Regulation of neuraminidase expression in Streptococcus pneumoniae
© Gualdi et al.; licensee BioMed Central Ltd. 2012
Received: 13 February 2012
Accepted: 5 September 2012
Published: 11 September 2012
Sialic acid (N-acetylneuraminic acid; NeuNAc) is one of the most important carbohydrates for Streptococcus pneumoniae due of its role as a carbon and energy source, receptor for adhesion and invasion and molecular signal for promotion of biofilm formation, nasopharyngeal carriage and invasion of the lung.
In this work, NeuNAc and its metabolic derivative N-acetyl mannosamine (ManNAc) were used to analyze regulatory mechanisms of the neuraminidase locus expression. Genomic and metabolic comparison to Streptococcus mitis, Streptococcus oralis, Streptococcus gordonii and Streptococcus sanguinis elucidates the metabolic association of the two amino sugars to different parts of the locus coding for the two main pneumococcal neuraminidases and confirms the substrate specificity of the respective ABC transporters. Quantitative gene expression analysis shows repression of the locus by glucose and induction of all predicted transcriptional units by ManNAc and NeuNAc, each inducing with higher efficiency the operon encoding for the transporter with higher specificity for the respective amino sugar. Cytofluorimetric analysis demonstrated enhanced surface exposure of NanA on pneumococci grown in NeuNAc and ManNAc and an activity assay allowed to quantify approximately twelve times as much neuraminidase activity on induced cells as opposed to glucose grown cells.
The present data increase the understanding of metabolic regulation of the nanAB locus and indicate that experiments aimed at the elucidation of the relevance of neuraminidases in pneumococcal virulence should possibly not be carried out on bacteria grown in glucose containing media.
KeywordsSialic acid Metabolic regulation Carbon catabolite repression
Streptococcus pneumoniae is a common inhabitant of the upper respiratory tract and it is also a major human pathogen. The self-limited carriage episodes represent the most common interaction between pneumococci and the host. However, in some cases, such asymptomatic interaction can progress to invasive disease. Of the many factors influencing the interaction of the bacterium with the host, numerous extracellular glycosyl-hydrolases and carbohydrate transporters have been found to play significant roles. The sialidases or neuraminidases, which are able to cleave terminal sialic acid (neuraminic acid, NeuNAc) residues present in O-linked and N-linked glycans, have since long received special attention as virulence determinants[3, 4]. Direct interaction of the microbial sialidases with host glycoproteins resulting in exposure of additional attachment sites on host cells was the mechanisms most frequently found to be involved in virulence[5–7]. Recently such interaction was found to be directly involved in invasion[8, 9]. Despite the impact of sialidases in pneumococcal pathogenesis, metabolic implications have received less attention, including the utilisation of sialic acid as a carbon source on the glucose-free mucosal surfaces[10–16]. Sialic acid has recently been described by us and others to act as a molecular signal for pneumococci, resulting in increased carriage and translocation of bacteria to the lung[10, 14, 17].
Given the prominent role of sialidases in host-pathogen interaction, it is not surprising that pneumococci harbour three sialidases, two of which, NanA and NanB, are common to all pneumococci and the third, NanC, is present in only 51% of strains. Structural and functional analysis of the three enzymes indicated possible different roles. NanA is a first-line virulence factor for sialic acid removal, the trans-sialidase NanB is involved in the metabolic use of sialic acid, and NanC has a regulatory role, being able to produce and remove an intermediate metabolic compound which also acts as sialidase inhibitor[19, 20]. The conserved nanAB locus that comprises the genes between SPG1583 and SPG1601 in strain G54 (SP1674-94 in TIGR4) was identified as the cluster responsible for uptake and metabolism of sialic acid[16, 21–23]. In addition to the extracellular sialidases NanA and NanB, the regulon encodes two ABC transporters, one of which responsible for sialic acid and N-acetyl mannosamine uptake SPG1589-91 (satABC) and the other (SP1596-8) for uptake of N-acetyl mannosamine alone[14, 23]. In addition to the ABC transporters the locus encodes a PTS uptake system for glucosamine, and the remaining genes encode for enzymes involved in sialic acid metabolism. In vitro this operon was found to be the main cluster showing differential expression in pneumococcal opacity variants and was predicted to be composed of four predicted transcriptional units. During infection, the nanAB operon was found to be upregulated in pneumonia and meningitis compared to growth in blood[24, 25]. Much less information is available on the nanC operon, except for the analysis of the enzymatic function of the sialidase NanC and its recent implication as an alternative system for the uptake of sialic acid.
The present work aims at performing a functional analysis of the operon in order to gain further insight into the metabolic regulation of this locus.
The NanAB locus conservation in oral streptococci
List of gene annotation in the nanAB locus
S. pneumoniae TIGR4
S. pneumoniae G54
S. mitis B6
S. oralis Uo5
S. gordonii V288
S. sanguinis SK36
satA ABC transporter permease
satB ABC transporter permease
satC ABC transporter substrate-binding protein
PTS system, IIBC components
NanE, ManAc-6P 2-epimerase
ABC transporter permease
ABC transporter permease
ABC transporter substrate-binding protein
Acetyl xylan esterase
Neuraminidase locus induction in S. pneumoniae
Repression of the nanAB locus in the presence of glucose
According to the presence of three cre sites within the pneumococcal neuraminidase locus, we observed a biphasic growth curve when bacteria grew on glucose plus ManNAc or NeuNAc (Figure4A,B, open squares). To demonstrate that this phenotype was due to carbon catabolite repression, we investigated the transcriptional behaviour of the neuraminidase locus in the presence or absence of glucose in the medium. Growth conditions used were as follows: ManNAc with and without glucose (Figure4A, open triangles and open squares), NeuNAc with and without glucose (Figure4B, open triangles and open diamonds) and glucose as the sole carbon source as a reference condition (Figure4A and4B, closed circles). Growth curve data show that addition of glucose to both ManNAc and NeuNAc resulted in an initial growth on glucose as a preferred carbon source followed by a second slower growth phase, in which the amino sugars were metabolised. To assess glucose repression during growth on glucose gene expression analysis was carried out by sampling the bacteria at an OD590 of 0.05 (Figure4A,B, arrows). As shown in Figure4C, the over-expression of all genes of the nanAB locus occurred during growth on ManNAc or NeuNAc as the sole carbon sources (Figure4C, open and grey bars), while it was completely repressed in the presence of glucose (Figure4C, striped bars).
Regulation of neuraminidase A production and activity by ManNAc
Pneumococcal neuraminidases are the most studied surface located glycosyl-hydrolases due to their role in pathogenicity as factors involved in adhesion and invasion of S. pneumoniae to host cells[5, 6, 8, 9, 27, 28]. In addition, their role in the release of free sialic acid from oligosaccharides has been proposed as an important source of carbon and energy[13, 14, 29, 30]. More recently, the cleavage of sialic acid from O-glycans has been related to pathogenesis, by proposing sialic acid as a molecular signal to promote in vitro biofilm production and in vivo nasopharyngeal carriage and lung invasion by S. pneumoniae[10, 17]. In this context, the regulatory mechanisms of the neuraminidase locus expression are of importance. So far nearly all data on virulence and expression of the two loci containing neuraminidases has been carried out on the nanAB locus only, since the D39 reference strain does not carry the nanC locus. The main finding on expression of the nanAB locus reported its organisation in four predicted transcriptional units, of these the one harbouring NanA and the one encoding for the enzymes of the sialic acid metabolism were differentially expressed in transparent and opaque pneumococcal colony variants. Additionally the increased expression of this locus during infection[10, 24, 25], further underlines the importance of neuraminidases in the interaction of pneumococci with the host. It should be noted that most of the above work on pneumococcal virulence is done utilising strain D39, which is unable to ferment sialic acid due to a frame shift in the neuraminate lyase of the nanAB locus[23, 31], a fact which apparently does not influence regulation of the locus and virulence of the bacterium.
We have recently shown that the two ABC transporters of the nanAB locus, and also the sodium symporter of the nanC locus to a lesser extent, are not only involved in sialic acid uptake, but also in the transport of ManNAc, which represents the first metabolic intermediate in pneumococcal NeuNAc catabolism. In this work we focus our attention on the contribution of the nanAB locus, since deletion mutants for the nanC locus had been shown not to influence growth on ManNAc and NeuNAc during the first 18–24 hours of incubation, implying a limited or absent regulatory crosstalk between the two regulons[14, 23]. The two ABC transporters were shown to be able to support growth on amino sugars, with SPG1596-8 and SPG1589-91 being the main transporters for ManNAc and NeuNAc, respectively. In this work we have combined genomic information, gene expression and growth phenotypes to further clarify these data. When performing in silico analysis of the nanAB locus we observed the presence of part of the locus in related oral streptococci. Here we utilised this genomic information to strengthen the correlation between orthologous transporters and metabolic functions. S. sanguinis and S. gordonii, harbouring an operon including the orthologue of the SPG1596-8, were found to be able to efficiently metabolise ManNAc, but not NeuNAc. To the contrary S. mitis and S. oralis, which are much more closely related to pneumococci, harboured a locus, in addition to all the metabolic genes, also encoding for a neuraminidase and the orthologue of the satABC SPG1589-91 transporter. The finding that S. mitis can efficiently metabolise NeuNAc and ManNAc, confirm that the substrate specificity identified for the pneumococcal transporters is generally well conserved in orthologues of related species. Interestingly, all oral streptococci share the core part of metabolic enzymes of the operon, suggesting comparable capability to metabolise both NeuNAc and ManNAc. These observations match earlier data that described detectable levels of metabolism of NeuNAc in most oral streptococci, while sialidase activity could only be found in few species. Amongst the oral streptococci, pneumococci carry a composite locus, probably assembled from the gene pool of related species. The association of the SPG1594 oxidoreductase with ManNAc metabolism and of two small hypothetical proteins (SPG1586 and SPG1588) with NeuNAc metabolism remains unexplained, as all necessary enzymes for sialic acid metabolism appear to be already present. The PTS transporter, found to transport glucosamine, appears to be unique in pneumococci. The fact that glucosamine is the last metabolic intermediate in sialic acid catabolism may indicate a convenience for the bacterium in co-utilisation of GlcN and ManNAc, even if it is not clear where pneumococci should feed on GlcN, a rare sugar in the human nasopharynx, but of which on the contrary the pneumococcal cell wall is exceptionally rich.
When pneumococci grow on ManNAc and NeuNAc as the sole carbon sources, the generation time is much longer than on glucose or on the yeast-extract derived carbohydrates of the CAT medium, which is in accordance with previous data. Growth on ManNAc (Figure3B, Figure4A) shows a profile with a change in generation time. In the case of growth on glucose repression of the whole locus indicates sequential utilisation of sugars. This is less clear for the growth on yeast extract derived dextran and ManNAc, where only part of the locus is induced with the exception of the predicted central transcriptional unit encoding the principal ManNAc ABC transporter SPG1596-8. The data here presented thus do not rule out, that during growth on yeast derived sugars also ManNAc may be co-metabolised. The differential impact of regulation on the three operons is reminiscent of data on expression of this locus in transparent colony variants, where also the nanB and ManNAc-uptake operon is not involved in differential expression, while the other two transcripts are upregulated. The fact that both ManNAc and NeuNAc are able to efficiently induce the operon is in accordance with our finding that the SPG1583 regulator acts a positive regulator, as documented by absence of metabolism in its mutant and also by its annotation as a phosphor-sugar binding regulator. Since NeuNAc is imported by an ABC transporter, which does not phosphorylate during uptake, and is first hydrolysed to ManNAc before becoming phosphorylated (Figure1B), both amino sugars may equally originate the inducer of the positive regulator; probably ManNAc-phosphate.
The sequential utilization of carbon sources is generally regulated by carbon catabolite repression, and in bacteria it has been linked not only to metabolic use, but also to more general mechanisms involved in host-pathogen interactions[34, 35]. As in other Gram-positive bacteria, also in S. pneumoniae carbon catabolite repression involves the catabolite control protein A (CcpA) which regulates operons by binding to a specific operator sequence, named as catabolite-repressible element (cre site)[36–39]. Multiple cre sites were recently predicted upstream SPG1601, SPG1597 and SPG1593 in the nanAB locus[37, 38], and array analyses proved the role of CcpA in its regulation and interestingly relief of ccpA repression shows much more pronounced effects on the “NeuNAc-operon” (SPG1593-84) than on the “ManNAc operon” (SPG1599-4). The cre sites and CcpA-mediated regulation is in accordance with the transcriptional units described earlier. Our data here confirm that glucose completely represses the expression of all three predicted transcriptional units of the nanAB locus. The above gene expression data are also consistent with the neuraminidase activity assay on whole cells, which indicates twelve times more enzymatic activity in induced cells with respect to glucose grown cells. The repression of both neuraminidases and the intracellular enzymes for sialic acid metabolism had already been reported for a large number of viridians streptococci, which thus share with S. pneumoniae a strong effect of carbon catabolite repression on the loci responsible of NeuNAc metabolism.
In summary, the data obtained in our study confirmed and demonstrated that, (i) pneumococci carry a composite locus, in part shared by related species, which is predicted to metabolise both ManNAc and NeuNAc, (ii) pneumococci could use both ManNAc and NeuNAc as the sole carbon sources for growth, (iii) uptake of ManNAc and NeuNAc involved preferentially the SPG1596-8 and the satABC SPG1589-91ABC transporters, respectively, (iv) ManNAc and NeuNAc could induce the nanAB locus, which is subjected to carbon catabolite repression by glucose and (v) a quantitative neuraminidase activity assay allowed to tentatively quantify neuraminidases on the surface of pneumococci grown in amino sugars to numbers around 100–500 enzymes per cell. Interestingly, some growth conditions were found to mimic the transcriptional profile observed for pneumococcal transparent colony variants, suggesting a metabolic influences on pneumococcal phase variation. Still, the differential induction of the predicted transcriptional units by the two amino sugars, indicates that probably carbon catabolite repression and activation by the regulator act at different strength on the three transcriptional units. Finally as already shown in oral streptococci, the amount of NanA significantly increases and neuraminidase activity during growth on ManNAc or NeuNAc, indicating that experimental conditions based on mid log glucose-grown bacterial cells may be biased in estimating the actual contribution of neuraminidases to host-pathogen interaction.
Bacterial strains and culture media
Bacterial strains used in this work were S. pneumoniae strain G54 (serotype 19F) and its un-encapsulated derivative FP65, since the pneumococcal reference strain D39 has a frame shifted neuraminate lyase gene and TIGR4 did not grow efficiently in CAT medium. Most experiments are performed with the un-encapsulated FP69 as strains without are non virulent and no influence on sugar metabolism has been observed (data not shown). Oral streptococci where S. mitis NCTC12261 (kindly provided by Morgens Kilian) and S. gordonii V288 Challis. Bacteria were plated on Tryptic soy agar plates (TSB; Liofilchem Roseto degli Abruzzi, Italy) containing 3% v/v of horse blood. Stocks grown in TSB at 37°C to OD590 of 0.2 were supplemented with 20% glycerol and stored at −80°C. For fermentation assays and growth curves, bacteria were grown in CAT medium composed of bacto casitone 10 g/l (Becton Dickinson), bacto yeast extract 1 g/l (Becton Dickinson), tryptone 5 g/l (Oxoid Hampshire, UK) and sodium chloride 5 g/l. Just before use, CAT medium was supplemented with 3% w/v of K2HPO4 0.5 M, a carbon source and catalase 200 U/ml. The sugars were glucose (Sigma-Aldrich), N-Acetylneuraminic acid (NeuNAc, Carbosynth, Compton, UK) and N-Acetyl-D-mannosamine (ManNAc, Carbosynth, Compton, UK). Due to the presence of bacto-yeast extract (Beckton Dickinson), the carbohydrate non-supplemented CAT medium contained 0.16 g/l of total carbohydrate.
Mutants were constructed by direct transformation of S. pneumoniae with PCR generated recombinant DNA fragments. For deletion of the whole nanAB locus, primers NanA1 (TGTAGCCGTCATTTTATTGCTAC), NanA2 (TCCACTAGTTCTAGAGCGATTTTCTGCCTGATGTTGGTAT), NanA3 (ATCGCTCTTGAAGGGAATGCTATTTACACCATACTTCCT), and NanA4 (CAGCTTCGCCTTGCCGTAGGT) were used to amplify segments to allow the integration of the spectinomycin marker aad9 and the deletion of the whole nanAB locus (SPG1583 -SPG1600). For deletion of the SPG1583 regulator, primers DC_09 (TGTCTACGATAGCCGTTGAG), DC_10 (ATCAAACGGATCCCCAGCTTGAACCAGCATCATGGATGAAAATTG), DC_11 (ATATTTTACTGGATGAATTGTTTTAGAAAGCCGTCTTGGTCTGTC), and DC_12 (AATCGCTCGCTATTTTTTGC) were used to amplify segments to allow the substitution of the kanamycin maker aphIII with the whole nanAB locus, as previously described.
Comparative genomic analysis was performed using the ACT (Artemis Comparison Tool). Genbank files for sequence comparison were downloaded directly from the NCBI website. The S. pneumoniae genomes utilised were of strain TIGR4 and G54 (NC_003028 and NC_011072). The genomes used for comparison were from S. gordonii strain Challis (NC_009785), S. mitis strain B6 (NC_013853), S. oralis strain Uo5 (NC_015291), and S. sanguinis strain SK36 (NC_009009).
The method for evaluation sugar uptake and fermentation has been recently described. Briefly, bacteria grown on agar plates were resuspended to an OD590 = 0.6 in CAT medium and diluted 1:1 with CAT medium supplemented with K2HPO4,the appropriate sugar and catalase as reported above. After o.n. incubation, pH changes were visualised by addition of phenol red (0,1 mg/ml) (P4633 Sigma-Aldrich).
Growth curve and sample collection
In order to characterize the gene expression pattern in a specific point of the growth curve, we sampled bacteria during growth. Strains were grown on TSA plates at 37°C in a CO2 enriched atmosphere for 18 hours. Bacteria were then collected with a swab and resuspended at the OD590 of 0.2 in non-supplemented CAT medium. Bacterial samples were diluted 1:100 in CAT medium either without added sugar or with addition of either glucose, ManNAc, NeuNAc, glucose + ManNAc, or glucose + NeuNAc, all at 1 g/L. Bacterial growth curves were performed in 96-well plates in a thermostated spectrophotometer at 37°C. Plates were shaken gently for 10 seconds prior to each reading, and the optical density was read automatically in 10 min intervals at a wave length of 590 nm. Triplicate samples were collected from microwells for gene expression analysis and cytofluorimetry. For RNA extraction and retrotranscription, the samples were transferred to microtubus, centrifuged at 13000 rpm at 4°C for 1 min, and the pellet was conserved at −20°C. For flow-cytometry analysis, the samples were centrifuged at 8000 rpm at room temperature for 5 min and immediately analysed.
RNA extraction, retrotranscription and qPCR
RNA was extracted using the NucleoSpin RNA II kit (Macherey-Nagel) according to the manufacturer’s instructions, and the RNA samples were frozen in aliquots until use. cDNA synthesis was carried out using the Transcriptor First strand cDNA synthesis kit (Roche) according to the manufacturer’s instructions. Annealing was performed at 25°C for 10 min, extension at 37°C for 1 h, and finally inactivation at 70°C for 15 min. The qPCR was performed as previously described, by mixing 2 μl of cDNA template, 10 pmol of primers, and 2 μl of Light Cycler DNA-Master SYBR Green I (Roche). The reaction was carried out in a Light Cycler apparatus (Roche). Primer efficiency was verified by serial dilution of cDNA ranging from 102 to 106 target copies per reaction. Primers were designed on gyrB (reference gene; CAGATCAAGAAATCAAACTCCAA and CAGCATCATCTACAGAAACTC), nanA SPG1600 (AGCAACCTCTGGCAAATGAA and ATAGTAATCTCTTGGAATT), SPG1598 (GGTCAACTCAGATGCTT and GAGGAACAGAGTAGTAATC), SPG1592 (CCAACCACGATAGCAAC and CTGAATACAACCTCTCC) and SPG1591 (CAGGTGCTTTCCCAGTC and GTGTTGTAGTATGGTGAG)[24, 50]. The relative gene expression was analysed by using the 2–ΔΔCT method. At least three replicas were used for any given sample. Statistical analysis was conducted by using the two-tailed Student t test.
Flow cytometry assay
FP65 pneumococci grown in media with carbohydrate supplementations at 1 g/L to late log phase were resuspended in 500 μl of phosphate-buffered saline (PBS; pH 7.4) containing 1% bovine serum albumin and incubated at 37°C for 30 min. Samples were spun down and pellets were resuspended in anti-NanA rabbit serum diluted 1:100 in PBS/BSA and incubated at 4°C for 1 h (negative controls were incubated without antibody). After two washes with 1 ml of PBS, 100 μl of fluorescein isothiocyanate (FITC)-conjugated anti-rabbit (1:64; Sigma-Aldrich) was added to bacterial pellets. The resuspensions were incubated at 37°C for 30 min and then washed twice in PBS. Samples were finally resuspended in 300 μl of paraformaldehyde 1% in PBS and subjected to flow cytometry (FACScan, Becton Dickinson, San Diego, CA). Statistical analysis was carried out by using two-tailed Student t test.
The neuraminidase activity was measured using the fluorogenic substrate 2′-(4-methylumbelliferyl)-α-D-N-acetylneuraminic acid (4MU-Neu5Ac) (M8639, Sigma-Aldrich, St. Louis, Miss.). The time dependence of the variation of fluorescence (λexcitation, 335 nm; λemission, 400 nm) in the presence of cell or enzyme samples was recorded with a EnVision multilabel plate reader (Perkin Elmer, Waltham, Mass.) using 50 μM 4MU-Neu5Ac in 10 mM MES buffer at pH 6.0, in a final reaction volume of 200 μl. S. pneumoniae FP65 was grown in CAT medium, containing alternatively glucose or N-acetylmannosamine as the carbon source, respectively, for 18 hours at 37°C. The sample was prepared as follows; the culture was centrifuged at 10,000 × g (4°C) and the cell pellet washed once in an equal volume of 10 MES buffer pH 6.0, centrifuged and resuspended at a final A600 = 0.4 in 10 mM MES pH 6.0. The method was initially optimized and calibrated using purified NanA neuraminidase of S. pneumoniae D39 produced in E. coli (0.88 mg/ml) (data not shown). The activity was computed as the variation of fluorescence vs time using a linear regression of the data. In our conditions, 1 μg of purified NanA yielded a activity of 10,690 ΔF/min.
Sialic acid (N-acetylneuraminic acid)
- ABC transporter:
ATP binding cassette transporter
- PTS transporter:
Phosphotransfer system transporter
- CAT medium:
Casitone yeast extract medium.
The work was in part funded by the European Commission grant PNEUMOPATH FP7-HEALTH-222983 and by Ricerca Regionale Toscana in Materia di Salute 2009–201.
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