Reverse transcriptase-PCR differential display analysis of meningococcal transcripts during infection of human cells: Up-regulation of priA and its role in intracellular replication
© Talà et al; licensee BioMed Central Ltd. 2008
Received: 16 February 2008
Accepted: 29 July 2008
Published: 29 July 2008
In vitro studies with cell line infection models are beginning to disclose the strategies that Neisseria meningitidis uses to survive and multiply inside the environment of the infected host cell. The goal of this study was to identify novel virulence determinants that are involved in this process using an in vitro infection system.
By using reverse transcriptase-PCR differential display we have identified a set of meningococcal genes significantly up-regulated during residence of the bacteria in infected HeLa cells including genes involved in L-glutamate transport (gltT operon), citrate metabolism (gltA), disulfide bond formation (dsbC), two-partner secretion (hrpA-hrpB), capsulation (lipA), and DNA replication/repair (priA). The role of PriA, a protein that in Escherichia coli plays a central role in replication restart of collapsed or arrested DNA replication forks, has been investigated. priA inactivation resulted in a number of growth phenotypes that were fully complemented by supplying a functional copy of priA. The priA-defective mutant exhibited reduced viability during late logarithmic growth phase. This defect was more severe when it was incubated under oxygen-limiting conditions using nitrite as terminal electron acceptors in anaerobic respiration. When compared to wild type it was more sensitive to hydrogen peroxide and the nitric oxide generator sodium nitroprusside. The priA-defective strain was not affected in its ability to invade HeLa cells, but, noticeably, exhibited severely impaired intracellular replication and, at variance with wild type and complemented strains, it co-localized with lysosomal associated membrane protein 1.
In conclusion, our study i.) demonstrates the efficacy of the experimental strategy that we describe for discovering novel virulence determinants of N. meningitidis and ii.) provides evidence for a role of priA in preventing both oxidative and nitrosative injury, and in intracellular meningococcal replication.
Neisseria meningitidis (meningococcus) is a transitory colonizer of the human nasopharynx that sporadically provokes life-threatening disease. This microorganism has to interact with cellular barriers for its life cycle . After crossing the nasopharyngeal mucosa, meningococci occasionally spread into the blood stream before moving across the blood-brain barrier causing fatal sepsis and meningitis in otherwise healthy individuals [2–5].
The early stages of an infection with N. meningitidis are governed by specific interactions between the pathogen and the epithelial tissues and are quite well known. Indeed, this microorganism has evolved a diverse array of surface structures subjected to phase- and antigenic-variation, which promote adherence and entry into human cells, although it is still unclear whether cell invasion is important in human infections. Initial adherence of encapsulated bacteria requires type IV pili, fine hair-like structures protruding from the bacteria surface . Then, interaction with host cells is achieved by several meningococcal surface adhesins (Opa and Opc) that have been extensively studied [1, 6]. In contrast, later stages of infection, including the intracellular location of the meningococci and their strategies for intracellular survival, are only poorly understood .
In vitro studies with cell line infection models are beginning to disclose the essential role of the metabolic adaptation of meningococci to the intracellular environment of the infected cell. The adaptive response includes the stimulation of the capsular biosynthetic genes leading to increased resistance to cationic antimicrobial peptides (CAMPs), important components of the host innate defense system against microbial infections , and the activation of the GdhR regulon whose members are involved in metabolism of the available host carbon sources [8, 9].
In this work by using reverse transcriptase-PCR differential display (RT-PCR-DD) we have identified a set of meningococcal genes up-regulated during residence of the bacteria in the intracellular host environment including genes involved in L-glutamate transport (gltT operon), citrate metabolism (gltA), disulfide bond formation (dsbC), two-partner secretion (hrpA-hrpB), capsulation (lipA), and DNA replication/repair (priA). PriA is a single-stranded DNA-dependent ATPase, and a 3' to 5' DNA translocase/helicase that was discovered originally because of its requirement in vitro for the conversion of bacteriophage phiX174 viral DNA to the duplex replicative form [10, 11]. In Escherichia coli this protein, at the crossroads of DNA replication and recombination, plays a central role in origin-independent, replication restart of collapsed or arrested DNA replication forks and is also involved in DNA recombination [12–14]. These activities rely on the ability of PriA to load replication forks at a D loop, an intermediate that forms during homologous recombination, double-strand break-repair, and stable DNA replication. We investigated the role of priA in the meningococcal infectious cycle using a human cell line infection model.
RNA differential display analysis of meningococcal gene expression in the intracellular host environment
In an attempt to identify meningococcal genes selectively up- or down-regulated in the intracellular environment of infected host cells we used a previously published RT-PCR-DD strategy that relies on the presence of highly and moderately repetitive transcribed DNA sequences in the meningococcal genome . Oligonucleotides designed on the basis of the DUS (DUS-IN and DUS-OUT) or the 26L, 27L nemis sequences (26L-IN, 26L-OUT, 27L-IN, 27L-OUT) were used as primers in reverse-transcriptase (RT) assays to prepare cDNAs from intracellular meningococci (strain B1940) recovered from saponin-lysed HeLa cells after 7 h of infection or control bacteria grown in DMEM without HeLa cells as previously described . After 7 h of infection bacterial recovery from infected cells reached the highest values . We decided to use HeLa cells because studies with these cells have contributed to our understanding of the molecular mechanisms underlying the infectious cycle of N. meningitidis [15–20]. The analysis of the meningococcal transcriptome during the early stages of an infection has been previously performed using HeLa cells .
The nucleotide sequence analysis demonstrated that the band a- and f-associated cDNA corresponded to genes that have been shown to be induced in the intracellular environment and have been also implicated in meningococcal pathogenesis (Fig. 1C). The band a-associated cDNA corresponded to NMB1964, a gene of the GdhR-regulated gltT operon coding for the L-glutamate ABC transporter that is critical for meningococcal adaptation in the low-sodium intracellular environment . The band f corresponded to NMB0082 coding for LipA, a protein required for proper translocation and surface expression of the lipidated (α2→8)-linked polysialic acid capsule polymer [7, 22]. The band g-associated cDNA sequence fell within NMB1780-NMB1779 (hrpB-hrpA) operon coding for a two-partner secretion (TPS) system that has been recently shown to contribute to adhesion of un-encapsulated bacteria to epithelial cells . The bands c-, l- and n-associated cDNAs corresponded to genes whose role in meningococcal pathogenesis has never been reported so far, including NMB0551 (band c sequence) encoding PriA, the linked NMB0549 and NMB0550 (band l sequence) coding, respectively, for a thiol-disulfide oxidoreductase (DsbC) and the ATP-binding protein of an unknown ABC-type transporter (YbjZ), and NMB0954 (band n sequence) encoding GltA, the putative meningococcal citrate synthase (Fig. 1C). Fig. 1C also shows the genes surrounding priA (NMB0551). Upstream from NMB0549 (ybjZ) a gene coding for an AcrA/AcrE family protein (NMB0548) is located; downstream to priA and in the opposite direction a gene coding for a protein of unknown function (NMB0552) and that for a putative transposase (NMB0553) map.
The role of priA in meningococcal pathogenesis
The role of PriA in meningococcal pathogenesis was explored in more detail using the HeLa infection model. It is noteworthy that over-expression of priA was also observed in an independent screening by limited transcriptional analysis (Fig. 1B) that was useful to demonstrate up-regulation of lipA in a previous work . This screening was performed using a partial Sau3AI-restricted genomic library from B1940. The library was screened by Southern blot using cDNA probes derived from intracellular bacteria after 8 h of infection of HeLa cells or control bacteria grown for 8 h in cell culture medium. The screening led to isolation of a plasmid harboring two Sau3AI fragments, 983 and 1123 bp-long (marked by asterisks in Fig. 1B and 1C), spanning almost the entire priA gene.
The goal of our study was to assess the reliability of RT-PCR-DD as a tool to identify genes with increased or decreased expression during meningococcal growth in infected cells. Although this analysis was clearly not exhaustive as the repeat sequences that we used to prime the RT-PCR-DD reactions were not randomly distributed in the chromosome, and not found in every gene , nevertheless it enabled us to identify three up-regulated genes/operons (gltT, lipA, hrpA-hrpB) with known roles in virulence (thus validating this approach) and three novel potential meningococcal virulence factors (Fig. 1). One of these, priA, was selected for extensive further validation (Fig. 2) and characterization.
In infected cells meningococci have to adapt their metabolism to the available host carbon and nitrogen sources and circumvent or subvert a number of host defense mechanisms including lysosomal killing, antimicrobial peptides and oxidative injury. Up-regulation of the gltT operon, coding for an L-glutamate ABC type transporter that is critical for meningococcal adaptation in the low-sodium intracellular environment , and of gltA, coding for the citrate synthase, catalyzing the first committed step of the citric acid cycle is part of a metabolic strategy to survive and grow in the intracellular environment. Indeed, in the intracellular milieu there is little available glucose, as glucose entering cells is rapidly phosphorylated to glucose-6-phosphate , a substrate that, as well as the other glycolytic intermediates, cannot be assimilated by meningococci. The best intracellular carbon sources are pyruvate and lactate or/and several amino acids such as L-glutamate that stimulate the citric acid cycle [26, 30].
Stimulation of L-glutamate uptake and respiratory metabolism is also useful to prevent oxidative injury, a major source of DNA damage, as this amino acid is the precursor of glutathione . In this context the up-regulation of thiol-disulfide oxidoreductase (DsbC)- and PriA-encoding genes (Figs. 1 and 2), and the impaired ability of the priA-defective mutant to replicate in infected HeLa cells (Figs. 8 and 9) may be relevant. PriA plays a central role in origin-independent replication restart of collapsed or arrested DNA replication forks [12–14]. There is evidence that, even under normal aerobic conditions, most, if not all, replication forks do not proceed from the origin of replication to the terminus without hitting a roadblock, in the form of a damaged DNA template, a nick in the template, a "frozen" protein-DNA complex, or local positive superhelicity, which have the potential to arrest or collapse the fork. Inability to reassemble the replisome and resume replication in a timely manner after repair of DNA damage can lead to chromosomal rearrangements and consequently, a loss in viability .
Oxidative injury is a major cause of DNA replication fork arrest . This accounts for the growth defect mostly due to reduced viability of the priA-defective meningococcal strain (Figs. 4 and 6), which was much more sensitive to oxidative and nitrosative injuries when compared to the parental strain (Fig. 7). Reduced viability was also observed in E. coli priA-defective mutants [24, 33]. A growth defect was also shown in the Neisseria gonorrhoeae priA-defective mutant . This strain was also defective in DNA repair and DNA transformation compared to the isogenic parental strain. However, based on staining with Live/Dead BacLight kit the authors concluded that the growth defect could not be attributable to reduced viability. The different biology of the meningococcal and gonococcal infection may account for the different phenotype of the meningococcal and gonococcal priA-defective mutants. Indeed, substantial differences in oxidative defenses between meningococci and gonococci have been reported. When compared to meningococci, gonococci that are usually associated with inflamed urogenital tissues and activated polymorphonuclear leukocytes, have much higher catalase and cytochrome c peroxidase activities in addition to a specific manganese (II) uptake system involved in resistance to superoxide radicals .
The growth defect of the priA-defective meningococcal strain was more severe in the presence of nitrite under either aerobic or oxygen-limiting growth conditions (Fig. 4). Under these conditions meningococci use nitrite as a terminal electron acceptor in anaerobic respiration. Nitrite reduction via nitric oxide to nitrous oxide is the partial denitrification pathway for this mode of growth. In pathogenic Neisseriae the pathway involves both a copper-containing nitrite reductase (AniA) and a single subunit nitric oxide reductase (NorB) [36, 37]. Nitrite reduction leads to the production of nitric oxide, a toxic molecule that exhibits synergistic activity in combination with reactive oxygen species  and that in Salmonella induces DNA replication arrest . The inability to restart nitric oxide-promoted arrested replication forks may account for reduced viability of the priA-defective mutant under oxygen-limiting conditions.
The relevance of nitrite reduction and defence mechanisms against nitric oxide injury in neisserial pathogenesis is the subject of investigation. Nitrite is present in the diet and is naturally formed in human blood and tissues due to the oxygenation of nitric oxide that is produced by various cell types as a signaling molecule and as a weapon against pathogens and tumor cells. It has been proposed that in microaerobic environments including the human nasopharynx and in the nitric oxide-enriched intracellular environment, meningococcal partial denitrification contributes with oxygen respiration as a route for electron transfer in respiration [37, 40]. Interestingly, inside HeLa cells at variance with wild type and complemented bacteria, priA-defective meningococci co-localized with LAMP1 (Fig. 9) that marks highly oxidative and nitrosative cell compartments . Based on this evidence, it is reasonable to assume that failure of the priA-defective mutant to replicate efficiently in HeLa cells may reflect the reduced ability to restart arrested replication forks.
In conclusion, in this study we, on one hand, demonstrate the efficacy of the experimental strategy that we describe, i.e. the analysis of the meningococcal gene expression, for disclosing the mechanisms that N. meningitidis uses to survive and multiply inside the environment of the human cell. On the other hand, we provide evidence that priA, whose expression increases in the intracellular environment, plays a key role in preventing both oxidative and nitrosative injuries, and in intracellular meningococcal replication.
Bacterial strains and growth conditions
N. meningitidis serogroup B strain B1940 was used in this study. The origin and genotype of this strain have been previously reported . Meningococci were cultured either aerobically in GC broth or agar with 1% Polyvitox, at 37°C in a 5% CO2 incubator or under oxygen-limiting conditions in GC agar containing 5 mM sodium nitrite with 1% Polyvitox, at 37°C in an anaerobic jar with an anaerobic atmosphere generator (GENbox anaer, Biomerieux) and an indicator (Anaer indicator, Biomerieux).
E. coli strain DH5α [F-Φ80d lacZΔM15 endA1 recA1 hsdR17 supE44 thi-1 λ- gyrA96 Δ(lacZYA-argF) U169] was used in cloning procedures. This strain was grown in Luria Bertani (LB) medium. To allow plasmid selection, the LB medium was supplemented with ampicillin (50 μg ml-1).
Cell culture and infection
For standard invasion and intracellular viability assays, HeLa cells (ATCC Number CCL-2) were used. Several experiments were also repeated with HEp2 (ATCC Number CCL-23) and Chang conjunctiva cells (ATTC Number CCL-20.2). It should be noted, however, that, as a result of a well known contamination event, HEp2 (thought to be derived from an epidermoid carcinoma of the larinx) and Chang conjunctiva (thought to be derived from normal conjunctiva) cells present HeLa markers and have been established via HeLa cells contamination, as stated by ATCC http://www.atcc.org. These cells were grown at 37°C in a 5% CO2 incubator in DMEM supplemented with inactivated 10% fetal bovine serum (FBS), 2 mM L-glutamine, penicillin (50 U ml-1) and streptomycin (50 μg ml-1).
N. meningitidis invasion assays were performed as previously described [8, 7]. In brief, HeLa (or HEp2 or Chang conjunctiva) cells were infected at a multiplicity of infection (MOI) of 50 for 1 h. To start the infection bacteria were centrifuged (60 × g) onto cells. Cells were washed twice with phosphate-buffered saline (PBS) to eliminate the majority of extracellular bacteria and exposed to gentamicin to kill remaining extracellular bacteria. Cells were then washed extensively with PBS to remove gentamicin and dead extracellular bacteria, and then lysed with saponin. Gentamicin treatment was performed at 100 μg ml-1, a concentration 10-fold above the minimal inhibitory concentration (MIC) for 30 min. When required, cells were re-incubated in a fresh culture medium for various time intervals after gentamicin treatment. For quantification, bacteria released by saponin from HeLa cells (intracellular) were plated and colony-forming units (CFU) were counted the day after.
DNA procedures and genetic manipulation
Oligonucleotides used in this study
The Neisseria-E. coli shuttle vectors pDEX and pACNL1 have been previously described [9, 45]. pACNL1 is a pACYC184 derivative harboring a 1480 bp Sau3AI fragment, spanning the meningococcal leuS-Ψdam region in the BamHI site. To construct pDEXpriA, the DNA corresponding to the central segment of the ORF NMB0551 was amplified using the primers NMB0551-1 and NMB0551-2, and the BamHI-restricted 851 bp PCR product was cloned into the BamHI site of pDEX. NMB0551 (priA) was inactivated in B1940 by single cross-over event using pDEΔpriA originating the strain B1940ΩpriA. Transformations were performed by using 0.1 to 1 μg of plasmid DNA. Transformants were selected on GC agar medium supplemented with erythromycin (7 μg ml-1). Successful gene inactivation was demonstrated by Southern blot hybridization. NMB0551-specific probe was obtained by 32P labeling of BamHI-restricted PCR fragment. The size of this fragment was 851 bp (primers NMB0551-1 and NMB0551-2). B1940ΩpriA was complemented by transformation with the integrative plasmid pACpriA. To construct this plasmid, the priA gene (with flanking regulatory elements) was amplified from strain B1940 using the primers NMB0551-3 and NMB0551-4 (Table 1). The XbaI/HindIII-restricted 2565 bp PCR product was cloned into the XbaI/HindIII sites of pACNL1. Transformants were selected on GC agar medium supplemented with chloramphenicol (5 μg ml-1).
Total RNAs were extracted from intracellular bacteria during the infection of HeLa cells or control bacteria grown in culture medium as described .
The procedure for limited transcriptional analysis has been previously detailed [9, 8]. Briefly, a partial Sau3AI-restricted genomic library from the serogroup B strain B1940 was constructed. Individual clones were digested and a Southern blot analysis was performed using cDNA probes derived from intracellular bacteria after 8 h of infection of HeLa cells or control bacteria grown for 8 h in cell culture medium. This procedure detects mRNA species present in the initial population at a frequency of at least 1 in 200.
The protocol for RT-PCR-DD analysis has been also reported . Briefly, total RNAs were extracted from intracellular bacteria during the infection of HeLa cells or control bacteria grown in cell culture medium, and were used as templates for first-strand cDNA synthesis in the presence of the primers DUS-IN, DUS-OUT, 26L-IN plus 27L-IN, 26L-OUT plus 27L-OUT, RS3-IN, RS3-OUT listed in Table 1. Then second-strand cDNAs synthesis was carried out using the corresponding oligonucleotides and a mixture of random hexamers as primers, and the PCR products were analyzed by polyacrylamide gel electrophoresis. The gel was stained by the silver staining method . The slices of gel containing the differentially expressed transcripts were cut with a sharp scalpel, and the DNA fragments were allowed to diffuse into 100 μl of sterile water at 37°C for 4 h under stirring. The eluted DNA was ethanol precipitated using glycogen as a carrier. Then, it was used as a template in a PCR with the corresponding primers. The positive amplicons were cloned in a pGEM easy vector (Promega) and sequenced.
RT-PCR slot blot analysis of meningococcal priA-specific transcripts during infection of HeLa cells was performed as previously described . To prepare gene-specific cDNA probes, the RNAs were subjected to reverse transcription using the oligonucleotides NMB0551-2 or 16Suniv-2 (loading control) as primers. The labeling procedure consisted of a PCR, where 2 μl of cDNA was used as template in a 50 μl mixtures containing 0.2 mM of each dCTP and dTTP, 2.5 μM of each dATP and dGTP, 0.12 μM [α-32P]ATP (3000 Ci mmol-1) and [α-32P]GTP (3000 Ci mmol-1), 0.2 μM forward NMB0551-1 or 16Suniv-1 primers, and 0.05 U μl-1 of Taq polymerase (Perkin Elmer S.p.A). The amplification reaction consisted of 20–25 cycles including 45 sec of denaturation at 94°C, 45 sec of annealing at 55°C and 45 sec of extension at 72°C. The number of cycles was critical to operate in the linear range of the PCR, and it was determined in preliminary experiments. The 32P-labeled cDNA probes were hybridized to different amounts (0.05 to 100 ng) of denatured NMB0551 (priA)- or 16S rRNA gene-specific DNA fragments generated by PCR with the corresponding primer pairs NMB0551-1/NMB0551-2, and 16Suniv-1/16Suniv-2, and fixed onto positively charged Hybond-N+ nylon membranes. The hybridization reactions were carried out in Church buffer  at 63°C. Semi-quantitative analysis was performed by directly counting the radioactivity bands by a PhosphoImager SI (Molecular Dynamics, Inc., Sunnyvale, CA).
Semi-quantitative analysis of the priA-specific transcript, normalized to 16S rRNA, was also performed by real-time RT-PCR. Total RNAs (1 μg) from either intracellular or control bacteria grown in cell culture medium were reverse-transcribed by using random hexamer (2.5 μM) with Superscript RT (Invitrogen). About 0.1–1% of each RT reaction was used to run real-time PCR on a SmartCycler System (Cepheid) with SYBR® Green JumpStart Taq ReadyMix (Sigma-Aldrich) and the primer pairs 16Suniv-1/16S-r (specific for 16S rRNA) and NMB0551-f/NMB0551-r (specific for priA). PCR products were 185 bp for 16Suniv-1/16S-r, and 143 bp for NMB0551-f/NMB0551-r. Real-time PCR samples were run in triplicate. The real-time PCR conditions were: 30 sec at 94°C, 30 sec at 55°C, 30 sec at 72°C for 35 cycles; detection of PCR products was performed at 83°C.
Bacteria viability assay
The viability of meningococcal strains was determined by using the Live/Dead BacLight bacterial viability kit (Molecular Probe). To this purpose, meningococci were grown to either middle (0.5 OD600 nm) or late (1.0 OD600 nm) logarithmic phase in 50 ml of GC medium with 1% Polyvitox as described above. Then 1 ml of bacterial suspension was collected by low-speed centrifugation. Meningococci were washed, re-suspended in 1 ml 0.9% NaCl and mixed with an equal volume of 2X working solution of Live/Dead BacLight containing a 1:1 mixture of SYTO9 and propidium iodide. After 15 min dark incubation, 5 μl of mounted specimens were viewed with a Nikon Optiphot-2 microscope with an episcopic-fluorescence attachment (EFD-3, Nikon).
Hydrogen peroxide and sodium nitroprusside sensitivity assays
B1940, B1940ΩpriA and B1940ΩpriA/priA+ were grown to middle logarithmic phase (0.5 OD600 nm corresponding to about 1 × 109 CFU). Then, 5 ml aliquots ("input" CFU = 5 × 109 CFU for each strains) were placed into 15-ml conical tubes. H2O2 was added to the tubes at final concentrations of 0, 0.5, or 1 mM, and tubes were incubated with shaking for 20 min at 37°C. Cultures were immediately centrifuged and pellets were re-suspended into 5 ml GC broth. These re-suspensions were serially diluted into GC broth and spotted onto GC agar. The plates were incubated at 37°C in a 5% CO2 incubator and the colonies were counted after 24 h of growth. For the sodium nitroprusside sensitivity assay, dilutions of freshly grown liquid cultures of N. meningitidis to middle logarithmic phase (0.5 OD600 nm corresponding to about 1 × 109 CFU) were immediately spread onto GC agar plates containing 1% Polyvitox and the nitric oxide generator. Plates were incubated in an atmosphere of 5% CO2 at 37°C.
Immunofluorescence analysis was performed as previously described to distinguish between extracellular and intracellular bacteria . In brief, after infection, cells were washed once with PBS, and fixed with 3% paraformaldehyde. For staining of extracellular bacteria, incubation with primary antibodies was carried out for 20 min at room temperature. After washes in PBS, cells were incubated with secondary antibodies for 20 min in the dark, at room temperature. Subsequently, cells were permeabilized with saponin, incubated with primary antibodies to stain bacteria or intracellular markers and then incubated with secondary antibodies. Rabbit polyclonal anti-N. meningitidis antibody was from ViroStat while monoclonal H4A3 anti-LAMP1 was obtained from the Developmental Studies Hybridoma Bank at the University of Iowa. Primary and secondary antibodies were used at a 1:500 dilution. Mounted coverslips were examined using a Nikon Optiphot-2 microscope with an episcopic-fluorescence attachment (EFD-3, Nikon). Image processing was carried out with Adobe Photoshop version 7.0.
Scanning electron microscopy
Meningococcal strains B1940 and B1940ΩpriA were grown to late (1.0 OD600 nm) logarithmic phase in 50 ml of GC medium with 1% Polyvitox as described above. Then 1 ml of bacterial suspension was collected by centrifugation. For SEM observations, meningococci were fixed with 1% glutaraldehyde, washed three times with distilled water by centrifugation, dehydrated in a graded alcohol series and critical-point dried. The sample was then mounted on Aluminum stubs, sputter-coated with gold and examined at an accelerating voltage of 20 kV with a Jeol 6060LV Scanning Electron microscope.
The authors are grateful to Miss Victoria Blake for English editing of the manuscript. This work was partially supported by grants from Italian MIUR to C. B. and P. A. (60%, COFIN 2004, COFIN 2006). The authors have no conflicting financial interests.
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