Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada T6G 2E91
Author for correspondence: William J. Page. Tel: +1 780 492 4782. Fax: +1 780 492 2216. e-mail: bill.page{at}ualberta.ca
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ABSTRACT |
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Keywords: Azotobacter vinelandii, catecholate siderophores, isochorismate synthase, Fur, superoxide stress
Abbreviations: CFX, cell-free extract; FdI, ferredoxin I; Fpr, ferredoxin:NADPH reductase; Fur, ferric uptake regulator protein; IRP, iron-repressible promoter; Lux, bioluminescence; MV, methyl viologen; PDHE1, pyruvate dehydrogenase E1 subunit; SOD, superoxide dismutase; Sox, superoxide stress
The GenBank accession number for the sequence reported in this paper is AF238500.
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INTRODUCTION |
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Respiration by iron-limited cells presents a considerable hazard: not only are superoxide radicals and hydrogen peroxide generated, but also iron-limited cells have very low superoxide dismutase (SOD) activity (Cornish & Page, 1998 ). Vigorous aeration of iron-limited A. vinelandii cultures causes the upregulation of catecholate siderophore synthesis, while azotobactin is not similarly affected (Cornish & Page, 1998
). It has been shown that the generation of hydroxyl radicals by the iron-catalysed Fenton reaction is effectively limited when iron is chelated to azotochelin or protochelin (Cornish & Page, 1998
). Therefore, it has been hypothesized that catecholate siderophores could play an additional role in preventing oxidative damage to iron-limited cells and that catecholate siderophore synthesis may be under the dual regulation of iron and oxidative stress.
The expression of high-affinity, siderophore-mediated uptake systems for iron accumulation is controlled at the level of transcription by the dissociation of the ferric uptake regulator (Fur) from an iron-box operator sequence (de Lorenzo et al., 1987 ). In iron-limited medium, decreased levels of the corepressor, intracellular Fe2+, allow Fur dimer dissociation from the promoter region and ensuing transcription of iron-regulated genes (Bagg & Neilands, 1987
). This is a highly conserved control mechanism, found in most aerobes and facultative aerobes (Achenbach & Yang, 1997
). Thus differential control of A. vinelandii siderophore synthesis could be explained by differences in Fur affinity for catecholate or azotobactin Fur-binding operator sequences. Unfortunately, siderophore-specific operator sequences have not been identified in A. vinelandii and there has been no proof of the existence of a Fur homologue in this organism.
Escherichia coli deals with oxidative stress through the increased transcription of genes activated by SoxS in response to superoxide or OxyR in response to hydrogen peroxide (Demple, 1996 ). Since SOD activity is low in iron-limited A. vinelandii, it is most likely that a superoxide stress (Sox) response may be involved. Such a control system is plausible, since recent work presents strong evidence for a superoxide-dependent regulator in A. vinelandii (Isas et al., 1995
; Yannone & Burgess, 1997
, 1998
).
In this study we describe the regulation of the first gene in the A. vinelandii catecholate siderophore biosynthesis operon, which encodes an isochorismate synthase, and report its dual regulation by iron and oxidative stress.
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METHODS |
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Cell-free extract preparation and SOD assay.
A. vinelandii strain UW was harvested and lysed in a French pressure cell to prepare a cell-free extract (CFX) (Cornish & Page, 1998 ). One unit of SOD activity was defined as the amount of protein required to inhibit the maximal rate of nitro blue tetrazolium reduction by
by 50% (Cornish & Page, 1998
; Oberley & Spitz, 1985
). Values reported are means calculated from at least duplicate assays in which the standard deviation was not greater than 10%.
Bioluminescence (Lux) activity in liquid cultures.
A. vinelandii strain F196 was grown for 16 h in Burks medium containing varied amounts of ferric citrate. Methyl viologen (MV) was added to increase superoxide stress (Korbashi et al., 1986 ) and Lux activity was assayed after 3 h induction. Two millilitres of culture was dispensed into a 3 ml spectrofluorometer cuvette and 0·1 vol. pure decanal was added. Maximum light production was measured as emission during mixing (aeration) at 200 r.p.m. for 200 s in a Hitachi F-2000 spectrofluorometer. Lux activity was calculated as the difference between the maximum and the minimum light intensity (observed when stirring was turned off). Lux specific activity was calculated as intensity per c.f.u.
DNA isolation and cloning.
Chromosomal DNA was extracted from A. vinelandii F196 following the procedure described by Robson et al. (1984). The DNA was partially digested with Sau3A under conditions optimized to generate fragments of approximately 23 kb (Sambrook et al., 1989 ). The digested DNA was ligated into the cosmid vector pLAFR3 and packaged using the Gigapack II Gold kit (Stratagene). The cosmid library was amplified in E. coli VCS257 and clones containing Tn5luxAB were isolated on LB-Kan medium. The KanR clones were then screened for iron-repressible Lux activity by Petri plate contact printing (Sevinc & Page, 1992
). Standard procedures were used for cloning, subcloning and restriction mapping (Sambrook et al., 1989
).
Southern hybridization.
DNA samples were transferred to 0·45 µm Hybond-N nylon membrane (Amersham Life Sciences) by the method of Southern (1975) . The probe for luxA was a random primer labelled 330 bp PstI fragment from within the luxA gene of pTn5luxAB (Feinberg & Vogelstein, 1983
; Mehrotra, 1997
).
DNA sequencing.
Clone pAS40 was used as the template for double-stranded sequencing starting with primer WJP11 (5'-CGGTCTGAGATAGCTCAGG-3'), which was complementary to luxA sequence. Sequence downstream of the transposon was obtained, starting with primer WJP17 (5'-GTCAGATCCTGGAAAACGG-3'), which was complementary to the right border of Tn5 (Auserwald et al., 1981 ). The sequence was determined using T7 Sequenase and Thermo Sequenase kits (Amersham Pharmacia Biotech).
DNA:Sox binding assays.
The Sox protein of A. vinelandii was detected in the DNA-binding assay described by Yannone & Burgess (1997, 1998) using 15 µg CFX protein per reaction. The Sox-binding site of the ferredoxin:NADPH reductase gene (fpr) was synthesized as a double-stranded 50-mer oligonucleotide (Yannone & Burgess, 1998 ) and was used as a positive control. The Sox-boxes identified in this study were synthesized as double-stranded 50-mer oligonucleotides and end-labelled by standard procedure: 5'-TGACGCTAGCATTATTACATACATGAAGGCGCCAGTGCCTTCCCCTAGGT-3' (Box 1) and 5'-TTCCGATTGCAGGGATTGGTCCGGATTCATGCTCTCTCCAAGTGATGTAA-3' (Box 2).
DNA:Fur binding assays.
The binding of the E. coli Fur protein (a gift from Dr J. Neilands, University of California at Berkeley) to iron-box sequences was carried out as described by de Lorenzo et al. (1988) , using Mn2+ as a corepressor. A 250 bp target containing the csbC promoter region was generated by PCR, using the oligonucleotide primers: WJP21 (5'-ctctgtcgacGCTTCCGATTGCAGGGATTG-3') and WJP22 (5'-ctacagatctTTACGGCTAGAGGACGAGCA-3'), which contained SalI (WJP21) and BglII (WJP22) restriction sites (lower case), to facilitate ligation in pQF50, generating pAS50. The PCR reaction mixture consisted of 10 µl 10x Stemke buffer (0·7 M Tris, pH 8·8, 40 mM MgCl2, 1% Triton X-100, 1 mg BSA ml-1), 10 µl dNTPs (1 mM), approximately 30 pmol each of the primers, 20 ng pAS40 template and 5 µl Taq polymerase (diluted 1:10 in 1x strength Stemke buffer) and deionized water (total volume 100 µl). The PCR program (Minicycler, MJ Research) was: 5 min denaturation at 95 °C, followed by 30 cycles of 30 s denaturing step at 95 °C, 30 s annealing at 52 °C and 1 min extension at 72 °C, and finally one 5 min extension at 72 °C. The Fur-binding site of the aerobactin (iucA) operator was excised as a 250 bp EcoRIPvuII fragment of pCON6 and was used as a positive control (de Lorenzo et al., 1988
).
Detection of Fur protein by Western blotting.
Cytoplasmic extracts were prepared from exponential-phase cultures (Maniatis et al., 1982 ) and the proteins were resolved by SDS-15% PAGE (Page & Huyer, 1984
). Molecular mass was estimated using prestained standards from New England BioLabs. Proteins were transferred to a nylon membrane, which was then blocked in 1x Blotto [10 mM Tris/HCl, pH 8·0, containing 0·15 M NaCl (TBS), 5% skim milk, and 0·02% sodium azide] for 30 min. A 1:500 dilution of polyclonal rabbit anti-Pseudomonas aeruginosa Fur antiserum (a gift from M. Vasil, University of Colorado) was added and incubated with shaking overnight (Prince et al., 1991
). The blot was washed with TBS, and Fur was localized by incubating with secondary antibody (anti-rabbit IgG horseradish peroxidase conjugate, 1:1000 in TBS) for 3 h at room temperature, followed by development with TBS containing 0·5 mg ml-1 chloronaphthol in methanol and 0·02% H2O2.
Isolation of RNA; Northern and dot-blot hybridization.
A. vinelandii and E. coli cultures were harvested in exponential phase for RNA extraction using a modified hot-phenol procedure (Frost et al., 1989 ; Miller, 1972
). RNA (10 µg in 3·7 µl distilled H2O) was denatured with 2·7 µl freshly deionized 6 M glyoxal, 8 µl DMSO and 1·6 µl 100 mM sodium phosphate buffer (pH 7·0) and incubated at 50 °C for 1 h. The cooled samples were loaded onto a 1% agarose gel (in 10 mM sodium phosphate buffer, pH 7·0) and separated by electrophoresis at 5560 V for at least 4 h. In dot-blot analysis, each RNA sample (5 µg in deionized water) was denatured and loaded into the dot-blot well (Hybri-Dot manifold, BRL) as described by Thomas (1980)
. Northern hybridization was conducted at 60 °C (Sambrook et al., 1989
). The probe used to detect the csbC transcript was a 310 bp NotIPstI fragment cut from pAS310 and labelled using the random primer method. The probe used to determine even RNA loading was a universal oligonucleotide for the 16S rRNA gene (a gift from G. W. Stemke, University of Alberta).
Primer extension.
Primer extension mapping was done as described by Sambrook et al. (1989) , using end-labelled primer and 50 µg total RNA per reaction. RNA was denatured at 85 °C for 10 min, cooled to 45 °C, and hybridized with radiolabelled antisense primer at 45 °C for 1 h [3x hybridization buffer, 0·5 µl (17 units) RNA guard]. Extension reactions were done with 25 units AMV reverse transcriptase (Boehringer Mannheim) at 42 °C for 1 h. The oligonucleotide WJP18 (5'-GGTAATGGGTGAACAGCAC-3') was used as the primer, as it was approximately 140 bp from the putative 5' start of csbC.
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RESULTS |
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Cloning and sequencing the iron-repressible promoter (IRP) of strain F196
A. vinelandii strain F196 was used to further examine the control of catecholate siderophore synthesis. Strain F196 is a catecholate-minus mutant, which was generated previously by mutation of strain UW with Tn5luxAB (Sevinc & Page, 1992 ) so that Lux activity was regulated by iron availability (Fig. 2a
). To isolate the IRP region of strain F196, a genomic library was prepared and a KanR Lux+ clone, pAS1, was identified. However, Lux activity was poorly regulated by Fe3+ in E. coli VCS257(pAS1) (Fig. 2b
). Iron-repressible Lux activity was restored when E. coli VCS257(pAS1) was transformed with pMH15, which encoded the E. coli fur gene on a plasmid with a copy number of 1012 (Fig. 2c
). Iron-repressible Lux activity was also observed when pAS1 was transformed into A. vinelandii UW (Fig. 2d
) and into the Fur-overproducing E. coli strain HB101(pMH15) (data not shown). Therefore it was concluded that the IRP region was contained in pAS1 and that difficulties in observing Lux regulation in E. coli were due to repressor (Fur) dilution.
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The 11·5 kb SalI fragment cloned in pUC119 (pAS40) was used as the template for sequencing. A total of 874 bp of double-stranded sequence upstream of the transposon and 489 bp of sequence downstream of the transposon were obtained. The sequence was analysed using FramePlot version 2·1 (Bibb et al., 1984 ) and two ORFs with opposite orientation were detected (Fig. 3
). The complete sequence of the upstream ORF (orfA) is currently being determined. The 1084 bp sequence of the downstream ORF was subjected to a homology search, using the Gapped BLAST GenBank program version 2.0 (Altschul et al., 1997
). There was an extremely high probability (P=3 x 10-65) that the downstream ORF was an isochorismate synthase gene. It shared 44% identity and 55% similarity at the amino acid level with the isochorismate synthase gene from Bacillus subtilis and shared significant homology at the amino acid level with the corresponding genes from Pseudomonas fluorescens, Mycobacterium tuberculosis, Vibrio cholerae, Aeromonas hydrophila and E. coli. The gene encoding the isochorismate synthase of A. vinelandii (GenBank accession no. AF238500) was named csbC, for catecholate siderophore biosynthesis C, in keeping with the E. coli lettering system, where C denotes isochorismate synthase.
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Primer extension analysis was done to identify the csbC transcript initiation site. Total RNA was extracted from strain UW grown under iron-limited (1 µM Fe3+) and iron-sufficient growth conditions, as well as suitable E. coli controls. One definite product was obtained after reverse transcription from primer WJP18 that was only observed using RNA extracted from iron-limited cells. The start of transcription was an adenine at nucleotide 214 that was 7 bp downstream of the proposed -10 sequence (Fig. 3, asterisk).
Northern analysis
The RNA transcript from csbC expressed in E. coli or in A. vinelandii appeared as a smear of hybridization, running through the length of the gel when examined by Northern analysis (data not shown). These results are typical of those obtained by Northern analysis of the ent operon of E. coli (T. Brickman, personal communication). The transcript was only detectable in iron-limited cells and the csbC transcript was completely repressed under iron sufficient (710 µM Fe3+) growth conditions. Exact transcript sizes were hard to determine, but the largest transcript was approximately 3·2 kb in strain F196 and approximately 9·5 kb in the wild-type strain UW. This difference in size was most likely due to the termination of transcription at the 3' end of luxAB in strain F196. Since luxAB accounted for approximately 2·4 kb, and the sequence between the putative promoter and start of luxA was about 660 bp, the predicted truncated transcript in strain F196 was about 3060 bp, as observed. When the Northern blot was stripped and probed with a universal oligonucleotide for 16S rRNA, bands of approximately even intensity were seen in all lanes, indicating that absence of csbC product under iron-sufficient growth conditions was due to repression, not to problems in RNA isolation or loading (data not shown).
DNA binding by the E. coli Fur protein
In order to further investigate the possibility that a Fur-like protein regulated csbC, DNA-binding assays using purified E. coli Fur protein were done. Although it would have been better to use the A. vinelandii Fur protein in these assays, this product was not available. Use of the E. coli Fur protein seemed reasonable since Fur is highly conserved and the E. coli Fur will complement fur mutations in many bacteria (Achenbach & Yang, 1997). The DNA target was the 250 bp PCR fragment from pAS50 containing the putative promoters and iron-boxes of csbC and orfA (Fig. 4). A DNA shift was observed at
25 nM Fur (Fig. 4a
, lane 2), and a second shift was detected at
500 nM Fur (Fig. 4a
, lane 6). This was not unexpected, since there were two iron-boxes within the target DNA, with relatively high (csbC iron-box) or low (orfA iron-box) homology to the iron-box consensus sequence. When the corepressor Mn2+ was absent, the DNA shift was eliminated (data not shown). The assay was repeated in exactly the same way using a 250 bp EcoRIPvuII fragment containing the E. coli aerobactin (iucA) promoter. In this positive control, a similar shift was observed only in the presence of Mn2+, at
50 nM Fur (data not shown).
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Cell extract of A. vinelandii strain UW contained a single protein that cross-reacted strongly with anti-P. aeruginosa Fur antiserum. This protein had a molecular mass of approximately 17 kDa, slightly larger than the Fur protein found in E. coli (Fig. 4b).
Regulation of csbC transcription by iron and oxidative stress
In order to determine if csbC transcription was also regulated by O2 stress, cultures were grown for 22 h in different concentrations of iron citrate, with the aeration altered by varying the culture volume per flask. Increased aeration increased catecholate siderophore production and delayed the repressive effect of added Fe3+ (Fig. 5a). The transcription of csbC was repressed by lower concentrations of ferric citrate under low aeration conditions than under high aeration conditions (Fig. 5b
), suggesting that control by Fur and a Sox-element may be in competition with each other.
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DISCUSSION |
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The regulatory region upstream of csbC is reminiscent of the divergent promoter to the E. coli fepBentC region (Ozenberger et al., 1987 ), where the -35 sequence of the entC promoter is separated from the -35 sequence of fepB by 31 bp. In A. vinelandii the -35 sequence of csbC is separated by 30 bp from the -35 sequence of the divergent promoter of orfA, which however does not share any homology with fepB. Our preliminary results on the sequencing of this ORF (unpublished work in progress) indicate some homology to antibiotic efflux transport proteins. One such protein is a chloramphenicol-resistance determinant that encodes a putative transmembrane pump in Streptomyces lividans (Dittrich et al., 1991
). This protein shares 20% homology with the integral membrane protein FhuB involved with the ferric-hydroxamate siderophore uptake system in E. coli. It is possible that the orfA product is involved in catecholate siderophore transport and may be coordinately regulated with catecholate biosynthesis.
It is clear that csbC transcription is negatively regulated by iron. The transcription of a csbC::luxAB fusion is negatively affected by E. coli Fur (introduced on pMH15) and E. coli Fur binds to the iron-boxes in the orfAcsbC intergenic region. An A. vinelandii Fur homologue exists, but we have been unable to obtain this product to use in these binding assays. The csbC iron-box has a good degree of homology with the 19 bp Fur binding consensus sequence (de Lorenzo et al., 1987 ) and is somewhat palindromic (Fig. 8a
). The orfA iron-box, on the other hand, has a lower homology with the 19 bp consensus sequence (Fig. 8a
). In a new interpretation of the iron-box (Escolar et al., 1999
), it has been suggested that the consensus is comprised of at least three 6 bp repeats (Fig. 8b
). The thymines present in the AT-AT motif are involved in binding to the repressor (Dalet et al., 1999
). In this analysis, the csbC iron-box has three contiguous repeats with at least an AT--T motif. The orfA iron-box has weaker homology, with only two contiguous repeats with an AT--T motif (Fig. 8b
). These iron-boxes should have different affinities for Fur binding. Indeed, two shifts in the mobility of the orfAcsbC intergenic region were observed with the addition of Fur-Mn2+ (Fig. 4a
). The highest affinity observed was like that of the iucA iron-box of E. coli, which suggests that csbC transcription should be tightly controlled by iron availability, if the only regulatory feature was Fur. However, csbC transcription continues at iron concentrations greater than 3 µM but less than 10 µM. At 3 µM iron, azotobactin synthesis is repressed (Page & von Tigerstrom, 1988
), indicating that an active Fur complex exists in the cytoplasm for repression of siderophore synthesis.
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However, the binding of the presumed Sox protein to Box 1 cannot be considered equivalent to its binding to the fpr Sox-box. The GCAY motif of Box 1 is located at the -10 region of the csbC promoter (Fig. 3). A protein binding in this region could be a class II activator (Ishihama, 1992
). The best example of such an activator is the MerR protein, which controls the mercury-resistance locus of Tn501 (Summers, 1992
). This protein, which is related to the superoxide stress regulator SoxR (Nunoshiba, 1996
), acts as a repressor until activated by mercuric ions. A conformational change results in underwinding of the DNA at the MerR target, allowing RNA polymerase to initiate transcription (Ansari et al., 1995
; Rhodius & Busby, 1998
). Such a model strongly suggests that the protein binding to the csbC Box 1 may act as a repressor, until activated or removed by secondary factors reporting oxidative stress in the cell.
Yannone & Burgess (1998) have shown that the Sox protein of A. vinelandii has a much larger molecular mass and is not serologically cross-reactive with E. coli SoxS. As well, our results show that the binding of the putative Sox protein of A. vinelandii is constitutive, rather than inducible like the E. coli SoxS protein (Demple, 1996 ). Recently it was shown (Regnström et al., 1999
) that the A. vinelandii protein that binds to the fpr Sox-box is the E1 subunit of pyruvate dehydrogenase (PDHE1). This protein has previously unrecognized DNA-binding activity and specifically binds FdI, so may be sensitive to the redox status of the cell. However, it remains to be shown that PDHE1 modulates transcription of the fpr gene. Our future studies will be directed towards understanding the control of the csbC promoter of A. vinelandii by native Fur and the native Sox protein.
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ACKNOWLEDGEMENTS |
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Received 18 October 1999;
revised 8 March 2000;
accepted 13 March 2000.