Abstract
The Escherichia coli endoribonuclease LS was originally identified as a potential antagonist of bacteriophage T4. When the T4 dmd gene is defective, RNase LS cleaves T4 mRNAs and antagonizes T4 reproduction. This RNase also plays an important role in RNA metabolisms in E. coli. rnlA is an essential gene for RNase LS activity, but the transcriptional regulation of this gene remains to be elucidated. An Fe-S cluster protein, IscR, acts as a transcription factor and controls the expression of genes that are necessary for Fe-S cluster biogenesis. Here, we report that overexpression of IscR suppressed RNase LS activity, causing the loss of antagonist activity against phage T4. This suppressive effect did not require the ligation of Fe-S cluster into IscR. β-Galactosidase reporter assays showed that transcription from an rnlA promoter increased in iscR-deleted cells compared to wild-type cells, and gel-mobility shift assays revealed specific binding of IscR to the rnlA promoter region. RT–PCR analysis demonstrated that endogenous rnlA mRNA was reduced by overexpression of IscR and increased by deletion of iscR. From these results, we conclude that IscR negatively regulates transcription of rnlA and represses RNase LS activity.
AN mRNA degradation activity in Escherichia coli is rigidly controlled under various cellular conditions. The degradation of E. coli mRNA is usually initiated by endonucleolytic cleavage (Kushner 2002) and a major endonuclease, RNase E, triggers the degradation of most mRNAs (Bernstein et al. 2004). E. coli has additional endonucleases such as RNase I, III, G, P, and Z that can cleave mRNAs, although their spectrum of action is limited (Bardwell et al. 1989; Cannistraro and Kennell 1991; Alifano et al. 1994; Umitsuki et al. 2001; Perwez and Kushner 2006). We discovered another endonuclese, RNase LS, as a potential antagonist of T4 phage. When a T4 dmd mutant infects E. coli cells, RNase LS activity remarkably increases after early and middle genes of T4 phage are expressed (KAI et al. 1998; Ueno and Yonesaki 2001) and causes rapid degradation of most mRNAs at late stages, leading to a growth defect of T4 phage (Kai et al. 1996). In vitro analysis confirmed that the dmd encodes an inhibitor of RNase LS (Otsuka et al. 2007). In addition to T4 mRNA decay, RNase LS also plays a role in the metabolism of many E. coli mRNAs and 23S rRNA (Otsuka and Yonesaki 2005). Especially, RNase LS degrades an adenylate cyclase (cyaA) mRNA, resulting in the accumulation of cAMP and a transcription factor Crp (Iwamoto et al. 2008). rnlA is essential for RNase LS activity and encodes an endonuclease activity (Otsuka and Yonesaki 2005; Otsuka et al. 2007). Recently, we found that rnlB (formerly yfjO), which is located downstream of rnlA, has a role in the regulation of RNase LS activity (M. Koga, and T. Yonesaki, unpublished results). rnlA and rnlB are reasonably assumed to form an operon, but the transcriptional regulation of these genes has not been assessed.
We isolated five E. coli mutants defective in RNase LS activity and on which a T4 dmd mutant was able to grow (Otsuka et al. 2003). Two of these (std-2 and -5) have mutation(s) in rnlA. Interestingly, the deletion of iscR, which encodes transcription factor to repress some genes depending on the cellular Fe-S level (Schwartz et al. 2001), completely eliminated the ability of other three (std-1, -3, and -4) mutation(s) to support the growth of a T4 dmd mutant, indicating a requirement of iscR for their effects. Although the relationship between these mutations and iscR is still uncertain, iscR could be one of the key players in the regulation of RNase LS activity.
The isc operon, consisting of iscRSUA-hscBA-fdx, encodes proteins essential for Fe-S cluster formation (Tokumoto and Takahashi 2001). IscR was originally discovered by its role in the negative control of this operon (Schwartz et al. 2001). Transcriptome analysis identified 40 genes in 20 predicted operons, which were regulated by IscR under aerobic and anaerobic conditions (Giel et al. 2006). IscR itself is an Fe-S cluster protein and an Fe-S cluster in IscR is necessary for transcriptional repression of the isc operon (Schwartz et al. 2001). Recently, Nesbit et al. (2009) reported that the Fe-S cluster is dispensable for IscR regulation of some of its target promoters. Whether or not an Fe-S cluster is necessary for IscR-mediated transcriptional regulation appears to depend on the type of IscR-binding sequence (Giel et al. 2006; Nesbit et al. 2009).
In this study, we found that overexpression of IscR suppressed RNase LS activity and alleviated the growth defect of a T4 dmd mutant. Ligation of the Fe-S cluster with IscR was not required for suppression of RNase LS activity. In addition, we characterized transcription from the promoters for rnlA and rnlB, and IscR was found to negatively regulate transcription from an rnlA promoter but not from an rnlB promoter.
MATERIALS AND METHODS
Phages and bacterial strains:
Wild-type bacteriophage T4 is T4D. The amSF16 mutant contains an amber mutation in the dmd gene (Kai et al. 1996; Ueno and Yonesaki 2001). T4 GT7 phage was used for transduction (Wilson et al. 1979). The E. coli strains MH1 (sup0 hsdR ΔlacX74 rpsL) and MG1655 were used as wild types. Strain MH1 ΔiscR∷kan was constructed by GT7-mediated transduction of a kanamycin-resistance marker from strain JW2515 (Baba et al. 2006) provided by National BioResource Project (NIG, Japan). E. coli strain MH1 ΔrnlAB has a deletion of rnlA and rnlB (M. Koga and T. Yonesaki, unpublished results). MG1655 Δisc has a deletion of the isc operon from iscR to iscX (formerly ORF3) (Tokumoto and Takahashi 2001).
Plasmids:
To clone iscR, a DNA fragment was amplified by PCR using the primers 5′-GAGATCCACGCCCTGCTTCTTACATTC and 5′-CGGATCCTGATCAGTACCTTCAAGTTC, and DNA from E. coli W3110 strain as a template. The amplified fragment was digested with NruI and EcoRI and blunted. The resulting fragment (1.3 kb) containing the only ORF of iscR, its promoter, and the Shine-Dalgarno sequence was ligated into pBluescript II KS+ previously digested with EcoRV to construct pBS477NE, where iscR was oriented in the opposite direction as the lac promoter. The 531-bp DNA fragment containing the Shine-Dalgarno sequence and the iscR ORF was obtained by digestion of pBS477NE with EcoRI and SmaI and cloned into pRKNSE (Nakamura et al. 1999) to construct pRKSmE, where iscR was oriented in the same direction as the lac promoter. pRKC92AR, pRKC98AR, and pRKC104AR encoded alanine-substituted IscR at Cys92, Cys98, and Cys104, respectively. These mutants were generated by PCR using mutagenic oligonucleotides and pRKSmE as a template.
To construct pQ-ORF2-95 for expression of His-tagged IscR, a DNA fragment containing iscR was PCR amplified with MG1655 DNA as a template and the primers 5′-GGATCCAGACTGACATCTAAAGGGCG and 5′-GTCGACTATTAAGCGCGTAACTTAACGTC, digested with BamHI and SalI, and ligated into pQE30 (Qiagen).
A DNA fragment containing the N-terminal 39 amino acids of RnlA and 67 bp upstream of rnlA was amplified by PCR with W3110 DNA as a template. The antisense downstream primer was 5′-GGAATTCCTGGCATAGGACCAATTG and the sense upstream primer was 5′-GGAATTCCATACACTTCAG. The amplified fragment was digested with EcoRI and ligated into pRS552 (Simons et al. 1987) to construct an rnlA–lacZ fusion gene, generating pRSrnlA67. pPN–lacZ containing 200 bp upstream of the initiation codon and the N-terminal 50 amino acids of RnlA fused to β-galactosidase was constructed in a similar manner. pRSrnlB-long was constructed as follows. A DNA fragment was amplified by PCR with W3110 DNA as a template and the primers 5′-GGAATTCCATATCTCACTGGAGCCA and 5′-CGGATCCCCTGAGACGTTAATTCCGG. The resulting fragment containing 854 bp upstream of rnlB and the N-terminal 11 amino acids of RnlB was digested with EcoRI and BamHI and ligated into pRS552.
Burst size assay:
MH1 cells with or without different plasmids were grown to 5 × 108 cells/ml in LB medium and infected with wild-type T4 or a dmd mutant at a multiplicity of 0.1 at 30°. At 8 min, the cells were diluted 10−4-fold with fresh LB medium and further incubated for 70 min. After cells were lysed with chloroform, the total number of progeny phages was counted by plating. The burst size is the ratio of the number of progeny to the number of input phage and infection of wild-type cells with wild-type T4 gives a burst size of 80–110. The relative burst size is expressed as a percentage of wild-type T4 for wild-type cells harboring no plasmid or a vector plasmid. Each value is the mean of at least three independent experiments with a standard deviation.
RNA purification, Northern blot, primer extension, and RT–PCR analysis:
Isolation of total RNA and northern blot analysis were carried out as described previously (Kai et al. 1996). For primer extension analysis to identify transcription start sites of rnlA and rnlB, we used primers 5′-GGAATTCCTGGCATAGGACCAATTG for rnlA and 5′-CGGATCCCCTGAGACGTTAATTCCGG for rnlB, respectively. For RT–PCR analysis, reverse transcription was performed by incubation at 42° for 45 min with 2 μg of total RNA, 100 units of ReverTra Ace reverse transcriptase (TOYOBO), 1 mm of dNTPs, and 5 pmol of gene-specific primers in 20 μl of reverse transcription buffer. Primers, rnlA-dw N134 (5′-CTGGCATAGGACCAATT), ompA-dw (5′-TTGGATTTAGTGTCTGCACG), lpp dw (5′-TTATCTTGCGGTATTTAGTAG), or b2531-up (5′-TTTATCGCCGCCCTGGCAGCC) were used for reverse transcription of rnlA, ompA, lpp, or iscR, respectively. PCR amplification was performed with 0.2 mm dNTPs, 2 μl of reverse transcription mixture for rnlA, 1 μl for ompA and lpp, or 1.5 μl for iscR, 10 pmol of sense and antisense primers, and 0.3 units of KOD Dash (TOYOBO) in 25 μl of PCR buffer. A thermal cycle of 95° for 30 s, 51° for 15 s, and 72° for 30 s was repeated 20 times for rnlA, 16 times for lpp, or 12 times for ompA. A thermal cycle of 95° for 15 s, 60° for 15 s, and 72° for 30 s was repeated 20 times for iscR. Primers for PCR were 5′-ATGTTTCTATGGGATCCAGG and rnlA-dw N134 for rnlA, 5′-ATGAAAAAGACAGCTATCGC and ompA-dw for ompA, 5′-TTATCTTGCGGTATTTAGTAG and lpp-dw for lpp, 5′-GTCTGCGTAAAAATGGTCTG and b2531-up for iscR, respectively. The products from each reaction were separated through a 5% polyacrylamide gel.
Western blot analysis:
Proteins were separated on a 15% polyacrylamide gel containing SDS and electroblotted onto Immuno-Blot PVDF membrane (Bio-Rad). The membranes were probed with a rabbit antibody against IscR and successively with horseradish peroxidase-conjugated donkey anti-rabbit IgG (GE Biosciences). The blot was developed with Immobilon Western Chemiluminescent HRP Substrate (Millipore).
β-Galactosidase assay:
Twenty microliters of bacterial culture was mixed with 80 μl of permeabilization buffer (100 mm Na2HPO4, 20 mm KCl, 2 mm MgSO4, 0.8 mg/ml CTAB, 0.4 mg/ml sodium deoxycholate, and 5.4 μl/ml β-mercaptoethanol) to lyse cells, and 600 μl of substrate solution (60 mm Na2HPO4, 40 mm NaH2PO4, 1 mg/ml ONPG, 2.7 μl/ml β-mercaptoethanol) was added and incubated at room temperature for 5–15 min. After stopping the reaction by adding 700 μl of 1m Na2CO3, absorbance was measured at OD420nm. The Miller unit is calculated using the following formula: 1 Miller unit = 1,000A420/(bacterial density at A600)(ml of bacterial culture)(min of reaction time).
Purification of IscR:
MH1 cells harboring pQ-ORF2-95 were grown at 37° to a density of 3 × 108 cells/ml in 100 ml of LB containing 50 μg/ml of ampicillin. After addition of 0.2 mm IPTG, cells were incubated for 2 hr and harvested by centrifugation. All the following procedures were performed below 4°. Cells were suspended with 5 ml of lysis buffer (50 mm NaH2PO4, 300 mm NaCl, 10 mm imidazole, 10% (v/v) glycerol, and 1 mm PMSF, pH 8.0) and disrupted with an ultrasonic generator, UD-201 (Tomy Seiko). After centrifugation at 30,000 × g for 30 min, the cleared lysate was loaded onto a Ni-beads column (Ni-NTA Superflow, Qiagen) according to the manufacturer's instruction. The fraction containing His-tagged IscR was eluted with 250 mm imidazole and dialyzed against TEGX buffer [20 mm Tris·Cl (pH 8.0), 0.5 mm EDTA (pH 8.0), 10% (v/v) glycerol, 0.2% Triton-X 100] containing 0.1 m NaCl. After the sample was loaded onto an Affi-Gel Blue column (Bio-Rad), the column was washed with TEGX buffer containing 0.3 m NaCl and His-tagged IscR was eluted with TEGX buffer containing 1 m NaCl. The purified protein was precipitated with ammonium sulfate, dialyzed against TEGX buffer containing 0.1 m NaCl and 50% (v/v) glycerol, and stored at −20°.
Gel mobility shift assay:
A DNA probe (222 bp) containing the rnlA promoters was prepared by PCR with pBRMpNO carrying from yfjM to rnlB as a template and the primers 5′-[32P]CTGGCATAGGACCAATT and 5′-GGAATTCCGGAGTGCCCCCTATTC. A DNA probe (448 bp) containing the rnlB promoter was prepared by PCR with pBRMpNO as a template and the primers 5′-[32P] CGGATCCCCTGAGACGTTAATTCCGG and 5′-CCGCATCTCCACGTGACTGC. For each binding assay, 4 × 103 cpm of gel-purified DNA probe and the indicated amount of His-tagged IscR were added to the binding reaction mixture (15 μl) consisting of 20 mm Tris-HCl (pH 8.0), 50 mm KCl, 4 mm MgCl2, 0.5 mm EDTA, 0.02 mg/ml BSA, 5 mm DTT, 10% (v/v) glycerol, and 200 ng of poly-[dI-dC] (Roche). After incubating at room temperature for 20 min, half of the reaction mixture was loaded on an 8% polyacrylamide gel in 0.25 × TBE and electrophoresed at 4° for 2–2.5 hr at 150 V. The gel was analyzed by Bio-Image Analyzer (Fuji BAS-1800).
RESULTS
Overexpression of IscR partially restores the growth of a T4 dmd mutant:
To investigate the effect of iscR on the growth of a T4 dmd mutant, wild-type T4 or a dmd mutant was plated to measure the efficiency of plating (Figure 1A). A T4 dmd mutant grew normally on MH1 ΔrnlAB cells lacking RNase LS, but its efficiency of plating decreased to <10−4 on parental MH1 cells or MH1 ΔiscR cells harboring a vector plasmid, pBluescript II SK− (pBSSK−). Deletion of iscR has no effect on the growth of wild-type T4. Introduction of iscR cloned in a plasmid, pBS477NE, allowed T4 dmd mutants to form plaques on MH1 or MH1 ΔiscR cells with an efficiency of plating of nearly 1, as on MH1 ΔrnlAB cells. Because the high-copy plasmid-encoded iscR but not the genome-encoded iscR restored the growth of a T4 dmd mutant, this effect could be caused by overproduction of IscR. Indeed, overproduction of IscR was clearly demonstrated by Western blot; more than 10-fold IscR was accumulated in cells harboring pBS477NE than in cells harboring pBSSK− (Figure 1C).
Effect of IscR on RNase LS activity. (A) A solution containing wild-type T4 or dmd mutant phages was serially diluted in 10-fold steps, and 2-μl samples containing the number of phages indicated on the left were spotted onto a plate seeded with MH1 or its derivative cells carrying a plasmid as shown below the figure. Photographs were taken after overnight incubation at 30°. (B) MH1 cells with pBSSK− or pBS477NE were infected with wild-type T4 or a dmd mutant and newly synthesized proteins were pulse labeled for 3 min at the times indicated above the figure, as described previously (Ueno and Yonesaki 2001). Labeled proteins from an equal portion of infected cells were separated by 12.5% SDS–PAGE and analyzed by Bio-Image Analyzer (Fuji BAS-1800). The numbers in the right margin show representative late genes encoding the proteins. The 23* indicates a processed product encoded by gene 23. (C) MH1 cells with pBSSK− or pBS477NE were grown to 5 × 108 cells/ml in LB containing 50 μg/ml of ampicillin and total proteins from an equal portion of cells were analyzed by Western blot with an antibody against IscR. (D) MH1 cells with pBSSK− or pBS477NE grown in LB at 30° to a mid-log phase were infected with wild-type T4 or a dmd mutant and total RNAs were extracted at 25 and 35 min after infection. Two micrograms of each RNA was analyzed by Northern blot with a 32P-labeled DNA probe for soc as described previously (Kai and Yonesaki 2002).
We also examined the effect of overexpressed IscR on progeny production by measuring a number of progeny per infected cell (burst size). A T4 dmd mutant grew very poorly on MH1 cells, with a burst size only 2.3% of that of wild-type phages (Table 1). The burst size of a T4 dmd mutant on MH1 cells harboring pBS477NE was reproducibly higher (21%) than on MH1 cells. Thus, suppression by overexpression of IscR was remarkable, though partial, as with the std-1, -3, and std-4 mutations (Otsuka et al. 2003). The burst size of the wild-type phage in MH1 cells harboring pBS477NE was reduced to ∼86%, compared to parental MH1 cells.
Effect of iscR cloned in a multi-copy plasmid on the growth of a T4 dmd mutant
Because deprivation of intracellular iron is known to induce the expression of IscR, we measured the burst size of a T4 dmd mutant on MH1 cells in the presence of 0.25 mm 2, 2′-dipyridyl, a membrane-permeant ferrous iron chelator that causes deprivation of intracellular iron (supporting information, Table S1). Treatment with this reagent partially restored the growth of a T4 dmd mutant, although it reduced the growth ability of wild-type T4. This result suggested that an increase of intracellular IscR counteracts RNase LS activity.
Next, we investigated the effect of IscR on gene expression in a T4 dmd mutant. Gene expression at each stage after T4 infection was examined by pulse labeling newly synthesized proteins (Figure 1B). Consistent with previous reports, protein synthesis by a T4 dmd mutant at late times (23 and 40 min) was impaired in MH1 cells carrying pBSSK−. In contrast, protein synthesis in MH1 cells harboring pBS477NE infected with a dmd mutant was almost as high as in MH1 cells infected with wild-type T4.
Suppression of the growth defect of a T4 dmd mutant should accompany the stabilization of late-gene mRNAs. To confirm this expectation, the steady-state level of T4 late-gene soc mRNA was examined by Northern blot, because its degradation has been extensively characterized (Kai and Yonesaki 2002). As shown in Figure 1D, the amount of soc mRNA at late stages (25 and 35 min) after T4 dmd infection to MH1 cells with a vector alone was hardly detected because of rapid degradation. However, when a T4 dmd mutant infected MH1 cells with pBS477NE, soc mRNA was present as abundantly as in MH1 cells infected with wild-type T4. Our primer extension analysis also confirmed the loss of RNase LS-mediated specific cleavages in MH1 cells with pBS477NE (Figure S1). All of the above results clearly indicated that overexpression of IscR decreased the RNase LS activity to allow the growth of a T4 dmd mutant.
Ligation of the Fe-S cluster with IscR is not required for inhibition of RNase LS activity:
We examined whether ligation of the IscR with Fe-S cluster is necessary for the suppression of the growth defect of a T4 dmd mutant. Cys92, Cys98, and Cys104 are predicted Fe-S cluster ligands in IscR and indeed, IscR-C92A with an alanine substitution did not contain an Fe-S cluster, when it was purified under anaerobic condition (Nesbit et al. 2009). Cells harboring a plasmid expressing IscR with individual alanine substitutions of these amino acids were examined for supporting the growth of a T4 dmd mutant (Table 2). pRKSmE expressing wild-type IscR raised the burst size of a T4 dmd mutant from 1.1 without plasmid to 28.3 with plasmid. Each of these substitutions (pRKC92AR, pRKC98AR, or pRKC104AR) resulted in a burst size similar to that for wild-type IscR. In addition, soc mRNA in infection of MH1 cells harboring these mutant plasmids with a T4 dmd mutant was accumulated as abundantly as that in cells harboring pRKSmE (Figure 2). These results demonstrated that ligation of the IscR with Fe-S cluster had almost no effect on IscR-mediated repression of RNase LS activity.
Effect of an Fe-S cluster in IscR on RNase LS activity. MH1 cells with the pRKNSE vector, pRKSmE, pRKC92AR, pRKC98AR, or pRKC104AR grown in LB medium at 30° to a mid-log phase were infected with a T4 dmd mutant, total RNAs were extracted at the indicated times after infection, and soc mRNA was analyzed by Northern blot as described previously (Kai and Yonesaki 2002).
Effect of alanine substitutions in IscR on the growth of a T4 dmd mutant
Genes downstream of iscR in isc operon are not involved in inhibition of RNase LS activity:
iscR is part of the isc operon and negatively regulates its own expression (Schwartz et al. 2001). Repression of downstream genes in this operon by IscR might be responsible for inhibition of RNase LS activity. To investigate this possibility, we measured progeny production of a T4 dmd mutant on MG1655 and MG1655 Δisc. The deletion of isc operon did not alleviate the growth defect of a T4 dmd mutant (Table S2). This result suggested that components of iscS to iscX were not involved in the inhibition of RNase LS activity.
Transcription start sites for rnlA and rnlB were identified by primer extension analysis:
We tested whether IscR can directly inhibit RNase LS activity in vitro using S30 extract from MH1 cells, but IscR could not inhibit RNA cleavages by RNase LS (Figure S2). Next, we investigated another possibility that IscR regulates RNase LS activity via transcriptional control of rnlA and/or rnlB. To identify promoters experimentally, we mapped the 5′ ends of rnlA and rnlB transcripts. Unfortunately, we could not detect endogenous rnlA and rnlB transcripts by primer extension or Northern blot analysis because their expression was very weak. To circumvent this problem, we constructed two plasmid derivatives of pBR322: pPN-lacZ containing 200 bp upstream of the translation start site of rnlA and 150 bp encoding the N-terminal 50 amino acids of RnlA, and pRSrnlB-long containing 854 bp upstream of the translation start site of rnlB and 33 bp encoding the N-terminal 11 amino acids of RnlB. MH1 cells transformed with either of these plasmids were incubated until log phase and then total RNA was extracted. Primer extension analysis identified four 5′ termini specific to rnlA transcripts 65, 46, 32, and 24 bp upstream of the initiation codon (Figure 3A). In addition to a strong signal for the last site, this site solely matches a transcription site from the promoter predicted by the GENETYX program (Figure 7A). Therefore, rnlA mRNA would be mainly transcribed from 24 bp upstream of the rnlA initiation codon. This idea was confirmed by β-galactosidase reporter assays in the next section. On the other hand, the other three sites might correspond to unexpected reverse transcriptase stop sites or RNA processing sites in transcripts originating from a weak plasmid promoter. Two 5′ termini specific to rnlB transcripts were also detected 123 and 124 bp upstream of the initiation codon (Figure 3B), which are within the rnlA ORF. Two starts depending on a single promoter are often observed in E. coli (for example, refer to Otsuka et al. 2003). Although a promoter corresponding to these sites was not predicted by GENETYX, another program, BPROM (http://linux1.softberry.com/berry.phtml?topic=bprom&group=programs&subgroup=gfindb), identified a promoter matching these sites as transcription start sites (Figure 7B). Indeed, gene expression driven by a sequence containing this region was confirmed in the next section.
Identification of rnlA and rnlB transcription start sites. (A) Total RNAs were extracted from MH1 cells with pPN–lacZ grown in LB medium at 30° when the OD600 reached 0.7. Ten micrograms of RNA was used for primer extension analysis as described in materials and methods. (B) Total RNA was extracted from MH1 cells harboring pRSrnlB-long (rightmost lane) when the OD600 reached 0.65 and was analyzed using primer extension analysis. A set of sequence ladders for rnlA or rnlB was obtained by dideoxy sequencing method with the same primer and run in parallel in each figure. Arrows indicate bands detected by primer extension.
IscR represses transcription from rnlA promoter but not from rnlB promoter:
To investigate whether IscR regulates transcription from the rnlA and rnlB promoters, we examined the effect of an iscR deletion on the expression of β-galactosidase from pRSrnlA67, from which the expression of rnlA–lacZ translational fusion gene depended on 67 bp of sequence upstream of rnlA, or pRSrnlB-long (Figure 4). First, a plasmid containing no promoter for lacZ resulted in a low level of β-galactosidase activity (background value of 75). On the other hand, β-galactosidase activity expressed from the rnlA and rnlB promoters was significantly higher than background, indicating that both inserted DNAs provided promoter activity. Second, deletion of iscR led to three- to fourfold increase of β-galactosidase activity driven by the rnlA promoter at any cell growth stage. In contrast, deletion of iscR had no effect on the activity driven by the rnlB promoter. Third, β-galactosidase activity driven by the rnlA promoter increased with cell growth in both wild-type and iscR-deleted cells, but the activity driven by the rnlB promoter was nearly constant. Interestingly, β-galactosidase activity driven by the rnlB promoter was considerably higher than that driven by the rnlA promoter at any cell growth stage; the former activity was more than eightfold the latter even in the absence of iscR. This result indicates that transcription activity from the rnlA promoter is much weaker than from the rnlB promoter, so that RnlB would be synthesized more vigorously than RnlA in wild-type cells. Putting it all together, we conclude that the rnlA and rnlB promoters are regulated independently and that IscR represses transcription from the rnlA promoter (refer to Figure 7A).
β-Galactosidase reporter assay with rnlA or rnlB promoter. MH1 or MH1 ΔiscR cells with pRSrnlA67 (A) or pRSrnlB-long (B) were grown in LB medium at 30° and β-galactosidase activities were measured as described in materials and methods, when the OD600 reached the value indicated in the figure. The β-galactosidase activity is shown as Miller units. Each value is given after subtracting the background value of 75, which was obtained for cells harboring pRS552, and shows the mean ± SD from two or three independent experiments.
IscR can bind to rnlA promoter:
Since the above results suggested that IscR specifically binds to the rnlA promoter, we performed gel mobility shift assays with different concentrations of purified His-tagged IscR and 32P-labeled DNA probes. The DNA probe for rnlA contained a region from −99 to +117, and the DNA probe for rnlB from −410 to +33. As shown in Figure 5, a shifted rnlA DNA probe was apparent in the presence of 50 nm IscR, although 200 nm IscR did not significantly shift the rnlB DNA probe.
Binding of His-tagged IscR to rnlA promoter region. His-tagged IscR at increasing concentrations from 0 to 200 nm was incubated at room temperature for 20 min with a 32P-labeled DNA probe (4 × 103 cpm) containing the rnlA promoters or the rnlB promoter. The mixtures were separated through an 8% polyacrylamide gel in 0.25 × TBE at 4°. F and C indicate a free probe and a DNA–protein complex, respectively.
IscR represses transcription from chromosomal rnlA:
Finally, we confirmed that IscR represses transcription of rnlA in the chromosome. The amount of endogenous rnlA mRNA in MH1 cells harboring pBSSK− or pBS477NE was measured by RT–PCR (Figure 6A). Simultaneously, lpp and ompA mRNAs were measured as loading controls and iscR mRNA was also measured to confirm its overexpression. As expected, MH1 cells harboring pBS477NE overexpressed iscR mRNA by approximately threefold (bottom panel) and instead underexpressed rnlA mRNA by approximately twofold (lane 4), compared to MH1 cells with pBSSK− (lane 3). On the other hand, the amount of endogenous rnlA mRNA in MH1 ΔiscR cells was approximately twofold more than that in MH1 cells (Figure 6B). Finally, we observed that MH1 cells under oxidative stress overproduced iscR mRNA by approximately threefold and simultaneously underexpressed rnlA mRNA by ∼1.5-fold (Figure 6C).
Negative correlation between the levels of rnlA mRNA and iscR mRNA in vivo. (A) MH1 cells (lane 1), MH1 ΔrnlAB cells (lane 2), and MH1 cells with pBSSK− (lane 3) or pBS477NE (lane 4) were grown to mid-log growth phase in LB medium and total RNAs were extracted. RT–PCR analyses for rnlA, ompA, lpp, and iscR mRNAs were performed as described in materials and methods. Various amounts of pBRMpNO carrying sequence from yfjM to rnlB were used as a template to demonstrate a semiquantitative profile of PCR conditions; lane 5, 2 pg; lane 6, 4 pg; lane 7, 8 pg; and lane 8, 16 pg. An asterisk indicates a band of nonspecific product. Lane 9 shows size markers. (B) MH1 or MH1 ΔiscR cells were grown to mid-log growth phase in LB medium and total RNAs were analyzed for rnlA and iscR mRNAs by RT–PCR as described above. (C) MH1 cells were grown to mid-log growth phase in M9C medium and treated with or without 1 mm of H2O2 for 10 min. Total RNAs were analyzed by RT–PCR for rnlA and iscR mRNAs as described above.
DISCUSSION
In this study, we demonstrated that overexpression of IscR repressed RNase LS activity and allowed the growth of a T4 dmd mutant (Figure 1). The β-galactosidase reporter assay in Figure 4 strongly suggested that IscR represses transcription from an rnlA promoter. Furthermore, His-tagged IscR bound to DNA containing the rnlA promoter (Figure 5). Finally, rnlA mRNA was reduced by overexpression of IscR and increased by deletion of iscR in vivo (Figure 6). Taken together, we conclude that IscR represses the transcription of rnlA via its binding to the promoter region and thus reduces RNase LS activity. Analysis using IscR mutants containing an amino acid substitution at the predicted Fe-S ligands demonstrated no effect on the reduction of RNase LS activity or the growth of a T4 dmd mutant (Figure 2 and Table 2). Therefore, IscR appears able to repress rnlA transcription regardless of the presence of an Fe-S cluster.
There are two types of IscR-binding sites: Type 1, consisting of the 25-bp ATASYYGACTRWWWYAGTCRRSTAT (R, purine; Y, pyrimidine; S, G or C; and W, A or T) and type 2, consisting of the 26-bp AWARCCCYTSNGTTTGMNGKKKTKWA (N, any; K, T or G; and M, A or C) (Giel et al. 2006). Because IscR regulation of promoters containing type 2 sites appears not to require the ligation of an Fe-S cluster, we searched the sequence around the rnlA promoter for a sequence homologous to type 2 sites and found a sequence with 65% (17/26 bp) homology to the type 2 consensus (Figure 7A), which also partly matches “AxxxCCxxAxxxxxxxTAxGGxxxT” suggested for IscR-binding motif (Nesbit et al. 2009). These features suggest that IscR binds to this sequence for transcriptional repression.
Nucleotide sequence in the rnlA and rnlB promoter region. (A) The −35 and −10 sequences corresponding to an rnlA promoter are underlined. “IC” and asterisks show the initiation codon and the transcription start site, respectively. The predicted IscR-binding type 2 site is boxed. The numbers above the sequence show nucleotide positions from the first nucleotide of the initiation codon. (B) The −35 and −10 sequences corresponding to an rnlB promoter are underlined.
In β-galactosidase reporter assays, we found several interesting features in the regulation of rnlA and rnlB expression (Figure 4). First, these genes can be regulated independently. We identified promoter specific for rnlB within the ORF of rnlA. Because there is a transcription terminator-like sequence downstream of rnlB but no terminator upstream of the rnlB promoter, rnlB can be transcribed in two different modes, one as a polycistronic mRNA transcribed from the rnlA promoter and another as a monocistronic mRNA transcribed from its own promoter. Second, transcription activity from the rnlB promoter was much higher than from the rnlA promoter. High rnlB expression seems to be important for cell viability because our unpublished data suggest that RnlA in the absence of RnlB induces cell death (M. Koga and T. Yonesaki, unpublished results). Finally, transcription from rnlA promoter increases from mid to late log phase, suggesting its dependence on cell growth stage. Because this increase does not require IscR, other transcription factors may function in this regulation. Because transcription promoted by σ38 is gradually activated starting in late log phase (Gruber and Gross 2003), we examined the effect of σ38 on the transcriptional activation of rnlA. However, this activation was still observed for a strain lacking rpoS encoding σ38 (K. Miki and T. Yonesaki, unpublished results). Nonaka et al. (2006) reported that rnlA has a promoter regulated by σ32, which controls heat-shock response and that this promoter is located downstream of the rnlA promoter. However, cells were cultivated at a low temperature (30°) and a 5′ end corresponding to the σ32-regulated promoter was not detected by primer extension analysis in this study. In this connection, RNase LS activity appears very weak at 42° in comparison to that at 30° (Kai et al. 1996) so that the effect of σ32 on transcription of rnlA remains puzzling.
Because expression of IscR is induced under oxidative stress or iron deprivation, RNase LS activity would be repressed under these conditions. At present, it is unknown whether repression of RNase LS activity is necessary for adaptation or cell survival under these stresses. Our previous data showed that RNase LS plays a role in the metabolism of many mRNAs and of 23S rRNA under normal growth condition (Otsuka and Yonesaki 2005; Iwamoto et al. 2008). It might be important for cells adjusting to these stresses to inactivate RNase LS activity and stabilize RNase LS target mRNAs or rRNA.
Acknowledgments
We cordially thank John W. Drake at the National Institute of Environmental Health Sciences for invaluable help with the manuscript. We thank the staff of the Radioisotope Research Center at Toyonaka, Osaka University for facilitating our research, because all of our experiments using radioisotopes were carried out at the center. This work was supported in part by a grant from the program Grants-in-Aid for Scientific Research from the Ministry of Education, Culture, Sports, Science and Technology of Japan.
Footnotes
Supporting information is available online at http://www.genetics.org/cgi/content/full/genetics.110.114462/DC1.
Communicating editor: S. Gottesman
- Received January 19, 2010.
- Accepted April 23, 2010.
- Copyright © 2010 by the Genetics Society of America