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. Author manuscript; available in PMC: 2016 Jun 2.
Published in final edited form as: Microb Pathog. 2009 Jan 6;46(3):166–170. doi: 10.1016/j.micpath.2008.12.003

Transcript analysis of nrrF, a Fur repressed sRNA of Neisseria gonorrhoeae

Thomas F Ducey a,b,*,1, Lydgia Jackson a,b, Joshua Orvis a,b, David W Dyer a,b
PMCID: PMC4890603  NIHMSID: NIHMS789225  PMID: 19162160

Abstract

Like most microorganisms, Neisseria gonorrhoeae alters gene expression in response to iron availability. The ferric uptake regulator Fur has been shown to be involved in controlling this response, but the extent of this involvement remains unknown. It is known that in addition to working directly to repress gene expression, Fur may also work indirectly by controlling additional regulatory elements. Using in silico analysis, we identified a putative small RNA (sRNA) homolog of the meningococcal nrrF locus, and demonstrate that this sRNA is iron-repressible, suggesting that this is the gonococcal analog of the rhyB locus in Escherichia coli. Quantitative real-time RT-PCR analysis indicates that this transcript may also be temporally regulated. Transcript analysis identified the 5′ start of the transcript, using a single reaction, fluorescent-based, primer extension assay. This protocol allows for the rapid identification of transcriptional start sites of RNA transcripts, and could be used for high-throughput transcript mapping.

Keywords: Small RNA, nrrF, Fluorescent primer extension

1. Introduction

For almost all organisms, iron (Fe) is an element essential for life, playing a prominent role in a variety of metabolic pathways. Iron serves as a cofactor in a number of proteins, such as catalases, cytochromes, peroxidases, the oxygen transporting proteins hemoglobin and myoglobin, and ribonucleotide reductase [1]. Paradoxically, despite its importance, iron is a difficult nutrient to manage, and given the biological conditions (aqueous, neutral pH, oxygenated), ferrous iron (Fe2+) quickly oxidizes to the ferric state (Fe3+) [2]. Ferric ions are extremely insoluble (Ksp ≈ 10–37 M) and toxic, being responsible for driving the Fenton reaction that results in free radical production, which in turn causes lipid peroxidation, DNA damage and protein degradation [3]. To counter this toxicity, and keep iron soluble, mammals sequester iron in a number of proteins intracellularly (hemoproteins, ferritin) and extracellularly (lactoferrin, transferrin) [1]. In addition to managing Fe successfully for the host, this sequestration results in a non-specific suppression of microbial growth, known as “nutritional immunity” as free Fe concentrations (approximately 10−18 M) are far below that necessary to support microbial growth, which typically requires Fe concentrations of 10−6 M or greater [4].

To counter this nutritional immunity, pathogens such as Neisseria gonorrhoeae have evolved specific strategies to acquire iron in the host. This obligate human pathogen expresses several receptors capable of binding and removing Fe from human hemoglobin (HmbR), hemoglobin–haptoglobin complexes (HpuAB), lactoferrin (LbpAB) and transferrin (TbpAB) [5]. The gonococcus also can use exogenously-produced enterobactin (a siderophore) via the FetA receptor; presumably, this is important for allowing the organism to metabolize catecholate siderophores found in mixed microbial environments such as the female urogenital tract [6]. Expression of these receptors is Fe-repressible, as the genes encoding these proteins are transcriptionally regulated by the ferric uptake regulator (Fur). Fur, with Fe as a cofactor, dimerizes and binds to specific DNA regulatory elements known as Fur boxes [7–9]. Fur boxes have been predicted in the promoters of fetA, hmbR, fbpABC, hpuAB, lbpAB and tbpAB [10]. There also are accounts of Fur serving as an activator [11,12], and other regulators within the Fur superfamily are involved in manganese, nickel, and zinc homeostasis [13]. We have reported that the gonococcal iron regulon is controlled by what appears to be a regulatory cascade, with Fur serving as a primary regulator [14]. In Escherichia coli, RyhB, a small RNA (sRNA) has been shown to repress a number of genes by binding to their mRNA in the presence of the RNA chaperone Hfq [15]. These sRNA:mRNA hybrids are then quickly targeted for RNase degradation [16]. In E. coli, rhyB is repressed under iron-replete conditions [15]. Small RNAs behaving in a similar fashion have been identified in Pseudomonas aeruginosa, Vibrio cholerae, and Neisseria meningitidis [17]. Here we report the transcript analysis of the Fe associated sRNA nrrF, originally identified in N. meningitidis [17]. We identified the gene for this sRNA using a bioinformatics approach similar to Wilderman et al. [18], and we demonstrate nrrF repression by Fe. We hypothesize that NrrF participates in the gonococcal Fe response similarly to the hfq and rhyB loci in E. coli. Quantitative real-time RT-PCR data suggest that NrrF also is temporally regulated. We also report the fluorescent-based primer extension mapping of the 5′ end of nrrF and the determination of its transcriptional start.

2. Results

2.1. In silico identification of a Fur-regulated small RNA in N. gonorrhoeae

Based on the analysis of a number of sRNAs of E. coli [19,20], in particular the Fur-regulated sRNA rhyB [15], Wilderman et al. developed an approach to identify Fur-regulated sRNAs in P. aeruginosa [18]. This approach resulted in the identification of two Furregulated sRNAs in P. aeruginosa, prrF1 and prrF2 [18]. We adopted a similar bioinformatics approach to identify Fur-regulated sRNA genes in N. gonorrhoeae. This in silico screening resulted in the identification of one region containing the aforementioned characteristics. This region has a predicted intergenic Fur box and a Rho-independent terminator sequence, separated by a gap of no more than 200 bp, and contains a string of at least three terminal T nucleotides (U in RNA). This region was clustered ≈200 bp downstream of NGO2002 and ≈300 bp upstream of NGO2004 (Fig. 1A). Further analysis of this region identified a strong σ70 promoter, with placement of the putative Fur box in the classical position between the −35 and −10 promoter regions (Fig.1B). From promoter to poly-T tail, the region spans 195 bp, from complemented nucleotides 1,975,968 to 1,976,163 of the annotated FA1090 gonococcal genome. In addition, mFOLD prediction of this RNA species (Fig. 1C) suggests a secondary structure similar to ryhB of E. coli [15]. The absence of start codons and the presence of multiple stop codons throughout the reading frames of this region indicate that this gene does not encode a protein product. This region likewise shares 94% identity with nrrF, a previously identified Fur-regulated sRNA in N. meningitidis [17].

Fig. 1.

Fig. 1

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N. gonorrhoeae nrrF. (A) Map of nrrF. (B) Sequence of nrrF and promoter. The −35 and −10 regions of the promoter are marked. Predicted Fur box is indicated by the overhead line. Transcript start as determined by FPE (see Fig. 2) is identified with an overhead asterisk (*) and shading, stemloop is indicated by shading. qRT-PCR primer binding sites are underlined and labeled. (C) mFOLD prediction of nrrF.

2.2. 5′ Transcript mapping of nrrF

To confirm the location of the putative promoter, we used a single reaction, the fluorescent primer extension (FPE) reaction. FPE of cDNA generated from the nrrF transcript mapped the 5′ end to complemented base pair 1,976,123, a cytosine, of the gonococcal genome; seven bases from the end of the predicted −10 site of the sRNA promoter (Figs. 1B and 2). Comparison of FPE of cDNA generated from RNA harvested from iron-replete conditions (Fig. 2A) resulted in identically sized FPE of cDNA generated from RNA harvested from iron-deplete conditions (Fig. 2B), but at a lower fluorescent intensity (3.5-fold reduction). These results are consistent with the iron-repressible nature of this transcript (see below).

Fig. 2.

Fig. 2

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nrrF primer extension. Fragment analysis of fluorescent primer extension. The 125 bp peak is 6-FAM fluorescein labeled primer extension products of cDNA generated from RNA harvested from N. gonorrhoeae grown in iron-replete (A) or irondeplete (B) conditions. Other labeled peaks correspond to GeneScan 500-LIZ ladder.

2.3. Iron-regulated expression of nrrF

The presence of a predicted Fur box in the promoter of nrrF suggested that this transcript would be repressed under iron-replete conditions. Fur titration assays (FurTA) performed using E. coli expressing gonococcal Fur, confirm that this Fur box is capable of binding the gonococcal Fur protein [21]. In these analyses, a 897 bp fragment corresponding to complemented bases 1,975,608–1,976,505 of the gonococcal genome was found to titrate Fur [21]. This region includes the entirety of nrrF and its sole predicted Fur box [21]. RT-PCR analysis of nrrF transcripts isolated from gonococcal cells grown to mid-log under iron-deplete and iron-replete conditions confirmed the iron-repressible nature of this transcript. Appreciable differences in expression levels were seen, with lower levels of the nrrF transcript being seen under iron-replete conditions, with porI transcript, previously identified as a constitutively expressed gene [14], showing no appreciable differences (Fig. 3A). Expression levels of nrrF were accurately quantitated by qRT-PCR, through the course of a grown curve (Fig. 3B). NrrF levels increased approximately 170-fold after 3 h of iron starvation, but subsided at 4 h, suggesting that nrrF may be regulated by temporal signals in addition to iron availability.

Fig. 3.

Fig. 3

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Expression of nrrF under iron-deplete and iron-replete conditions. (A) rtPCR analysis of nrrF and porI transcript levels. (B) qRT-PCR analysis of nrrF transcript levels. Each column corresponds to the mean and SD of three independent assays.

3. Discussion

The identification of the gonococcal nrrF expands to six the number of regulatory elements we hypothesize to be involved in the gonococcal response to iron availability. In addition to Fur, our previous study identified two iron repressed AraC-like regulators (NGO0025 and NGO2115), one putative phage-like repressor (NGO1013), and a MerR-like regulator (NG0602) [14]. Additional work by Jackson et al. has identified an additional eight regulators that appear to be members of the Fur regulon, bringing the total to 14 distinct regulatory genes involved in the gonococcal response to iron availability [21]. In addition, microarray data suggest that the MerR-like regulator may function independently in the gonococcal iron response regulon; this situation may be analogous to the multiple Fur homologs found in Staphylococcus aureus and Bacillus subtilis [22–24]. The addition of NrrF to this cascade may further explain some of the gonococcal responses to iron availability which cannot be directly attributed to Fur. Further work is needed to extensively map the regulon boundaries of each of these gonococcal regulators.

Like ryhB of E. coli, the transcription of nrrF is iron-repressible, and has a similar secondary structure as predicted by mFOLD. RyhB has been shown to be involved in the regulation of two genes in the tricarboxylic acid cycle, two ferritin genes and sodB [15]. In the case of sodB, RyhB functions by coordinating with Hfq, an RNA chaperone, to target message for RNase E degradation in low iron conditions [25]. When insertionally inactivated, a similar pair of sRNAs in P. aeruginosa, PrrF1 and PrrF2, results in an increase in the expression of several genes involved in iron storage, defense against oxidative stress and intermediary metabolism [18]. The gonococcus has homologs for both Hfq (NGO0326) and RNase E (NGO1785), suggesting that in conjunction with these loci, NrrF may enhance degradation of mRNA encoding for iron containing proteins during times of iron depletion.

We also have utilized a single reaction, fluorescent primer extension protocol that is ideally suited to capillary electrophoresis systems such as the ABI 3730xl. This protocol is an improvement in cost and labor intensiveness over standard primer extension assays which relyon multiple reactions per promoter and the incorporation of radionucleotides [26], and could be adapted easily as a high-throughput strategy for genome-wide identification of transcriptional start sites. Such data would be an extremely valuable adjunct for a variety of purposes, including genome annotation.

4. Materials and methods

4.1. Strains, plasmids, and growth conditions

N. gonorrhoeae FA1090 was stored as −80 °C freezer stocks GC (Difco) media supplemented with 20% glycerol. N. gonorrhoeae was routinely plated on GCB agar (Becton Dickinson) supplemented with 2% IsoVitaleX (Becton Dickinson). Incubation of organisms on solid media was carried out at 37 °C in a 5% CO2 atmosphere. For iron-regulation analyses, broth cultures of N. gonorrhoeae FA1090 were grown at 37 °C, in the Chelex-treated (Bio-Rad), chemically defined medium (CDM) of Morse and Bartenstein [27] as modified by Dyer et al. [28]. CDM was either supplemented with 100 µM FeNO3 (CDM-100), 10 µM FeNO3 (CDM-10) or not (CDM-0).

A perl script was written to examine the potential presence of sRNA in N. gonorrhoeae FA1090 using criteria established by Wilderman et al. [18]. This script searched intergenic space for stemloop structures containing 7–12 complementary bases, with a loop of 5–7 bases, followed by at least three T nucleotides (U in RNA) [18]. mFOLD was used to examine the folding of the putative sRNA [29]. The sRNA region was examined for a σ70 promoter by utilizing the sequence alignment kernel (SAK) [30].

4.3. RNA extraction, reverse transcriptase PCR (rtPCR) and quantitative real-time PCR (qRT-PCR)

RNA extraction from N. gonorrhoeae FA1090 was performed as previously described [14]. Briefly, an aliquot of bacterial culture was immediately added to an ice-cold phenol/ethanol (EtOH) (95:5) mixture at a 1:10 (vol/vol) ratio. Cells were pelleted by centrifugation at 5000 × g for 10 min, resuspended in TE (10 mM Tris–HCl, 1 mM EDTA) pH 8.0, lysed by the addition of a 1/10th volume of 10% sodium dodecyl sulfate (SDS), and incubated at 64 °C for 2 min. A 1/10th volume of 1 M sodium acetate, pH 5.2, was added and RNA was extracted by the addition of an equal volume of prewarmed water-saturated phenol followed by extraction with an equal volume of chloroform. Bulk RNA was then precipitated using a standard EtOH precipitation. Prior to rtPCR and qRT-PCR, 1 µg or 2 µg of RNA respectively, was treated with 5 U of RNase-free DNase according to manufacturer specifications (Invitrogen). For rtPCR, after heat inactivation at 75 °C for 15 min, the DNase-treated RNA was used directly in a reverse transcription reaction at 42 °C for 60 min using 200 U Superscript III reverse transcriptase, 40 U RNase inhibitor, and 1 ng of gene specific primer in a 20 µl volume according to manufacturer specifications (Invitrogen). For rtPCR, a 1/10th volume of the reverse transcription reaction was used in a standard Taq PCR reaction (Roche) with 100 ng of both forward and reverse primers. Complete removal of contaminating DNA from the RNA preparations was ensured by performing parallel reverse transcription reactions sans Superscript III. DNA products were analyzed by 2% agarose gel electrophoresis with Tris-acetate-EDTA (TAE) buffer. For qRT-PCR reactions, the DNase-treated RNA was utilized as previously described [14]. RNA was isolated from FA1090 grown in iron-deplete and iron-replete conditions as previously described [14], at 1, 2, 3 and 4 h time points. First strand cDNA synthesis was generated from 2 µg total RNA with random hexamers according to the TaqMan® Reverse Transcription Reagents Kit (PE Applied Biosystems). A negative reverse transcription reaction (minus the reverse transcriptase) was included for each sample to detect the presence of genomic DNA. Primers are listed in Table 1. Real-time PCR amplification was performed on the ABI PRISM™ 7500 Sequence Detection System (PE Applied Biosystems) using SYBR® Green PCR Master Mix (PE Applied Biosystems). Relative gene expression was quantified using the comparative threshold cycle 2−ΔΔCT method (PE Applied Biosystems User Bulletin #2) with porl (a constitutively expressed major outer membrane porin) as the endogenous reference. Validation experiments for all experimental primer pairs with the endogenous control primers were done to ensure that the efficiency of the target amplification and the efficiency of the endogenous control were equal (PE Applied Biosystems User Bulletin #2). Each gene was assayed in duplicate and the mean CT value from three separate growth curves was used for comparisons.

Table 1.

Oligonucleotides used in this study.

Oligonucleotide Sequence Reference
rt-porI-fwd TGTCCGTACGCTACGATTCTC Ducey et al. [14]
rt-porI-rev AGCCAACGTGGTAAGATTCGC Ducey et al. [14]
sRNA_up TCCGTTCCGAACCATTAAA This study
sRNA_lo GCGTTTCGGTTTTGAGTATCT This study
sRNA_lo_mod 6-FAM-GCGTTTCGGTTTTGAGTATCT This study
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4.4. Fluorescent primer extension (FPE)

Determination of the transcriptional start of the gonococcal nrrF gene was performed in a manner similar to that of Fekete et al. [31]. Thirty micrograms of both iron-deplete and iron-replete RNA were treated with 30 U RNase-free DNase (Invitrogen), ethanol precipitated and resuspended at a concentration of 1 µg/µl. Ten micrograms of each RNA were mixed with 40 µM of a 5′-labeled 6-fluorescein phosphoramidite (6-FAM) primer (Table 1), denatured at 90 °C, and cooled to 30 °C over 30 min. Then 2000 U of Superscript III, 20 U of RNase inhibitor, and 200 µM of each dNTP (Roche) were added to the annealed RNA/primer mixtures in an rtPCR reaction according to manufacturer specifications (Invitrogen). The reactions were run at 42 °C for 120 min. Unincorporated dNTPs and primers were removed using a Sephadex G50 (Sigma) packed spin column (Millipore). The purified DNA was EtOH precipitated, and subsequently resuspended in 10 µl ABI Hi-Di. To this suspension GeneScan 500-LIZ ladder was added, and the mix was electrophoresed on an ABI 3730xl according to manufacturer specifications for genotyping (Applied Biosystems). After capillary electrophoresis, a standard curve of the GeneScan 500-LIZ ladder was generated using the GeneMapper software (Applied Biosystems), which was used to calculate the length of the 6-FAM labeled cDNA products.

4.5. Nucleotide sequence accession number

The annotated sequence of nrrF is available at GenBank under accession number EU366283.

Acknowledgments

Joshua Orvis is currently located at the Institute for Genome Sciences, Baltimore, MD. We thank B. Todd Campbell and Jeff Novak for a critical review of this manuscript. This study was supported in part by a grant from the University of Oklahoma Health Sciences Center, College of Medicine Graduate Student Association.

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