importance of SlyA for

Salmonella

pathogenesis has been demonstrated by studies showingthat a

slyA

mutant is profoundly attenuated for virulence,unable to replicate in host phagocytes and sensitive tooxidative stress (Libby

et al

., 1994; Daniels

et al

., 1996;Buchmeier

et al

., 1997; Watson

et al

., 1999; Kaneko

et al

.,2002). SlyA is a member of the MarR family of transcriptionfactors which includes the MarR, EmrR, HpaR and HpcRproteins of

Escherichia coli

, RovA of

Yersinia

and PecS of

Erwinia carotovora

, and SlyA-Ef of

Enterococcus faecalis

(Ariza

et al

., 1994; Reverchon

et al

., 1994; Seoane andLevy, 1995; Praillet

et al

., 1997; Revell and Miller, 2000;Xiong

et al

., 2000; Nagel

et al

., 2001; Grkovic

et al

., 2002;Nasser and Reverchon, 2002; Galan

et al

., 2003; Wu

et al

., 2003; Martin and Rosner, 2004; Rouanet

et al

.,2004). Members of the MarR family have been shown toact as transcriptional activators, repressors, or both. Thesehomodimeric, winged-helix transcription factors arebelieved to modulate their DNA-binding activity by bindingsmall molecules within a cleft formed at the surfacebetween the subunits (Grkovic

et al

., 2002). MarR, whichrepresses expression of the

marAB

operon, is the best-studied member of this family. Upon interaction with sali-cylate or deoxycholate, MarR dissociates from the

marAB

promoter, thereby enabling transcription to occur (Ale-kshun and Levy, 1999; Prouty

et al

., 2004a). To date noligand for SlyA has been identified, although DNA bindingby SlyA has been demonstrated with purified polyhistidine-tagged protein (Stapleton

et al

., 2002). In Stapleton

et al

.(2002), a putative consensus SlyA-binding motif TTAGCAAGCTAA was proposed, with five full or partial copiesof this motif demonstrated within the

slyA

promoter. Theseputative SlyA binding sites may be involved in the auto-regulation of

slyA

expression (Stapleton

et al

., 2002).Two proteomic analyses of the SlyA regulon in

Salmo-nella

have been reported. Stapleton

et al

. (2002) foundthat

slyA

mutant

S.

Typhimurium exhibits altered levels ofouter membrane proteins and reduced levels of the FliCflagellin protein. Spory

et al

. (2002) overexpressed SlyAin both EIEC

E. coli

and

S.

Typhimurium to identify pro-teins with altered abundance by 2D-gel electrophoresisand mass spectrometry. In agreement with Stapelton

et al.

, Spory and colleagues found levels of FliC flagellinto be enhanced by SlyA overexpression.

In the present study we report the use of cDNA microar-rays to identify

S.

Typhimurium genes under the control ofSlyA. Unexpectedly, expression levels of a large numberof loci previously identified to be controlled by PhoP/PhoQwere found also to be regulated by SlyA, including genesrequired for virulence and resistance to antimicrobial pep-tides. The ability of purified SlyA to interact with the pro-

moter regions of two SlyA- and PhoP/PhoQ-co-regulatedgenes,

pagC

and

mig-14

, was determined

in vitro

. Analy-sis of mRNA and protein in

slyA

and

phoP mutant strainsrevealed an unusual mechanism of interaction betweenPhoP/PhoQ and SlyA, and has suggested novel modelsfor further study.

Results

Microarray analysis of SlyA-dependent gene expression

To identify genes under the control of SlyA, cDNA microar-ray analysis was performed using total RNA isolated fromwild-type S. Typhimurium ATCC 14028s and an isogenicslyA mutant grown to early stationary phase (OD600 = 2.0,see Experimental procedures). The expression of aslyA::lacZ fusion is nearly maximal at this growth phase(Buchmeier et al., 1997). Cy3- or Cy5-labelled cDNA wassynthesized from total RNA and hybridized to SalmonellaLT2 microarrays (Porwollik et al., 2004) (see Experimentalprocedures). A locus was considered to be SlyA dependentif hybridization intensity showed twofold or greater differ-ence between the wild-type and slyA mutant strain andalso displayed statistical significance by the method ofIdeker et al. (2000; 2001) (see Experimental proceduresand Supplementary material, Table S1). Only genes inwhich intensity was SlyA dependent in at least two of threebiological replicates are included in Table 1. Of the 4530S. Typhimurium transcripts covered in the array [ª 96% ofthe open reading frames (ORFs) in the LT2 genome], theexpression of 31 loci were consistently altered in the slyAmutant including 23 that were present in greater abun-dance in wild type compared with the slyA mutant (Table 1).Surprisingly, several of these SlyA-activated transcriptswere previously identified as being positively regulated bythe PhoP/PhoQ two-component regulatory system, includ-ing pagC, phoN, pagJ, pgtE, sopD2, mig-14, virK, envEand ugtL (Miller et al., 1989; Belden and Miller, 1994; Guinaet al., 2000; Brodsky et al., 2002; Brumell et al., 2003;Detweiler et al., 2003; Shi et al., 2004b). The pagC locuswas the most profoundly SlyA dependent, demonstratinga 40- to 100-fold reduction in expression as compared withwild-type under these conditions.

To specifically determine whether regulation of theseloci by SlyA requires PhoP/PhoQ, microarray analysis wasused to compare gene expression in phoP mutant andslyA phoP double mutant strains. This analysis revealedthat SlyA-dependent upregulation of 19 genes (pagC,sseAB, envE, ugtL, mig-14, virK, pgtE, phoN, pipB2,sopD2, pagJ, ybcY, STM0306, STM1055, STM1254,STM1330, STM1940 and STM2287) was abolished in theabsence of phoP. The effect of PhoP on the SlyA regula-tion of two genes (ssrA and STM1328) was difficult todetermine solely from our array analysis due to a relatively

494 W. W. Navarre et al.

© 2005 Blackwell Publishing Ltd, Molecular Microbiology, 56, 492–508

low degree of SlyA dependence and wide confidenceintervals (see Supplementary material). SlyA regulation ofnmpC, which was difficult to observe in the wild-type back-ground, was found to be more strongly SlyA dependent inthe phoP background. The stimulatory effects of SlyA ontwo loci (ssrB and STM1249) remained largely unaffected

by a phoP mutation, demonstrating that SlyA can upreg-ulate some genes independently of PhoP, and implyingthat slyA expression is not completely PhoP dependent.Of the SlyA-repressed loci (ydhIJ, yggM, STM1498/1499,STM1530 and ychN), all but one (STM1499) wereobserved to be repressed more strongly in the wild-type

Table 1. SlyA regulated genes in LB media, OD600 = 2.0.

Gene numberGenesymbol

Wild-typeversus slyAe

phoP versusphoP slyAe Description

SlyA-activated genesdependent on PhoP

STM1246a pagC 54.3 ± 0.88 1.0 ± 0.67 Outer membrane protein.STM1397b sseA 20.9 ± 1.8 1.0 ± 0.76 SPI2 type three secretion system (TTSS) chaperone.STM2782a mig-14 10.5 ± 1.2 1.0 ± 0.91 Required for virulence and resistance to antimicrobial peptides.STM1638d ybcY 8.2 ± 1.5 1.4 ± 1.3 Putative SAM-dependent methyltransferase.STM2781a virK 8.0 ± 0.63 1.0 ± 0.69 Virulence protein homologous to virK in Shigella.STM1254a 6.7 ± 0.84 1.0 ± 0.92 Putative outer membrane lipoprotein. Unknown function.STM1330a 5.7 ± 0.58 1.0 ± 0.67 Putative inner membrane DNA/RNA non-specific nuclease. Unknown

function.STM1601c ugtL 5.0 ± 1.4 1.0 ± 0.78 Putative membrane phosphatase. Involved in antimicrobial peptide

resistance.STM1055b 4.2 ± 0.75 1.4 ± 0.96 Gifsy-2 prophage protein. Unknown function.STM2395a pgtE (prtA) 4.0 ± 0.61 1.0 ± 0.68 Outer membrane protease, OmpT/Pla family. Resistance to antimicrobial

peptides.STM1398a sseB 3.9 ± 0.84 1.0 ± 0.68 SPI2 TTSS effector proteinSTM2287c 3.9 ± 1.2 1.0 ± 1.1 Cytoplasmic protein. Unknown function.STM0306 3.4 ± 0.70 1.0 ± 0.81 Putative outer membrane adhesin. Homologue of kek from uropathogenic

E. coli (UPEC).STM1940a 3.5 ± 0.49 1.0 ± 0.86 Putative cell wall-associated hydrolase. Putatitve lipoprotein/outer

membrane location.STM2585b pagJ 3.4 ± 0.32 1.0 ± 0.45 Gifsy-1 prophage protein. Unknown function.STM0972a sopD2 3.1 ± 0.84 1.0 ± 0.61 SopD homologue. Translocated into eukaryotic cells. Associates with

endosomes.STM1328a 3.2 ± 0.85 1.9 ± 0.65 Putative outer membrane protein. Unknown function.STM1392a ssrA (spiR) 3.1 ± 1.3 1.7 ± 0.76 Two-component sensor kinase. Regulates SPI2 TTSS.STM4319 a phoN 2.7 ± 0.70 1.0 ± 0.55 Non-specific acid phosphataseSTM2780a pipB2 2.3 ± 0.61 1.1 ± 0.32 Secreted virulence protein homologous to PipB.STM1242a envE 2.0 ± 1.2 1.0 ± 0.75 Putatitive outer membrane protein.

(17.1 ± 1.4)f

STM1867b pagK 1.4 ± 1.1 1.0 ± 0.77 Predicted periplasmic location. Unknown function.(4.9 ± 0.54)f

STM1244c pagD 1.1 ± 2.0 -1.3 ± 0.61 Putative outer membrane virulence protein.(180 ± 0.16)f

STM1572d nmpC 1.9 ± 0.32 3.7 ± 0.38 Predicted outer membrane porin. Unknown function.

SlyA-activated genes independent of PhoP

STM1391a ssrB 4.3 ± 0.56 2.3 ± 1.1 Two-component response regulator transcriptional activator. Activates SPI2 TTSS.

STM1249a 2.6 ± 0.22 2.8 ± 0.36 Putative periplasmic/secreted protein. Unknown function.

SlyA-repressed genesSTM3361 yhcN –10.1 ± 3.0 -2.9 ± 1.3 Putative outer membrane protein.STM1442 ydhJ –6.4 ± 0.74 -1.4 ± 0.74 Putative multidrug resistance efflux pump. Transcribed divergently from slyA.STM3105 yggM –6.1 ± 0.75 -1.3 ± 1.3 Putative periplasmic protein.STM1443 ydhI –5.8 ± 0.85 1.0 ± 1.2 Putative inner membrane protein. Unknown function. Transcribed divergently

from slyA.STM1530 –5.2 ± 0.69 -2.6 ± 0.79 Putative outer membrane porin. OmpC homologue.STM1498 –3.9 ± 0.72 -1.4 ± 0.99 Putative dimethyl sulphoxide reductase.STM1499 –3.8 ± 0.44 -3.4 ± 1.0 Putative anaerobic DMSO/TMAO reductase, chain A1.STM1519 marA –3.5 ± 0.62 -1.6 ± 0.51 Transcriptional activator of defence/antibiotic resistance systems (AraC/XylS

family)

a. Not found in E. coli strain K12, may be found in other bacterial species.b. Unique to Salmonella enterica serovar Typhimurium.c. Unique to Salmonella sp.d. On a prophage in E. coli K12 but found on unrelated islet-like sequences in S. Typhimurium.e. Average of three biological replicates (18 total replicates) reported as fold difference ± SD.f. Fold difference ± SD comparing the effect of the slyA mutation in the phoQ24 background.

Co-regulation by SlyA and PhoP/PhoQ in S. Typhimurium 495

© 2005 Blackwell Publishing Ltd, Molecular Microbiology, 56, 492–508

than in the phoP mutant background. These data indicatethat the ability of SlyA to influence the expression of mostgenes we have identified here requires the presence of afunctional PhoP/PhoQ system.

To further characterize the influence of the PhoP/PhoQregulon on SlyA-dependent gene expression, transcriptlevels in a phoQ24 mutant were compared with a phoQ24slyA double mutant. The phoQ24 allele encodes analtered PhoQ sensor kinase with a single amino acidsubstitution that leads to constitutively high levels of phos-phorylated (active) PhoP response regulator protein(Miller and Mekalanos, 1990; Gunn et al., 1996). Thus, thephoQ24 strain is useful for examining the effects of PhoPactivation without a requirement for magnesium limitation.Most of the differentially expressed genes identified inarrays comparing slyA mutant Salmonella with wild typewere confirmed when comparing the effects of a slyAmutation in a phoQ24 background. However, two addi-tional genes (pagD and pagK) were identified as slyAdependent only in the phoQ24 mutant. Also, the weaklySlyA-dependent envE gene showed nearly 10-fold greaterdependence on SlyA in this background. Like the otherSlyA/PhoP-activated genes, the SlyA dependence of bothpagD and pagK was abolished in a phoP background.This suggests that SlyA has little effect on basal levels ofexpression of these genes but plays a role under condi-tions where the PhoP/PhoQ system is strongly activated.

Examination of the SlyA-regulated loci revealed a sur-prisingly large proportion to be monocistronic. Remark-ably, only two SlyA-activated genes, ybcY and nmpC,have clear homologues present in the E. coli K12genome. However, both ybcY and nmpC map to differentlocations on the Salmonella and E. coli chromosomes andreside on islet-like sequences or prophages that differsubstantially between the two species (Blattner et al.,1997; McClelland et al., 2001). This indicates that nmpCand ybcY were acquired by separate horizontal transferevents at some point after E. coli and Salmonelladiverged. Most SlyA-activated genes are located onregions of chromosomal DNA that bear the hallmarks ofhaving been acquired by horizontal gene transfer, carriedon prophages (STM1055), pathogenicity islands (ssrAB)or islets (pagC, mig-14). A substantial proportion of theSlyA-regulated genes are predicted to encode membrane,periplasmic or secreted proteins, including all of the SlyA-repressed proteins. Several of the genes identified areknown to be required for Salmonella virulence, includingsopD2, pipB2, virK, mig-14, pgtE and ssrAB (Deiwicket al., 1999; Valdivia et al., 2000; Brumell et al., 2003;Detweiler et al., 2003; Knodler et al., 2003). In addition,ugtL, virK, mig-14 and pgtE have been shown to play arole in resistance against polymyxin B and/or other cat-ionic antimicrobial peptides (Guina et al., 2000; Brodskyet al., 2002; Detweiler et al., 2003; Shi et al., 2004a).

Quantitative polymerase chain reaction confirmation of pagC and mig-14 regulation by SlyA

As an independent confirmation of the microarray results,real-time quantitative polymerase chain reaction (Q-PCR)was used to measure levels of pagC and mig-14 mRNAin slyA and phoP mutant backgrounds (Fig. 1). Thesetranscripts were selected for analysis as two of the moststrongly SlyA-dependent loci identified by our array anal-ysis. Levels of pagC transcript were reduced at least 200-fold in the slyA, phoP and slyA phoP double mutant strainsindicating that the pagC gene requires both PhoP andSlyA for expression. Our results indicate that the effectsof SlyA and PhoP on pagC transcript levels are not addi-tive but rather strongly synergistic. These results wereindependently confirmed by measuring expression of apagC::lacZ fusion in wild-type, phoP and slyA mutantbackgrounds (Fig. 2).

The expression of mig-14 was reduced 45-fold in aphoP mutant whereas expression was reduced eightfoldin a slyA mutant (Fig. 1), suggesting that the regulationof mig-14 has a stronger dependence on PhoP than onSlyA under these conditions. Although there is no con-sensus ‘PhoP box’ upstream of mig-14, there appears tobe a PhoP binding site in the promoter of the virK geneimmediately upstream (Fig. 1A). It is possible that SlyA-independent/PhoP-dependent mig-14 transcriptionobserved reflects readthrough from the virK promoter.To address this possibility we performed reverse tran-scription polymerase chain reaction (RT-PCR) on RNAisolated from the phoQ24 and phoP mutant strainsusing a primer set that overlaps the virK and mig-14coding sequence. A fragment corresponding to the inter-genic region between the two open reading frames wasamplified from RNA isolated from the phoQ24 mutant.This product could not be amplified from either RNA iso-lated from our phoP mutant strain or from controls inwhich no reverse transcriptase was added (Fig. 1A,inset). This finding suggests that a PhoP-dependenttranscript encompasses both the virK and mig-14 openreading frames. Together, these data indicate that bothmig-14 and pagC require SlyA and PhoP for full expres-sion, but there are major differences in the regulatorymechanisms.

The microarray data suggests that SlyA had no influ-ence over the expression or activity of the phoPQ locus.Given the broad overlap of these two regulons this ideawas tested further by measuring the expression levels ofthe PhoP-regulated genes phoP, mgtC, sodCI and mig-5by Q-PCR. The expression of each of these genes wasnot affected by a mutation in slyA but all were found to beupregulated in the phoQ24 mutant and lowered in a phoPmutant background (data not shown). This confirms thatSlyA has no influence on the expression of phoPQ and

496 W. W. Navarre et al.

© 2005 Blackwell Publishing Ltd, Molecular Microbiology, 56, 492–508

Fig. 1. Q-PCR analysis of the effects of mutations in the phoP and slyA genes on pagC, mig-14 and pagD transcript levels.A. Map of the pagC and pipB2/virK/mig-14 regions of the Salmonella Typhimurium LT2 chromosome. Hollow arrows designate open read-ing frames with each vertical hash mark representing 100 nucle-otides. The thin grey arrow represents a pseudogene (STM1245) in the pagC–pagD intergenic region. The transcription start site for pagC (Pulkkinen and Miller, 1991; Gunn et al., 1995) is indicated by a bent arrow, and the region demonstrated to be sufficient for response to low Mg2+ is designated with a framed double-headed arrow. Transcript start sites of pipB2, virK and mig-14 have not been mapped. Exper-imentally verified SlyA binding sites are designated by grey boxes marked with an ‘S’. The putative PhoP binding site near virK (sequence: CATTGATAAACTGTTTAA) is designated with a white box marked (P). Inset. Ethidium bromide stained agarose gel showing the results of RT-PCR to determine whether virK and mig-14 are encoded on a single, phoP-dependent transcript. RNA samples isolated from phoQ24 (phoPQ ‘constitutive’) and a phoP mutant strain of Salmo-nella were reverse transcribed using the primer WNp325 (approxi-mate position in the mig-14 region designated by a half-arrow). Presence of the transcript was verified by subsequent PCR on iso-lated cDNA with primers WNp324 and WNp325 (half-arrows), pre-dicted to yield a 614-nucleotide product. To eliminate the possibility of chromosomal DNA contamination PCR was also performed on control RNA samples treated identically but without reverse transcri-pase as indicated. A 100 bp marker is shown in the lane marked ‘M’ with the 600 bp band indicated by the black arrowhead.B. Q-PCR results of pagC and mig-14 expression levels in wild-type Salmonella 14028s and phoP and slyA mutant strains. To control for variability in the recovery of RNA, transcript levels are normalized to mRNA for gyrB, a housekeeping gene used as an internal control with relatively constant expression in the wild-type and mutant strains. Expression levels are arbitrarily set at 1 for wild type.

Fol

d ex

pres

sion

com

pare

d w

ith w

ild ty

pe(lo

g sc

ale)

Wild

type

phoQ

24

phoQ

24

phoP

-

phoP

-

slyA

-

slyA

-

slyA

-

Wild

type

phoQ

24

phoQ

24

phoP

-

phoP

-

slyA

-

slyA

-

slyA

-

co-regulates only a subset of the Salmonella PhoP/PhoQregulon.

The effect of PhoP/PhoQ on levels of SlyA mRNA or protein

Transcription of the slyA gene has been shown to involveat least three distinct promoters (Stapleton et al., 2002;Norte et al., 2003). Two groups have reported that PhoPis able to activate transcription of the slyA gene via themost distal (P3) promoter and have postulated that this isthe mechanism by which PhoP influences the expressionof SlyA-regulated genes (Norte et al., 2003; Shi et al.,2004a). We therefore sought to determine whether theeffect of PhoP on SlyA-dependent genes occurs simply

Fig. 2. Overexpression of SlyA is not alone sufficient to enhance pagC expression. Strains harbouring a chromosomal pagC::lacZ translational fusion and a low-copy plasmid with or without the SlyA open reading frame under the control of an arabinose-inducible pro-moter were grown in LB media supplemented with 0.2% arabinose to an OD600 of 2.0.A. Anti-SlyA immunoblot of one of two independent experiments. Equal amounts of total protein were loaded from pagC–lacZ strains corresponding to wild-type 14028s (strain WN255, lanes 1 and 2), phoQ24 (strain WN256, lanes 3 and 4), slyA (strain WN312, lanes 5 and 6), phoQ24 slyA double mutant (strain WN313, lanes 7 and 8) and phoP (strain WN318, lanes 9 and 10) backgrounds. Strains contained either the control plasmid pSL2570 (odd lanes) or plasmid pSL2571 with slyA under the control of an arabinose-inducible pro-moter (even lanes). An asterisk designates an irrelevant cross-reac-tive protein.B. b-Galactosidase activity was measured as an indicator of pagC promoter activity. Strains containing the empty control vector (pSL2570) are designated with a ‘–’, while strains harbouring the slyA encoding vector (pSL2571) are designated with a ‘ +’.Results are aligned with their corresponding immunoblot from (A). The results presented in (B) are the averages of two independent experiments each performed in triplicate.

pagC–lacZ

Wild type phoQ24 phoQ24slyA

phoPslyA

b-G

alac

tosi

dase

act

ivity

Co-regulation by SlyA and PhoP/PhoQ in S. Typhimurium 497

© 2005 Blackwell Publishing Ltd, Molecular Microbiology, 56, 492–508

by direct activation of slyA transcription, leading toincreased levels of SlyA protein. To test this hypothesis,levels of slyA transcript were compared using Q-PCR inwild-type, phoQ24 and phoP mutant strains. Unexpect-edly, levels of slyA mRNA in phoP and phoQ24 mutantsnormalized to either gyrB or rpoD housekeeping geneswere found to differ by less than twofold from wild-typelevels (data not shown). Similarly, Western blot analysisof total protein from these strains at different growthstages revealed that SlyA protein levels are essentiallyequivalent between wild-type and phoP strains, andslightly elevated in a phoQ24 mutant (Fig. 3A). We con-clude that under our growth conditions [early stationaryphase in Luria–Bertani (LB) media], the influence of PhoPon the expression of SlyA mRNA and protein is minimal,and SlyA expression is primarily driven by one of thePhoP-independent promoters.

We also determined whether activation of PhoP/PhoQby low magnesium alters the level of SlyA mRNA(Fig. 3B). Wild-type and phoP mutant Salmonella weregrown to mid-logarithmic growth phase in N-minimalmedium containing 10 mM MgSO4. Cultures were washedand resuspended in N-minimal medium containing eitherhigh (10 mM) or low (10 mM) levels of MgSO4 for 30 minbefore harvesting RNA for analysis by Q-PCR. Levels ofpagC mRNA were observed to increase approximately180-fold within 30 min exposure to low magnesium(Fig. 3B), whereas levels of slyA mRNA increased lessthan twofold during the same time period. Western blotanalysis of these samples also demonstrated no signifi-cant alteration in SlyA protein under low magnesium con-ditions over this interval (Fig. 3B, inset).

These findings suggest that levels of slyA mRNA orSlyA protein do not correlate with activation of the pagC

Fig. 3. Effect of phoP mutations and Mg2+ on expression of slyA.A. Immunoblot (Western) analysis was used to measure SlyA protein levels in wild-type or phoP, phoQ24 (phoPQ constitutive), slyA and slyA-pSlyA mutant strains of Salmonella grown to late logarithmic phase, early stationary phase or stationary phase in LB medium. * designates an irrelevant cross-reactive protein.B. Wild-type and phoP mutant Salmonella were grown to mid-log phase (OD600 = 0.60) in N-minimal medium containing 10 mM MgSO4. Cells were washed three times in N-minimal medium containing either 10 mM (low) or 10 mM (high) Mg2+ and incubated for 30 min before harvesting RNA. Levels of slyA (top) and pagC (bottom) transcript were assessed using Q-PCR as described in Experimental procedures. An immunoblot analysis of the same cultures used for Q-PCR analysis (B, inset) shows that SlyA protein levels are comparable in wild-type (lanes 1 and 2) and phoP mutant (lanes 3 and 4) Salmonella in N-minimal medium containing either 10 mM (lanes 1 and 3) or 10 mM (lanes 2 and 4) MgSO4.

Wild

type

phoQ

24ph

oP-

slyA-

slyA- p

RB3::s

lyA

Fol

d ex

pres

sion

com

pare

d w

ith w

ild ty

pein

hig

h M

g2+ (

linea

r sc

ale)

Fol

d ex

pres

sion

com

pare

d w

ith w

ild ty

pein

hig

h M

g2+ (

log

scal

e)

Wild

type

high

Mg2+

Wild

type

low

Mg2+

phoP

-hi

gh M

g2+

phoP

-lo

w M

g2+

Wild

type

high

Mg2+

Wild

type

low

Mg2+

phoP

-hi

gh M

g2+

phoP

-lo

w M

g2+

498 W. W. Navarre et al.

© 2005 Blackwell Publishing Ltd, Molecular Microbiology, 56, 492–508

promoter. To further test this hypothesis, expression of achromsomally encoded pagC–lacZ fusion was measuredin phoP and slyA mutant strain backgrounds in which SlyAwas overexpressed from an arabinose-inducible plasmid(Fig. 2). In this assay, expression of pagC–lacZ was notdirectly related to levels of SlyA protein. Massive overex-pression of SlyA in a phoP background modestlyincreased expression of a pagC–lacZ fusion but tonowhere near the levels observed in wild-type andphoQ24 backgrounds in the absence of SlyA overexpres-sion (compare lanes 1, 3 and 10). In agreement with theQ-PCR results (Fig. 1B), expression of pagC–lacZ washigher in a phoQ24 slyA mutant than in phoP or slyAmutant strains (Fig. 2, compare lanes 5 and 7), indicatingthat PhoP can exert a modest influence on pagC expres-sion in the absence of SlyA. However, PhoP does notpromote the expression of pagC and other co-regulatedgenes simply by enhancing SlyA expression. Two novelmodels to accommodate these observations are thereforeproposed and discussed below (see Discussion).

SlyA binds to the promoter regions of pagC and mig-14

In order to determine whether SlyA physically associateswith the pagC promoter, EMSA (electrophoretic mobilityshift assay) analysis was performed with purified polyhis-tidine-tagged SlyA (His-SlyA, see Experimental proce-dures) and a 294 bp fragment containing the pagC

promoter region (728–435 bp upstream of the pagC startcodon) that encompasses a region sufficient to enableMg2+-dependent transcription (Chen and Schifferli, 2001).This fragment contains a putative SlyA binding site(TTTGGAATGTAA, -85) and the pagC transcriptionalstart site (Fig. 4). The ability of His-tagged SlyA to interactwith a 337 bp fragment containing a putative SlyA bindingsite (TTAGCATGTTAA, Fig. 4) located immediatelyupstream of the mig-14 open reading frame was alsodetermined. In these experiments His-SlyA was able toshift both the pagC and mig-14 promoter fragments in aconcentration-dependent manner. The specificity of His-SlyA binding was demonstrated by inhibition of binding tothe mig-14 and pagC promoter regions by the addition ofexcess unbiotinylated promoter fragment or by a double-stranded unlabelled oligonucleotide containing a consen-sus SlyA binding site (TTAGCATGTTAA), but not by asimilarly sized unlabelled fragment of the rpoD gene or anon-specific unlabelled oligonucleotide.

To more precisely determine the sequences recognizedby SlyA on the pagC and mig-14 promoter fragments,DNase I protection assays were performed using increas-ing amounts of His-SlyA protein added to biotinylatedDNA fragments shown to contain SlyA binding sites byEMSA (Fig. 5). His-SlyA protected a region approximately109 to 79 bp upstream of the pagC transcriptional startsite. A second putative SlyA binding site (TTAGCAT-TCAAA) lies 327 bp downstream of the pagC transcriptionstart site, within the unusually long (559 bp) pagC 5¢-

PpagC

[His-SlyA] [unlabelled PpagC] [unlabelled rpoD]

[His-SlyA] [unlabelled Pmig-14] [unlabelled rpoD]

[oligo 1] [oligo 2]

BoundDNA

FreeDNA

BoundDNA

FreeDNA

Pmig-14

Fig. 4. His-SlyA specific binding to the pagC and mig-14 promoter regions. 0.3 pg of pagC (top, lanes 1–15) or mig-14 (bottom, lanes 1–15) biotinylated promoter fragment was incu-bated without His-SlyA (lane 1), or with His-SlyA at a final concentration of 10 nM, 20 nM, 41 nM, 83 nM or 166 nM (lanes 2–6, respec-tively). To demonstrate His-SlyA binding speci-ficity, 41 nM of His-SlyA were incubated with 0.3 pg of either pagC or mig-14 biotinylated promoter fragment in the presence of 0.135 pg, 1.35 pg, 13.5 pg, 135 pg or 270 pg of non-bioti-nylated promoter fragment (lanes 7–11, respectively). Addition of 0.22 pg, 2.2 pg, 22 pg or 220 pg of an internal fragment of rpoD to a reaction containing either 0.3 pg of labelled pagC or mig-14 promoter with 41 nM His-SlyA was used to demonstrate specific binding of His-SlyA (lanes 12–15, respectively). In the PpagC binding experiments, specificity was fur-ther demonstrated by the inability of a non-specific, double-stranded oligonucleotide (oligo 1, see Experimental procedures) to compete away His-SlyA binding at either 6.6 ng or 66 ng (lanes 16 and 17). Incubation of the SlyA–PpagC complex with 0.6 ng, 6.6 ng and 66 ng of an unlabelled double-stranded oligo (oligo 2; lanes 18–20) corresponding to the previously defined consensus SlyA binding site (Stapleton et al., 2002) was able to compete with His-SlyA bind-ing to the labelled PpagC fragment.

Co-regulation by SlyA and PhoP/PhoQ in S. Typhimurium 499

© 2005 Blackwell Publishing Ltd, Molecular Microbiology, 56, 492–508

untranslated region. This site lies outside the region of thepagC promoter that is sufficient to confer Mg2+-dependentactivation of reporter genes (Chen and Schifferli, 2001).Both EMSA (data not shown) and DNase I footprint anal-ysis of this downstream site demonstrate that purified His-SlyA also interacts with affinity similar to that of to theupstream site. On the mig-14 promoter fragment, His-SlyAprotected a region approximately 115 to 95 bp upstreamof the mig-14 open reading frame. The regions protectedby His-SlyA overlap the predicted SlyA-binding motif asdefined by Stapleton et al. (2002) confirming their earlierfindings regarding the DNA binding specificity of purifiedSlyA protein.

A slyA mutant displays increased sensitivity to polymyxin B

Salmonella mutants lacking either phoP or phoQ exhibitdramatically increased sensitivity to polymyxin B and cat-ionic antimicrobial peptides. Detailed studies have shownthat PhoP/PhoQ promotes resistance to these peptidesby regulating lipopolysaccharide (LPS) modifications tomake the outer membrane more positively charged. Aswe found that SlyA regulates expression of mig-14 andugtL, two genes known to be required for polymyxin Bresistance, we hypothesized that SlyA would be requiredfor inducible resistance to polymyxin B (Table 2). Wild-type, slyA, phoP and slyA phoP double mutant Salmonellastrains were adapted in low (10 mM) magnesium for 3 hbefore exposure to 1 mM polymyxin B for 1 h at 37∞C. Pre-adaptation in low magnesium has been shown to induce

high levels of polymyxin B resistance in wild-type Salmo-nella but not in phoP mutant strains (Groisman et al.,1997). A slyA mutant strain was found to be approximately60–70 times more sensitive to polymyxin B than itsisogenic wild-type parent (P = 0.012, see Table 2). Resis-tance to polymyxin B in the slyA mutant was almost com-pletely restored by complementation with the slyA geneon a low-copy plasmid, confirming that the slyA mutationwas responsible for the loss of resistance to polymyxin B.Cultures of the phoP and slyA phoP double mutant strainswere completely killed under these conditions (survival ofless than 0.0001%, P = 0.011), indicating that resistanceto polymyxin B is more impaired in a phoP than in a slyAmutant. This is consistent with the observation that SlyAcontrols only a subset of the PhoP-activated genesrequired for resistance to polymyxin B (e.g. ugtL and mig-14 but not pmrAB). It is also consistent with the observa-tion that a slyA mutation has a less profound effect than

Fig. 5. His-SlyA protects regions of pagC and mig-14 DNA. The left and right panels repre-sent His-SlyA DNase I protection footprints of pagC and mig-14 DNA, respectively. The first lane in each panel contains a DNase I-only ladder. The SlyA concentrations used with pagC are 2.41, 3.62, 5.43, 8.15, 12.2 and 18.3 nM from left to right. The SlyA concentra-tions used with mig-14 are 1.81, 2.72, 4.07, 6.11, 9.17 and 13.75 nM from left to right. The indicated co-ordinates of protection are 109 to 73 bp upstream of the pagC transcriptional start site and 115 to 94 bp upstream of the predicted mig-14 translational start site.

Table 2. Polymyxin survival defect of slyA and phoP mutant strains.

Strain % Survival

14028s 46 ± 8.7slyA 0.7 ± 0.2phoP <0.0001phoP slyA <0.0001slyA pSlyA 37 ± 3

For per cent survival, approximately 3 ¥ 106 wild-type, phoP mutantor slyA- mutant Salmonella were grown in low magnesium (10 mM)minimal medium for 3 h. Cells were then treated with 1 mg ml-1 poly-myxin B for 1 h and plated to determine viability (see Experimentalprocedures).

500 W. W. Navarre et al.

© 2005 Blackwell Publishing Ltd, Molecular Microbiology, 56, 492–508

a phoP mutation on the expression of some genes asso-ciated with polymyxin resistance (e.g. mig-14). A similarfinding regarding the polymyxin sensitivity of slyA mutantS. Typhimurium has been recently reported by Shi et al.(2004a) and attributed to reduced expression of ugtL. Itremains to be determined whether reduced virK and mig-14 expression also contributes to the polymyxin B sensi-tivity of a slyA mutant strain.

Discussion

The regulatory proteins SlyA and PhoP/PhoQ play majorroles in Salmonella virulence and stress resistance. In thepresent study, we have used cDNA microarrays to dem-onstrate overlap between the PhoP/PhoQ and SlyA reg-ulons and have identified more than 25 genes regulatedby both PhoP and SlyA (Table 1). A substantial proportionof the SlyA-regulated loci, including all SlyA-repressedgenes, are predicted to encode membrane, periplasmic,or secreted proteins. This suggests that a major role ofSlyA is to alter the cell surface in order to protect the cellfrom toxic compounds produced by the host. Indeed, ugtL,virK, mig-14 and pgtE were previously identified as PhoP/PhoQ-regulated genes that play a role in resistanceagainst polymyxin B and/or cationic antimicrobial peptides(Guina et al., 2000; Brodsky et al., 2002; Detweiler et al.,2003; Shi et al., 2004a). S. Typhimurium carrying aslyA mutation is highly sensitive to polymyxin B, but to alesser degree than a phoP mutant strain. The differencein the degree of polymyxin sensitivity of slyA and phoPmutants may be explained, in part, by the SlyA-independent regulation of the pmr locus by PhoP/PhoQ.

The profoundly attenuated virulence of slyA mutant Sal-monella can be rationalized by the large number of viru-lence-associated genes identified as SlyA regulated bymicroarray. In addition to the many PhoP-dependent genesdiscussed above, SlyA also regulates expression of theOmpR-dependent ssrAB locus (Lee et al., 2000; Fenget al., 2003; Kim et al., 2003). SsrAB controls expressionof genes carried by Salmonella pathogenicity island 2(SPI2), which is required for intracellular survival of Sal-monella and remodelling of the Salmonella-containing vac-uole to inhibit vacuolar maturation and oxidative killing bythe NADPH phagocyte oxidase (Vazquez-Torres et al.,2000; Waterman and Holden, 2003). Although an earlierreport suggested that PhoP regulates SPI2 gene expres-sion (Deiwick et al., 1999), other investigators have notobserved a role for PhoP in ssrAB regulation under PhoP/PhoQ-inducing conditions (Lee et al., 2000; Miao et al.,2002; Kim and Falkow, 2004). SlyA regulation of ssrABmay be a primary explanation for the inability of slyAmutant Salmonella to replicate in phagocytes and hosttissues (Libby et al., 1994; Daniels et al., 1996).

The results of our cDNA microarray analysis differ frompublished proteomic analyses of the SlyA regulon. In oneof these studies, SlyA was reported to repress the expres-sion of several outer membrane proteins, including PagC(Stapleton et al., 2002). PagC was recognized solely bysize on a Coomassie brilliant blue-stained 1D-SDS poly-acrylamide gel, and it is therefore possible that theobserved SlyA-repressed protein was misidentified. Theother study (Spory et al., 2002) examined differences inprotein abundance resulting from SlyA overexpression.Overexpression of SlyA has been shown to activate theexpression of the HlyE haemolysin in E. coli by antago-nizing repressive effects of H-NS on the hlyE promoter(Wyborn et al., 2004), even though SlyA does not appearto play a role in hlyE regulation under normal circum-stances. It is therefore possible that overexpression ofSlyA resulted in the artifactual activation or repression ofgenes not differentially expressed between wild-type andslyA mutant bacteria. Subtle variation in growth conditionsand the relative insensitivity of proteomic methods mayalso account for differences between previously publishedresults and the present study.

Using DNase I footprinting and EMSA, a direct interac-tion between purified SlyA protein and the pagC and mig-14 promoters was demonstrated (Figs 4 and 5). Publishedstudies employing slyA::lacZ fusions have provided evi-dence that PhoP is able to enhance transcription of slyA(Norte et al., 2003; Eguchi et al., 2004), suggesting thatPhoP might interact with SlyA in a transcriptional regula-tory cascade somewhat analogous to PhoP and PmrD(Kox et al., 2000). However, in our experiments little, if any,influence of PhoP/PhoQ on slyA expression wasobserved. During a shift to low-magnesium medium weobserved a nearly 200-fold PhoP-dependent increase inpagC mRNA unaccompanied by significant increases inslyA mRNA or SlyA protein (Fig. 3B). Furthermore, weobserved a broad influence of the phoP mutation onnearly all SlyA-regulated loci despite no apparent varia-tion in the quantity of SlyA protein. Although it remainspossible that PhoP activation of slyA expression may beimportant under circumstances where Salmonella needsto respond rapidly to certain stresses (e.g. antimicrobialpeptides or low magnesium) and SlyA is otherwise notexpressed (e.g. log phase), our observations clearly indi-cate that PhoP/PhoQ influences expression of a largenumber of SlyA-co-regulated loci without significantlyaltering levels of SlyA protein per se.

It is therefore necessary to propose novel mechanismsto account for the co-ordinate regulation of a large num-ber of genes by SlyA and PhoP/PhoQ. Our observationsare consistent with at least two possible models (Fig. 6).In the first model PhoP/PhoQ may exert a regulatoryeffect by altering the ability of SlyA to act as a transcrip-tional activator. Because SlyA belongs to the MarR family

Co-regulation by SlyA and PhoP/PhoQ in S. Typhimurium 501

© 2005 Blackwell Publishing Ltd, Molecular Microbiology, 56, 492–508

of DNA-binding proteins, at least some of which areknown to interact with small molecules (Grkovic et al.,2002), it is possible that activation of PhoP/PhoQ resultsin a change in the concentration of a cognate ligand forSlyA. It is not likely that SlyA requires the ligand for DNA-binding activity, because purified SlyA binds to SlyA-regulated promoters in vitro. Rather, binding or release ofa ligand may enable bound SlyA to promote formation ofan open transcriptional complex. This situation would bein some ways analogous to the redox-responsive tran-scriptional activator OxyR, which binds to target promot-ers but can only activate transcription when a specificcysteine residue is oxidized, promoting a conformationalchange (Choi et al., 2001). It is possible that the bindingof SlyA to its cognate ligand alters its affinity for promot-ers, which may explain the observations that overexpres-sion of SlyA increases the expression of a pagC–lacZfusion even in the absence of phoP (Fig. 2, comparelanes 9 and 10). We suggest that artificially high concen-trations of SlyA partially compensates for the decreasedaffinity or activity of SlyA in a phoP mutant strain.Although the activation of SlyA by PhoP/PhoQ could intheory occur via some other type of post-translationalmodification (e.g. phosphorylation), no such modificationhas previously been described for members of the MarRfamily.

The scenario suggested above assumes that SlyA, notPhoP, is the proximal regulator of many PhoP/SlyA-co-regulated genes such as pagC. The absence of acanonical PhoP-box in the promoter region of pagC isconsistent with this model (Lejona et al., 2003). In

addition, attempts to demonstrate a direct interactionbetween PhoP and the pagC promoter either with orwithout SlyA by EMSA or DNase I footprinting have beenunsuccessful (data not shown). This model is also con-sistent with the observations that purified (and presum-ably ligand-free) SlyA protein acts as a repressor of itsown promoter in vitro, but slyA appears to be activatedby PhoP in vivo (Stapleton et al., 2002; Norte et al.,2003). Ligand-free SlyA might repress slyA transcriptionbut, upon binding of its cognate ligand, either dissociatefrom the promoter or activate its own transcription. Adefinitive test of this model awaits the identification of aputative SlyA-activating ligand.

A second model posits that each locus displayingdependence on both PhoP and SlyA possesses bindingsites for both transcription factors, as has recently beenreported for the ugtL promoter. Two recent reports havesuggested that SlyA and its homologue, RovA from Yers-inia, function as anti-repressors that compete with thenucleoid-like H-NS protein for binding sites within certainpromoter sequences (Heroven et al., 2004; Wyborn et al.,2004). SlyA might remodel the local nucleoprotein struc-ture of the bacterial chromosome by competing withrepressors like H-NS. In this scenario, activation of manySlyA-regulated genes would require the participation ofadditional activators such as PhoP or, in the case ofssrAB, OmpR (Lee et al., 2000). This second model isless parsimonious than the first because it requires thatat least 10 different loci would each contain both PhoPand SlyA binding sites and does not easily explain theeffect of the phoP mutation on SlyA-repressed genes. This

Fig. 6. Models of PhoP–SlyA co-regulatory interactions. In the ligand induction model (top), activation of the PhoP/PhoQ system by low magnesium concentrations is proposed to lead indirectly to a change in the concentration in a small molecule ligand (dark oval) that interacts with SlyA as a co-activator. This model posits that a SlyA–ligand interaction promotes a con-formational change allowing SlyA to activate transcription from a subset of promoters includ-ing pagC. In the overlapping regulon model (bottom), SlyA interacts cooperatively with dif-ferent regulators at different promoters (e.g. PhoP at pagC and OmpR at ssrAB), perhaps by acting as an anti-repressor by antagonizing the activity of H-NS or a similar factor (Heroven et al., 2004; Wyborn et al., 2004). The two pro-posed models are not mutually exclusive, and it is conceivable that PhoP interacts with SlyA directly at some loci (e.g. ugtL) while also mod-ulating SlyA functionality.

502 W. W. Navarre et al.

© 2005 Blackwell Publishing Ltd, Molecular Microbiology, 56, 492–508

model is supported, however, by the finding that thephoQ24 mutation can affect levels of pagC transcript evenin the absence of SlyA (Figs 1 and 2), although the effectof PhoP on pagC expression in the absence of SlyA maybe indirect. In addition, the nucleoprotein restructuringmodel would more easily account for binding of SlyAdownstream of the ugtL and pagC transcriptional startsites, unusual locations for binding by transcriptional acti-vators that interact directly with RNA polymerase (Shiet al., 2004a). Local nucleoprotein restructuring by SlyAcould also explain mild effects observed on the expressionof genes in the proximity of more strongly activated genes(e.g. pagD, envE and STM1254 near pagC; virK andpipB2 near mig-14; ssrA near ssrB). According to theclassification scheme of Shen-Orr et al. (2002), the over-lapping regulon model would be considered as a standard‘dense overlapping regulon’. The ligand-induction modelwe propose represents a modification of the standard‘feedforward loop’ mechanism as recently proposed forthe interaction of PhoP and SlyA (Shi et al., 2004a)because PhoP would influence the activity rather than theabundance of SlyA protein. However, these two modelsare not mutually exclusive and it is possible or even likelythat PhoP both alters SlyA activity and interacts directlywith SlyA at selected promoters.

Our findings indicate that SlyA has evolved to serve afunction in Salmonella that is significantly different from itscounterpart in E. coli, despite the 89% identity and 95%similarity between SlyA proteins of the two bacterial spe-cies. A large number of the SlyA-activated genes identi-fied by microarray analysis are unique to Salmonella, andonly two of these genes, ybcY and nmpC, have a closehomologue in the E. coli K12 genome. We suggest thatoverlap between the PhoP/PhoQ and SlyA regulonsevolved at some point after the divergence of S. entericaand E. coli from a common ancestor. Given the largenumber of SlyA/PhoP-co-regulated genes that areinvolved in virulence and survival within the host, theprogressive specialization of SlyA to promote resistanceto exogenous membrane-damaging stresses may havebeen a critical step in the evolution of Salmonella as aunique pathogenic species.

Experimental procedures

Strains and growth conditions

Wild-type S. Typhimurium 14028s and the isogenic phoQ24and phoP::Tn10dCm mutant strains were obtained from thelaboratory of Samuel Miller at the University of Washington.A strain containing the phoP7953:Tn10Tet mutant wasobtained from Eduardo Groisman at Washington University,St. Louis. Construction of the putA::pagC–lacZ allele wasdescribed previously (Prouty et al., 2004b). Each of thesealleles was moved into the same strain backgrounds used for

our array analysis by transduction using phage P22 HT105/1 int-201 (Schmieger, 1971). A null mutation in slyA wasconstructed by the protocol of Datsenko and Wanner (2000)using the red-gam recombinase as described. The tetRAtetracycline resistance genes were amplified from plasmidpBR322 (Watson, 1988). Complementation of slyA mutantswas accomplished by cloning the 680 bp PCR-amplified slyAfragment from pSL2237 (Libby et al., 1994) into vector pRB3(Berggren et al., 1995). Strains were grown in LB or N-minimal medium, pH 7.4, supplemented with 10 mM or10 mM MgSO4 as described (Hmiel et al., 1986; Sonciniet al., 1996).

cDNA microarray analysis

The Salmonella whole ORF PCR product microarray wasconstructed as previously described (Porwollik et al., 2003).Microarray analysis comparing transcript levels in wild-type14028s with slyA, phoP or slyA phoP double mutant Salmo-nella were each performed three times under identical con-ditions (three biological replicates). The array comparingphoQ24 with phoQ24 slyA mutant Salmonella was per-formed once with RNA harvested from early stationaryphase and once with RNA harvested from mid-log phasecells. Cells were subcultured 1:100 from an overnight culturegrown in LB broth with vigorous aeration at 37∞C into 50 mlof fresh LB broth. After growth to approximately OD600 = 2.0,cells were harvested by diluting into two volumes ofRNAprotect Bacteria Reagent (Qiagen, Valencia, CA) andusing the RNeasy midi kit according to the manufacturer’sinstructions.

Fluorescently labelled cDNA was synthesized from totalRNA using SuperScript-II reverse transcriptase (Invitrogen,Carlsbad, CA) primed with random hexanucleotides in abiased mixture of nucleotides (25 mM dCTP, dGTP, dATP and10 mM dTTP) supplemented with either Cy5- or Cy3-labelleddUTP (Amersham, Piscataway, NJ). After labelling, RNA wasremoved by hot-alkali treatment and labelled cDNA was puri-fied using a Qiaquick PCR Purification kit. Equal amounts ofoppositely labelled cDNA were mixed together and hybridizedto the Salmonella array. Dye switching was employed inwhich one array with Cy5-labelled control cDNA and Cy3-labelled mutant cDNA was compared with a second arraywith Cy3-labelled control cDNA and Cy5-labelled mutantcDNA. Arrays were scanned at the Institute for SystemsBiology (Seattle, WA) using a Packard Biosciences ScanAr-ray 5000 and quantified using DigitalGENOME (Molecular-ware) spot finding software. Smoothed background intensitywas estimated and subtracted from the mean intensity ineach spot boundary, followed by normalization to the medianintensities in Cy3 and Cy5. Statistical analysis was performedby combining six replicates for each experiment and deter-mining significant differential expression using software asdescribed (Ideker et al., 2000; 2001).

Quantitative RT-PCR analysis of gene expression

Expression levels of selected genes were analysed by one-step real-time RT-PCR analysis using a Rotor-Gene thermalcycler (Corbett Research, Mortlake, Australia). Salmonella

Co-regulation by SlyA and PhoP/PhoQ in S. Typhimurium 503

© 2005 Blackwell Publishing Ltd, Molecular Microbiology, 56, 492–508

RNA was prepared essentially as described above, exceptthat in most cases the RNeasy mini kit (Qiagen) was used.All reagents were from the Qiagen QuantiTect SYBR GreenRT-PCR system. First strand cDNA synthesis and PCRwere carried out according to the manufacturer’s instruc-tions. Each 20 ml of PCR reaction contained 10 ml of SYBRGreen master mix and 0.2 ml of reverse transcriptase (RTmix). Total Salmonella RNA (7.8 ml) at a concentration of5 mg ml-1 was added to each reaction. Forward and reverseprimers for each gene were added to a final concentrationof 1 mM each in a total volume of 2 ml. The amount of prod-uct generated after each cycle was quantified by measuringfluorescence of SYBR Green dye. Melting curve analysisverified that the reactions contained a single PCR product.Reported gene expression levels are normalized to levels ofgyrB transcript, a housekeeping gene used as an internalcontrol because it exhibits relatively constant levels of

expression between the mutant strains under these condi-tions. Standard curves were generated during every run foreach gene tested and established by comparing transcriptlevels in serial dilutions of total RNA from a control sample.Primer sets listed in Table 3 correspond to the followinggenes: pagC, WNp163 and WNp164; gyrB, WNp233 andWNp234; mig-14, WNp250 and WNp251; slyA, WNp252and WNp253.

RT-PCR analysis of the virK/mig-14 intergenic region

Four micrograms of total RNA (in 60 ml) isolated from strainsWN151 (phoQ24) and WN152 (phoP::Tn10dCm) were mixedwith 4 pmol of primer WNp325 (in 4 ml) and heated to 70∞Cfor 10 min before being placed on ice to allow the primer toanneal. After centrifugation the sample was split in two equal

Table 3. Strains, plasmids and primers used in this study.

Strain or plasmid Genotype or relevant characteristics Source or reference

Strains14028s ‘Wild-type’ Salmonella enterica serovar Typhimurium ATCCWN151 14028s phoQ24 (‘PhoP constitutive’, also known as CS022) Miller and Mekalanos (1990)WN152 14028s phoP::Tn10dCm (also known as CS015) Miller and Mekalanos (1990)WN228 14028s slyA::tetRA This workWN229 14028s phoQ24 slyA::tetRA This workWN230 14028s phoP::Tn10d-Cm slyA::tetRA This workWN255 14028s putA::pagC–lacZ Prouty et al. (2004b)WN256 WN151 putA::pagC–lacZ This workWN260 WN228 pRB3-slyA This workWN312 WN228 putA::pagC–lacZ This workWN313 WN229 putA::pagC–lacZ This workWN318 14028s putA::pagC–lacZ phoP7953::Tn10(tet) Fields et al. (1989)WN053 14028s pTP233 Schapiro et al. (2003)

PlasmidspRB3-slyA RK2-based plasmid with a 680 bp PCR fragment with the slyA

coding region and upstream region.Libby et al. (1994);

Berggren et al. (1995)pTP233 Lambda red recombinase Poteete and Fenton (1984)pSL2570 A low-copy pSC101 origin vector derived from pSX34-lacZ containing

the arabinose promoter and multiple cloning site of pBAD-18.Buchmeier et al. (1997)

pSL2571 pSL2570 with the slyA open reading frame. Buchmeier et al. (1997)

PrimersSL156 5¢-CTAATTATAAGCATATGAAATTGGAATC-3¢SL157 5¢-CTTTACGTGTGGATCCATGGCCACAC-3¢SL212 5¢-GCTTTAGTTTTAGCCAAAACTG-3¢SL213 5¢-ACCGTCTCTCCACGCTAAAC-3¢SL658 5¢-CGCTTCATGAAATAATCCACAATATC-3¢SL660 5¢-GGCTTGCGAGTGAATAGCGCG-3¢SL6370 5¢-GTTAACCACTCTTAATAATAATG-3¢SL6371 5¢-CGTCTAGACGTGACGCTCCATCCGCAATAC-3¢SL8147 5¢-GACATCGCTAAACGTATCGAAGAC-3¢SL8148 5¢-CACTGCTCGACGCAGAGCTTCATG-3¢WNp163 5¢-GGGTCTGTTGAGCCTGAAGG-3¢WNp164 5¢-GCCATCCTGAGTGGAATGTTC-3¢WNp233 5¢-GATGGGTTTTCCAGCAGGTATTC-3¢WNp234 5¢-AGGTCTGATTGCGGTGGTTTC-3¢WNp249 5¢-GGCGGTAGTATCAATATGCACCCA-3¢WNp250 5¢-GGCGCCATCGGAATAAGTATCTCA-3¢WNp251 5¢-AATCGCCACTAGGTTCTGATCTGG-3¢WNp252 5¢-GACCCAATGTGTCTGCGTCAATTC-3¢WNp324 5¢-CGACGAGATTTATGCGGTCAGTG-3¢WNp325 5¢-GGAAAAGGAAGACGGTTGCC-3¢slycons1 5¢-TTAGCATGTTAA-3¢slycons2 5¢-TTAACATGCTAA-3¢non-spec1 5¢-GAGAGAGAGAGAT-3¢non-spec2 5¢-ATCTCTCTCTCTC-3¢

504 W. W. Navarre et al.

© 2005 Blackwell Publishing Ltd, Molecular Microbiology, 56, 492–508

samples and mixed with 10 ml of Superscript II buffer, 5 ml of0.1 M dithiothreitol (DTT), 1 ml of dNTP mix (10 mM eachdGTP, dCTP, dATP and dTTP) and 1 ml of RNAsin (Promega)for a final volume of 50 ml. One microlitre of Superscript IIreverse transcriptase was added to one tube from each RNAsample while the other tube was incubated without reversetranscriptase to control for chromosomal DNA contamina-tion. Samples were incubated for 2 h at 42∞C before theaddition of 10 ml of TE containing 100 U of RNAse A(Qiagen). DNA from each sample was purified using theQiaquick PCR purification kit according to manufacturer’sinstructions. Amplification of the virK/mig-14 intergenicregion was accomplished by PCR using primers WNp324and WNp325.

Purification of His-SlyA

An N-terminal 6-His SlyA fusion protein was constructed inpET16B (Novegene, WI). The slyA coding region was ampli-fied by PCR using Pfu (Stratagene, La Jolla, CA) and prim-ers SL156 and SL157 (see Table 3) incorporating anengineered NdeI site at the ATG start codon, and the purifiedPCR product was cloned into the SmaI site of pSK(Stratagene). Plasmids containing the PCR fragment wererestricted with NdeI/BamHI, and the slyA fragment was direc-tionally cloned into the NdeI/BamHI site of pET16B. ThepET16B::slyA containing plasmid DNA was used to trans-form BL21 (DE3) pLysS. To induce production of His-SlyA,cells were grown to mid-log phase before IPTG was addedto 2 mM. Cells were harvested by centrifugation after 5 hincubation. His-SlyA was purified by nickel-affinity chroma-tography (Ni-NTA, Qiagen) according to the manufacturer’sprotocol. Fractions containing His-SlyA were pooled and dial-ysed in 20 mM Tris-HCl, pH 7.6, 0.1 mM EDTA and 5 mMDTT, before concentration and storage at -20∞C in 50% glyc-erol. The His-SlyA concentration was determined by measur-ing the absorbance at 280 nm using an extinction coefficientof 11 080 M-1 cm-1.

SlyA antibody production and purification

Production of rabbit antisera to purified His-SlyA was per-formed by Scantibodies (Ramona, CA). The antibody prepa-ration was purified to remove cross-reacting activity by serumaffinity chromatography. Briefly, 1 l of overnight culture con-taining slyA mutant WN228 was harvested by centrifugation,resuspended in 0.1 M NaHCO3 with 0.5 M NaCl, pH 8.3 (cou-pling buffer), then sonicated to lyse the cells. The lysate wasclarified by centrifugation at 15 000 g at 4∞C for 20 min andmixed with a slurry of CNBr-activated Sepharose 4B withgentle shaking at 4∞C overnight. Antisera was passed over acolumn containing this resin twice to remove cross-reactingantibodies not specific for SlyA. The column was washedextensively with alternating buffers containing 0.1 M Tris-HClwith 0.5 M NaCl, pH 8.0 or 0.1 M NaHCO3 with 0.5 M NaCl,pH 4.0. Eluate containing crude His-SlyA antiserum was con-centrated by ammonium sulphate precipitation by the addi-tion of saturated ammonium sulphate to a final concentrationof 50% followed by gentle stirring overnight at 4∞C. Precipi-tated serum was collected by centrifugation, resuspended in

phosphate-buffered saline (PBS), dialysed overnight againstPBS, then gently mixed with a slurry of Protein A SepharoseCL-48 overnight. The slurry was poured into a column andthe flow-through passed over twice, followed by extensivewashing with PBS. Antibody was eluted from the column in0.1 M glycine, pH 3.0 into tubes containing 1 M Tris-HCl,pH 9.0 to neutralize the elution buffer. Fractions exhibiting areaction to purified His-SlyA by dot-blot were pooled anddialysed in PBS. Pooled fractions were made in 0.02%sodium azide for long-term storage.

Western blot detection of SlyA

Bacteria were grown overnight in LB containing appropriateantibiotics. One millilitre of cells was collected by centrifuga-tion and washed twice in 20 mM Tris-HCl, pH 7.6, 1 mM DTT,0.1 mM EDTA and 5% glyercol (TGED), resuspended in500 ml of TGED, and lysed using 0.1 mm cubic zirconiumbeads in a mini-bead beater. The lysate was clarified bycentrifugation and the protein concentration determinedusing a Pierce BCA Microtiter plate assay. Approximately6 mg of total protein was mixed with SDS-PAGE sample bufferand loaded onto a 4–20% Tris-HCl SDS-PAGE Redi-Gel (Bio-Rad, CA). Proteins were transferred to nitrocellulose (PallMembrane, East Hills, NY), blocked in PBS containing 0.5%Tween 20 and 5% non-fat milk, reacted with column-purifiedanti-His-SlyA, and detected with Pierce Super Signal accord-ing to manufacturer’s instructions.

b-Galactosidase assay

For b-galacotsidase measurements, pagC–lacZ fusionstrains overnight cultures were grown at 37∞C in LB mediasupplemented with chloramphenicol (10 mg ml-1) to maintainplasmids pSL2570 or pSL2571. Subcultures (1:500) weremade in LB medium without chloramphenicol and supple-mented with 0.2% arabinose to induce expression of SlyA.b-Galactosidase activity was measured when the culturesreached early stationary phase (OD600 = 2.0) using standardmethodology (Miller, 1972). Samples were taken from eachculture for Western blot analysis of SlyA at the same time theenzyme assay was performed (see above).

EMSA assays

Promoter fragments were isolated by PCR amplificationusing primer sets SL658 and SL650 (mig-14 promoter) andSL6370 and SL6371 (pagC promoter, see Table 3). The 5-prime oligonucleotide was biotinylated (MWG Biosciences,High Point, NC). PCR products were gel-purified using aQiagen Gel extraction kit and quantified by spectrophotome-try. A 1¥ stock of Reaction-Storage buffer (10 mM Tris-HCl,pH 8.0, 0.1 mM EDTA, 5 mM MgCl2, 1 mM DTT, 5% glycerol)containing 10 mg ml-1 acetylated BSA was used for His-SlyAand promoter fragment dilution. Binding assays were per-formed in a total volume of 15 ml containing the following:1 mg of poly[IC], 0.1–0.6 pg of biotinylated DNA, various dilu-tions of His-SlyA and unlabelled competitor DNA as required.Competitor DNA included in some reactions was a non-

Co-regulation by SlyA and PhoP/PhoQ in S. Typhimurium 505

© 2005 Blackwell Publishing Ltd, Molecular Microbiology, 56, 492–508

specific PCR-amplified fragment of the rpoD gene (usingoligos SL8147 and SL8148), a double-stranded non-senseoligonucleotide (non-spec1 and non-spec2), or a double-stranded oligo corresponding to the consensus SlyA bindingsequence (slycons1 and slycons2). Binding reactions wereallowed to proceed for 20 min at room temperature, thenloaded onto pre-run 5% acrylamide gels in 1¥ Tris-BorateEDTA (Bio-Rad Precast Gels). The gels were run at 4∞C,100 V until the bromophenol blue dye reached the bottom ofthe gel, and DNA–protein complexes were transferred to anylon membrane (Biodyne B, Pall Corporation) using a semi-dry blotter (CBS Plastics, CA) at 180 mA for 20 min. The DNAwas UV cross-linked to the membrane, and biotinylated DNAon the membrane was detected using the LightShiftTMChemiluminescent EMSA Kit (Pierce Biotechnology, Rock-ford, IL) according to manufacturer’s protocol.

DNase I protection assay

DNA footprinting reactions were performed as described pre-viously (Feng et al., 2004). The 5¢ pagC and mig-14 regula-tory regions were amplified by PCR using 32P-labelledoligonucleotides. Each assay contained 3 ¥ 105 c.p.m.labelled template. For the binding reaction, SlyA was incu-bated for 20 min at room temperature in a buffer containing40 mM KCl, 4 mM Tris-HCl, pH 7.9, 1 mM EDTA, 1 mM DTT,3 mg poly(d[I-C]) and 12% (v/v) glycerol. DNase I was added,and the reaction was stopped after 30 s by the addition of20 mM EDTA, 360 mM Na acetate, pH 5.5 (final concentra-tion). The final products were precipitated with isopropanol,washed with 70% ethanol, dried and resuspended insequencing stop buffer. The products were separated byelectrophoresis on a sequencing gel along with a sequencingladder generated using the same primers and plasmidtemplates.

Polymyxin B survival assays

The polymyxin sensitivity assay was performed essentially asdescribed (Gunn et al., 1998) with incubation for 1 h at 37∞C.Survival was determined by plating serial dilutions on LB agarand comparing colony-forming units (cfu) in the polymyxin-treated and untreated samples.

Acknowledgements

W.W.N. was funded in part by a post-doctoral training fellow-ship from the Damon Runyon Cancer Research Foundation(DRG 1588). The National Institutes of Health provided sup-port to M.M. (AI034829 and AI052237), J.S.G. (AI43521),F.C.F. (AI39557) and S.J.L. (AI48622). We thank Bruz Mar-zlof and Krassen Dimitrov of the Institute for Systems Biol-ogy for their technical assistance with the analysis of thecDNA microarrays. We thank Joyce Karlinsey for assistancewith purification of the anti-SlyA antisera. We thank EduardoGroisman and Samuel Miller for the gifts of Salmonellastrains. We thank Dr Steffen Porwollik at the Sidney KimmelCancer Institute for his role in constructing the Salmonellaarrays.

Supplementary material

The following material is available from http://www.blackwellpublishing.com/products/journals/suppmat/mmi/mmi4553/mmi4553sm.htmTable S1. Complete results of expression analysis of slyAand phoP mutants by microarray analysis of labelled cDNA.

References

Alekshun, M.N., and Levy, S.B. (1999) Alteration of therepressor activity of MarR, the negative regulator of theEscherichia coli marRAB locus, by multiple chemicals invitro. J Bacteriol 181: 4669–4672.

Ariza, R.R., Cohen, S.P., Bachhawat, N., Levy, S.B., andDemple, B. (1994) Repressor mutations in the marRABoperon that activate oxidative stress genes and multipleantibiotic resistance in Escherichia coli. J Bacteriol 176:143–148.

Belden, W.J., and Miller, S.I. (1994) Further characterizationof the PhoP regulon: identification of new PhoP-activatedvirulence loci. Infect Immun 62: 5095–5101.

Berggren, R.E., Wunderlich, A., Ziegler, E., Schleicher, M.,Duke, R.C., Looney, D., and Fang, F.C. (1995) HIV gp120-specific cell-mediated immune responses in mice after oralimmunization with recombinant Salmonella. J AcquirImmune Defic Syndr 10: 489–495.

Blattner, F.R., Plunkett, G., 3rd, Bloch, C.A., Perna, N.T.,Burland, V., Riley, M., et al. (1997) The complete genomesequence of Escherichia coli K-12. Science 277: 1453–1474.

Brodsky, I.E., Ernst, R.K., Miller, S.I., and Falkow, S. (2002)mig-14 is a Salmonella gene that plays a role in bacterialresistance to antimicrobial peptides. J Bacteriol 184:3203–3213.

Brumell, J.H., Kujat-Choy, S., Brown, N.F., Vallance, B.A.,Knodler, L.A., and Finlay, B.B. (2003) SopD2 is a noveltype III secreted effector of Salmonella typhimurium thattargets late endocytic compartments upon delivery intohost cells. Traffic 4: 36–48.

Buchmeier, N., Bossie, S., Chen, C.Y., Fang, F.C., Guiney,D.G., and Libby, S.J. (1997) SlyA, a transcriptional regula-tor of Salmonella typhimurium, is required for resistance tooxidative stress and is expressed in the intracellularenvironment of macrophages. Infect Immun 65: 3725–3730.

Chen, H., and Schifferli, D.M. (2001) Enhanced immuneresponses to viral epitopes by combining macrophage-inducible expression with multimeric display on a Salmo-nella vector. Vaccine 19: 3009–3018.

Choi, H., Kim, S., Mukhopadhyay, P., Cho, S., Woo, J., Storz,G., and Ryu, S. (2001) Structural basis of the redox switchin the OxyR transcription factor. Cell 105: 103–113.

Daniels, J.J., Autenrieth, I.B., Ludwig, A., and Goebel, W.(1996) The gene slyA of Salmonella typhimurium isrequired for destruction of M cells and intracellular survivalbut not for invasion or colonization of the murine smallintestine. Infect Immun 64: 5075–5084.

Datsenko, K.A., and Wanner, B.L. (2000) One-step inactiva-tion of chromosomal genes in Escherichia coli K-12 usingPCR products. Proc Natl Acad Sci USA 97: 6640–6645.

506 W. W. Navarre et al.

© 2005 Blackwell Publishing Ltd, Molecular Microbiology, 56, 492–508

Deiwick, J., Nikolaus, T., Erdogan, S., and Hensel, M. (1999)Environmental regulation of Salmonella pathogenicityisland 2 gene expression. Mol Microbiol 31: 1759–1773.

Detweiler, C.S., Monack, D.M., Brodsky, I.E., Mathew, H.,and Falkow, S. (2003) virK, somA and rcsC are importantfor systemic Salmonella enterica serovar Typhimuriuminfection and cationic peptide resistance. Mol Microbiol 48:385–400.

Eguchi, Y., Okada, T., Minagawa, S., Oshima, T., Mori, H.,Yamamoto, K., et al. (2004) Signal transduction cascadebetween EvgA/EvgS and PhoP/PhoQ two-component sys-tems of Escherichia coli. J Bacteriol 186: 3006–3014.

Feng, X., Oropeza, R., and Kenney, L.J. (2003) Dual regula-tion by phospho-OmpR of ssrA/B gene expression in Sal-monella pathogenicity island 2. Mol Microbiol 48: 1131–1143.

Feng, X., Walthers, D., Oropeza, R., and Kenney, L.J. (2004)The response regulator SsrB activates transcription andbinds to a region overlapping OmpR binding sites at Sal-monella pathogenicity island 2. Mol Microbiol 54: 823–835.

Fields, P.I., Groisman, E.A., and Heffron, F. (1989) A Salmo-nella locus that controls resistance to microbicidal proteinsfrom phagocytic cells. Science 243: 1059–1062.

Galan, B., Kolb, A., Sanz, J.M., Garcia, J.L., and Prieto, M.A.(2003) Molecular determinants of the hpa regulatory sys-tem of Escherichia coli: the HpaR repressor. Nucleic AcidsRes 31: 6598–6609.

Grkovic, S., Brown, M.H., and Skurray, R.A. (2002) Regula-tion of bacterial drug export systems. Microbiol Mol BiolRev 66: 671–701.

Groisman, E.A. (2001) The pleiotropic two-component regu-latory system PhoP–PhoQ. J Bacteriol 183: 1835–1842.

Groisman, E.A., Kayser, J., and Soncini, F.C. (1997) Regu-lation of polymyxin resistance and adaptation to low-Mg2+environments. J Bacteriol 179: 7040–7045.

Guina, T., Yi, E.C., Wang, H., Hackett, M., and Miller, S.I.(2000) A PhoP-regulated outer membrane protease of Sal-monella enterica serovar Typhimurium promotes resis-tance to alpha-helical antimicrobial peptides. J Bacteriol182: 4077–4086.

Gunn, J.S., and Miller, S.I. (1996) PhoP–PhoQ activatestranscription of pmrAB, encoding a two-component regu-latory system involved in Salmonella typhimurium antimi-crobial peptide resistance. J Bacteriol 178: 6857–6864.

Gunn, J.S., Alpuche-Aranda, C.M., Loomis, W.P., Belden,W.J., and Miller, S.I. (1995) Characterization of the Salmo-nella typhimurium pagC/pagD chromosomal region. J Bac-teriol 177: 5040–5047.

Gunn, J.S., Hohmann, E.L., and Miller, S.I. (1996) Transcrip-tional regulation of Salmonella virulence: a PhoQ periplas-mic domain mutation results in increased netphosphotransfer to PhoP. J Bacteriol 178: 6369–6373.

Gunn, J.S., Lim, K.B., Krueger, J., Kim, K., Guo, L., Hackett,M., and Miller, S.I. (1998) PmrA–PmrB-regulated genesnecessary for 4-aminoarabinose lipid A modification andpolymyxin resistance. Mol Microbiol 27: 1171–1182.

Heroven, A.K., Nagel, G., Tran, H.J., Parr, S., andDersch, P. (2004) RovA is autoregulated and antago-nizes H-NS-mediated silencing of invasin and rovAexpression in Yersinia pseudotuberculosis. Mol Microbiol53: 871–888.

Hmiel, S.P., Snavely, M.D., Miller, C.G., and Maguire, M.E.(1986) Magnesium transport in Salmonella typhimurium:characterization of magnesium influx and cloning of atransport gene. J Bacteriol 168: 1444–1450.

Ideker, T., Thorsson, V., Siegel, A.F., and Hood, L.E. (2000)Testing for differentially-expressed genes by maximum-likelihood analysis of microarray data. J Comput Biol 7:805–817.

Ideker, T., Galitski, T., and Hood, L. (2001) A new approachto decoding life: systems biology. Annu Rev GenomicsHum Genet 2: 343–372.

Kaneko, A., Mita, M., Sekiya, K., Matsui, H., Kawahara, K.,and Danbara, H. (2002) Association of a regulatory gene,slyA with a mouse virulence of Salmonella serovar Chol-eraesuis. Microbio Immunol 46: 109–113.

Kim, C.C., and Falkow, S. (2004) Delineation of upstreamsignaling events in the salmonella pathogenicity island 2transcriptional activation pathway. J Bacteriol 186: 4694–4704.

Kim, C.C., Monack, D., and Falkow, S. (2003) Modulation ofvirulence by two acidified nitrite-responsive loci of Salmo-nella enterica serovar Typhimurium. Infect Immun 71:3196–3205.

Knodler, L.A., Vallance, B.A., Hensel, M., Jackel, D., Finlay,B.B., and Steele-Mortimer, O. (2003) Salmonella type IIIeffectors PipB and PipB2 are targeted to detergent-resis-tant microdomains on internal host cell membranes. MolMicrobiol 49: 685–704.

Kox, L.F., Wosten, M.M., and Groisman, E.A. (2000) A smallprotein that mediates the activation of a two-componentsystem by another two-component system. EMBO J 19:1861–1872.

Lee, A.K., Detweiler, C.S., and Falkow, S. (2000) OmpRregulates the two-component system SsrA–ssrB in Salmo-nella pathogenicity island 2. J Bacteriol 182: 771–781.

Lejona, S., Aguirre, A., Cabeza, M.L., Garcia Vescovi, E., andSoncini, F.C. (2003) Molecular characterization of theMg2+-responsive PhoP–PhoQ regulon in Salmonellaenterica. J Bacteriol 185: 6287–6294.

Libby, S.J., Goebel, W., Ludwig, A., Buchmeier, N., Bowe,F., Fang, F.C., et al. (1994) A cytolysin encoded by Sal-monella is required for survival within macrophages. ProcNatl Acad Sci USA 91: 489–493.

McClelland, M., Sanderson, K.E., Spieth, J., Clifton, S.W.,Latreille, P., Courtney, L., et al. (2001) Complete genomesequence of Salmonella enterica serovar TyphimuriumLT2. Nature 413: 852–856.

Martin, R.G., and Rosner, J.L. (2004) Transcriptional andtranslational regulation of the marRAB multiple antibioticresistance operon in Escherichia coli. Mol Microbiol 53:183–191.

Miao, E.A., Freeman, J.A., and Miller, S.I. (2002) Transcrip-tion of the SsrAB regulon is repressed by alkaline pH andis independent of PhoPQ and magnesium concentration.J Bacteriol 184: 1493–1497.

Miller, J. (1972) Experiments in Molecular Genetics. ColdSpring Harbor, NY: Cold Spring Harbor Laboratory Press.

Miller, S.I., and Mekalanos, J.J. (1990) Constitutive expres-sion of the phoP regulon attenuates Salmonella virulenceand survival within macrophages. J Bacteriol 172: 2485–2490.

Co-regulation by SlyA and PhoP/PhoQ in S. Typhimurium 507

© 2005 Blackwell Publishing Ltd, Molecular Microbiology, 56, 492–508

Miller, S.I., Kukral, A.M., and Mekalanos, J.J. (1989) A two-component regulatory system (phoP phoQ) controls Sal-monella typhimurium virulence. Proc Natl Acad Sci USA86: 5054–5058.

Minagawa, S., Ogasawara, H., Kato, A., Yamamoto, K., Egu-chi, Y., Oshima, T., et al. (2003) Identification and molec-ular characterization of the Mg2+ stimulon of Escherichiacoli. J Bacteriol 185: 3696–3702.

Nagel, G., Lahrz, A., and Dersch, P. (2001) Environmentalcontrol of invasin expression in Yersinia pseudotuberculo-sis is mediated by regulation of RovA, a transcriptionalactivator of the SlyA/Hor family. Mol Microbiol 41: 1249–1269.

Nasser, W., and Reverchon, S. (2002) H-NS-dependent acti-vation of pectate lyases synthesis in the phytopathogenicbacterium Erwinia chrysanthemi is mediated by the PecTrepressor. Mol Microbiol 43: 733–748.

Norte, V.A., Stapleton, M.R., and Green, J. (2003) PhoP-responsive expression of the Salmonella enterica serovarTyphimurium slyA gene. J Bacteriol 185: 3508–3514.

Porwollik, S., Frye, J., Florea, L.D., Blackmer, F., and McClel-land, M. (2003) A non-redundant microarray of genes fortwo related bacteria. Nucleic Acids Res 31: 1869–1876.

Porwollik, S., Boyd, E.F., Choy, C., Cheng, P., Florea, L.,Proctor, E., and McClelland, M. (2004) Characterization ofSalmonella enterica subspecies I genovars using microar-rays. J Bacteriol 186: 5883–5898.

Poteete, A.R., and Fenton, A.C. (1984) Lambda red-dependent growth and recombination of phage P22. Virol-ogy 134: 161–167.

Praillet, T., Reverchon, S., and Nasser, W. (1997) Mutualcontrol of the PecS/PecM couple, two proteins regulatingvirulence-factor synthesis in Erwinia chrysanthemi. MolMicrobiol 24: 803–814.

Prouty, A.M., Brodsky, I.E., Falkow, S., and Gunn, J.S.(2004a) Bile-salt-mediated induction of antimicrobial andbile resistance in Salmonella typhimurium. Microbiology150: 775–783.

Prouty, A.M., Brodsky, I.E., Manos, J., Belas, R., Falkow, S.,and Gunn, J.S. (2004b) Transcriptional regulation of Sal-monella enterica serovar Typhimurium genes by bile.FEMS Immunol Med Microbiol 41: 177–185.

Pulkkinen, W.S., and Miller, S.I. (1991) A Salmonella typh-imurium virulence protein is similar to a Yersinia entero-colitica invasion protein and a bacteriophage lambda outermembrane protein. J Bacteriol 173: 86–93.

Revell, P.A., and Miller, V.L. (2000) A chromosomallyencoded regulator is required for expression of the Yersiniaenterocolitica inv gene and for virulence. Mol Microbiol 35:677–685.

Reverchon, S., Nasser, W., and Robert-Baudouy, J. (1994)pecS: a locus controlling pectinase, cellulase and bluepigment production in Erwinia chrysanthemi. Mol Microbiol11: 1127–1139.

Rouanet, C., Reverchon, S., Rodionov, D.A., and Nasser, W.(2004) Definition of a consensus DNA-binding site forPecS, a global regulator of virulence gene expression inErwinia chrysanthemi and identification of new membersof the PecS regulon. J Biol Chem 279: 30158–30167.

Schapiro, J.M., Libby, S.J., and Fang, F.C. (2003) Inhibitionof bacterial DNA replication by zinc mobilization during

nitrosative stress. Proc Natl Acad Sci USA 100: 8496–8501.

Schmieger, H. (1971) A method for detection of phagemutants with altered transducing ability. Mol Gen Genet110: 378–381.

Seoane, A.S., and Levy, S.B. (1995) Characterization ofMarR, the repressor of the multiple antibiotic resistance(mar) operon in Escherichia coli. J Bacteriol 177: 3414–3419.

Shen-Orr, S.S., Milo, R., Mangan, S., and Alon, U. (2002)Network motifs in the transcriptional regulation network ofEscherichia coli. Nat Genet 31: 64–68.

Shi, Y., Latifi, T., Cromie, M.J., and Groisman, E.A. (2004a)Transcriptional control of the antimicrobial peptide resis-tance ugtL gene by the Salmonella PhoP and SlyA regu-latory proteins. J Biol Chem 279: 38618–38625.

Shi, Y., Cromie, M.J., Hsu, F.F., Turk, J., and Groisman, E.A.(2004b) PhoP-regulated Salmonella resistance to the anti-microbial peptides magainin 2 and polymyxin B. Mol Micro-biol 53: 229–241.

Soncini, F.C., and Groisman, E.A. (1996) Two-componentregulatory systems can interact to process multiple envi-ronmental signals. J Bacteriol 178: 6796–6801.

Soncini, F.C., Garcia Vescovi, E., Solomon, F., and Grois-man, E.A. (1996) Molecular basis of the magnesium dep-rivation response in Salmonella typhimurium: identificationof PhoP-regulated genes. J Bacteriol 178: 5092–5099.

Spory, A., Bosserhoff, A., von Rhein, C., Goebel, W., andLudwig, A. (2002) Differential regulation of multiple pro-teins of Escherichia coli and Salmonella enterica serovarTyphimurium by the transcriptional regulator SlyA. J Bac-teriol 184: 3549–3559.

Stapleton, M.R., Norte, V.A., Read, R.C., and Green, J.(2002) Interaction of the Salmonella typhimurium transcrip-tion and virulence factor SlyA with target DNA and identi-fication of members of the SlyA regulon. J Biol Chem 277:17630–17637.

Valdivia, R.H., Cirillo, D.M., Lee, A.K., Bouley, D.M., andFalkow, S. (2000) mig-14 is a horizontally acquired, host-induced gene required for Salmonella enterica lethal infec-tion in the murine model of typhoid fever. Infect Immun 68:7126–7131.

Vazquez-Torres, A., Xu, Y., Jones-Carson, J., Holden, D.W.,Lucia, S.M., Dinauer, M.C., et al. (2000) Salmonella patho-genicity island 2-dependent evasion of the phagocyteNADPH oxidase. Science 287: 1655–1658.

van Velkinburgh, J.C., and Gunn, J.S. (1999) PhoP–PhoQ-regulated loci are required for enhanced bile resistance inSalmonella spp. Infect Immun 67: 1614–1622.

Waterman, S.R., and Holden, D.W. (2003) Functions andeffectors of the Salmonella pathogenicity island 2 type IIIsecretion system. Cell Microbiol 5: 501–511.

Watson, N. (1988) A new revision of the sequence of plasmidpBR322. Gene 70: 399–403.

Watson, P.R., Paulin, S.M., Bland, A.P., Libby, S.J., Jones,P.W., and Wallis, T.S. (1999) Differential regulation ofenteric and systemic salmonellosis by. Slya Infect Immun67: 4950–4954.

Wosten, M.M., Kox, L.F., Chamnongpol, S., Soncini, F.C.,and Groisman, E.A. (2000) A signal transduction systemthat responds to extracellular iron. Cell 103: 113–125.

508 W. W. Navarre et al.

© 2005 Blackwell Publishing Ltd, Molecular Microbiology, 56, 492–508

Wu, R.Y., Zhang, R.G., Zagnitko, O., Dementieva, I., Maltzev,N., Watson, J.D., et al. (2003) Crystal structure of Entero-coccus faecalis SlyA-like transcriptional factor. J Biol Chem278: 20240–20244.

Wyborn, N.R., Stapleton, M.R., Norte, V.A., Roberts, R.E.,Grafton, J., and Green, J. (2004) Regulation of Escherichiacoli hemolysin E expression by H-NS and Salmonella SlyA.J Bacteriol 186: 1620–1628.

Xiong, A., Gottman, A., Park, C., Baetens, M., Pandza, S.,

and Matin, A. (2000) The EmrR protein represses theEscherichia coli emrRAB multidrug resistance operon bydirectly binding to its promoter region. Antimicrob AgentsChemother 44: 2905–2907.

Yamamoto, K., Ogasawara, H., Fujita, N., Utsumi, R., andIshihama, A. (2002) Novel mode of transcription regulationof divergently overlapping promoters by PhoP, the regulatorof two-component system sensing external magnesiumavailability. Mol Microbiol 45: 423–438.