1 Unidad de Genética Bacteriana (CSIC), Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28220, Majadahonda, Madrid, Spain
2 Bacterial Infection and Immunity Group, Institute of Food Research, Norwich Research Park, Norwich NR4 7UA, UK
Correspondence
Antonio J. Martín-Galiano
a.martin{at}wzw.tum.de
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ABSTRACT |
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CAI values for all genes of strain TIGR4 are available as supplementary data with the online version of this paper at http://mic.sgmjournals.org.
Present address: Lehrstuhl für Genomorientierte Bioinformatik, Wissenschaftszentrum Weihenstephan, Am Forum 1, 85354 Freising, Germany.
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INTRODUCTION |
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The approximate expression level of a gene can be predicted by comparing its codon bias with the profile of universally highly expressed genes, such as the ribosomal protein (RP) genes, which are commonly used as a reference set. Algorithms developed for this purpose (Sharp & Li, 1987a; Karlin & Mrazek, 2000
) are adequate for deciphering the general pattern of gene expression in the cell, and to detect special enhanced functions in some micro-organisms, such as DNA and protein repair in Deinococcus radiodurans and flagellar motility in Treponema pallidum (Karlin & Mrazek, 2000
). There is a good correlation of predicted highly expressed (PHE) genes with high two-dimensional gel abundances in Bacillus subtilis and Escherichia coli (Karlin et al., 2001
). However, these algorithms do not allow the detection of genes encoding proteins that are abundant due to their high stability rather than to a high translation rate (Karlin et al., 2001
) and, given the large translation capacity of ribosomes, codon usage restrictions of highly expressed genes should operate only at critical stages of rapid growth (Kurland, 1991
). In accordance with these ideas, the slow-growing Mycobacterium tuberculosis (2436 h doubling time) exhibits almost no alternative codon bias among genes that are PHE in other, fast-growing eubacteria (Andersson & Sharp, 1996
; Karlin & Mrazek, 2000
).
Codon bias could be an important factor in S. pneumoniae since its cell-division time under laboratory growth conditions is typically less than 45 min. However, to the best of our knowledge, systematic studies of the effect of codon usage on gene expression levels and gene function have not been reported for the lactic acid group of bacteria. In addition, there is one report on the correlations between codon usage bias and microarray data for E. coli (dos Reis et al., 2003). Given the medical significance of S. pneumoniae, Streptococcus pyogenes, and the viridans group streptococci, and the industrial importance of the food lactic acid bacteria, such as Lactococcus lactis and Lactobacillus acidophilus, a study of the relationship between codon usage, gene expression and gene function is required. The objective of this study was to analyse the relationships between the predicted level of gene expression based on codon usage, actual microarray expression values and gene function at the genomic level in S. pneumoniae.
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METHODS |
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Culture conditions, RNA extraction and microarray experiments.
S. pneumoniae R6 was grown in ToddHewitt medium (Difco) with 0·5 % yeast extract, adjusted to pH 7·8 (THYE medium). Cells corresponding to 50 ml cultures were collected at mid-exponential phase (OD620=0·25), washed with cold 0·9 % NaCl and stored at 80 °C. Pellets were thawed and cells lysed for 15 min at 37 °C in 10 mM Tris, 1 mM EDTA (pH 8·0), 0·1 % sodium deoxycholate. RNA was extracted with the RNeasy midi kit (QIAGEN), including a DNase treatment according to the manufacturer's instructions, precipitated with ethanol, washed, and suspended in 40 µl H2O. Concentration and purity of the RNA samples were measured using the 2100 Bioanalyser (Agilent). Details of the construction of the microarrays used in this study have been described previously (Dagkessamanskaia et al., 2004). The microarrays included probes for all strain TIGR4 annotated genes (2236) and probes for 117 R6-specific genes (i.e. less than 90 % similarity, as deduced by BLAST analysis). To obtain labelled cDNA, a 25 µl mixture was made with 15 µg RNA, 5 µg random primers (obtained with the Bioprime DNA labelling kit, Invitrogen), 12 µM DTT, 500 µM each dNTP (except for CTP, which was 240 µM), 2 nM Cy3- or Cy5-labelled CTP, and 200 units Stratascript (Stratagene) reverse transcriptase, in the buffer supplied by the manufacturer. The mixture was incubated overnight at 37 °C and the reaction stopped by addition of 1·5 µl 20 mM EDTA plus 15 µl 0·1N NaOH. After 15 min incubation at 70 °C, 15 µl 0·1N HCl was added. Labelled cDNA was treated with the QIAquick PCR purification kit (QIAGEN), the volume was reduced to 10 µl by lyophilization, and then 6·1 µg Cot1 human DNA was added, as well as 3x SSC, 0·2 % SDS, 0·02 M HEPES and 4x Denhardt's solution, to a final volume of 90 µl. Samples were treated for 2 min at 100 °C and 10 min at room temperature, centrifuged twice, and 40 µl of the supernatant was applied to a microarray slide. After overnight incubation at 63 °C, microarrays were washed and scanned with an Axon 4000A apparatus, using GenePix Pro 3.0 software. Fluorescence values, taken as the median of the intensity of all the pixels after subtracting the surrounding background, corresponded to the mean of three independent samples, each having four replicates for each gene.
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RESULTS AND DISCUSSION |
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Comparison of CAI and microarray fluorescence values
As 85 % of the genes of the R6 and TIGR4 strains have a similarity above 90 %, and a good correlation (r2=0·99) of CAI values among their homologous genes was observed (data not shown), Cy3- (two replicates) and Cy5- (one replicate) labelled cDNA obtained from R6 grown to mid-exponential phase (OD620=0·25) was hybridized to the microarrays, as described in Methods, and the mean fluorescence measurements for each gene were used to estimate the relative mRNA transcript levels. Fluorescence was detected for 1513 homologues of R6 and TIGR4. Given the median (1675 FU, fluorescence units) of the fluorescence distribution, and the proportion (12·56 %, 190 of 1513) of genes with values higher than 6000 FU (Fig. 3A), that value was chosen as the cut-off to assign highly expressed genes. Among the 114 PHE genes (CAI>0·5), 32·5 % showed high (>6000 FU), 33·3 % medium (20006000 FU), and 34·2 % low (<2000 FU) relative levels of expression (Fig. 3B
). Among the 25 genes with the highest CAI values (CAI>0·680), the majority (16 of 25, 64 %) gave high fluorescence values on the microarray, revealing a correlation between the levels of transcription and translation among a substantial proportion of highly expressed genes. A similar relationship has been recently observed in E. coli (dos Reis et al., 2003
). An increase in the proportion of genes with fluorescence values above 6000 FU was observed in groups of genes with CAI values of 0·4 to 0·6 (2125 %) compared to the genes with CAI values lower than 0·4 (410 %). The lower median (949 FU) and lowest percentage of genes over 6000 units (4 %) corresponded to the group of genes with CAI values lower than 0·2. Therefore, despite the fact that it is widely accepted that low-abundance polypeptides do not necessarily have low CAI values, in our experiments there was also a relationship between CAI and FU in genes with low CAI values. On the other hand, 10·4 % of non-PHE genes had high fluorescence values (>6000 FU), possibly reflecting the fact that these genes are upregulated under laboratory culture conditions. For instance, 55 % of the fatty-acid-metabolism genes (with medium or low CAI values) had values higher than 6000 units.
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Some of the genes involved in the complex pneumococcal network of sugar conversions were also PHE, such as the gene of the enzyme that cleaves lactose (lacG), genes of enzymes that convert galactose into glycolytic intermediates (lacA, lacB and lacD), and malQ, which encodes an enzyme involved in the degradation of maltodextrins, the first digestion product of starch. S. pneumoniae would be able to obtain energy easily under starvation conditions from glycogen, since the genes of glycogen phosphorylase (sp2106) and phosphoglucomutase (pgm) were PHE (Table 2). Additionally, the PHE gene sp1804 (Table 2
) shows high similarity (>70 %) with the Enterococcus hirae gls24 gene that encodes a stress protein playing an important role during glucose starvation (Giard et al., 2000
). In addition to the glycolytic and the two fermentation enzymes described above, malQ, sp2106 and pgm also showed high mRNA amounts.
Transcription and protein synthesis
As expected, genes of translation elongation factors were PHE genes (Fig. 2B, Table 2
), as well as others involved in translation and transcription, such as those of aminoacyl-tRNA synthetases and RNA polymerase subunits (Fig. 2B
, Table 2
). Most of these PHE genes also had high median fluorescence values in the microarray experiments. Aminoacyl-tRNA synthetases had a median FU value of 4762, whereas the value for RNA polymerase subunits was 12 506 FU. In contrast, the genes of proteolytic enzymes, although they generally had very high fluorescence values (median FU of 3853), were not PHE (Fig. 4B
), suggesting that proteolysis is enhanced under the laboratory culture conditions. Among the genes encoding chaperones, only dnaK and tig showed both high CAI and fluorescence values, being the only chaperones included in the 25 genes with the highest CAI values.
On the other hand, most RP genes had fluorescence values higher than the genome median but lower than 6000 FU (median 3210), plotting in the low-right quadrant of Fig. 4C, indicating that codon bias might be a more important factor than the amount of mRNA for the general abundance of RP proteins. Genes involved in amino-acid biosynthesis had quite homogeneous CAI values (generally <0·400), in accordance with the general tendency of the genome. However, much higher values were found in specific genes (ilvC, gdhA, metE, asd, cysM and glnA; Table 2
), a feature that has been associated with control-pathway enzyme genes (Karlin & Mrazek, 2000
). None of these genes showed high fluorescence values, which may be related to the abundance of casein-derived amino acids in THYE medium.
Transporters
S. pneumoniae has one of the highest proportions (30 %) of sugar transporter genes among the prokaryotic genomes (Tettelin et al., 2001), seeming to be highly adapted to compete for sugar nutrients with other respiratory tract micro-organisms. Several genes of sugar transporters and phosphotransferase systems were PHE (Table 2
). However, under the rich and stable sugar environment of the THYE medium, only a few of these genes showed high mRNA amounts: ptsH, ptsI and sp0758 of the phosphotransferase system, and maltosaccharide transporter malX.
In addition, some genes for Fe and Mn transporters were also PHE (Table 2), possibly reflecting an adaptation to pathogenicity, given the vital importance of the acquisition of these elements inside the host (Jakubovics & Jenkinson, 2001
). Among them, the psaABC operon encoding the Mn transporter also had relatively high levels of transcripts.
Oxidative metabolism
Genes involved in oxidant species detoxification and other redox reactions were PHE (trx, nox, sodA, fld and trxB; Table 2). Likewise, four of the genes classified as oxidoreductases in the unknown-specificity enzyme group (sp1325, sp1471, sp1472 and sp1588), and psaA, part of an Mn transporter involved in anti-oxidative defence, were also strongly PHE (Table 2
). Taken together, these data suggest that defence against oxidative species is highly developed in S. pneumoniae, possibly as a consequence of its ability to colonize and persist in the nasopharynx, where partial oxygen pressure is high. Consistent with this hypothesis, nox, sodA and psaA, which are essential for infection (Auzat et al., 1999
; Yesilkaya et al., 2000
; Tseng et al., 2002
) also appeared to be transcribed at high levels (11 200, 5630 and 12 987 FU, respectively). In spite of the anaerobic metabolism of S. pneumoniae, one of the highest CAI and fluorescence values (0·738 and 11 683 units, respectively) corresponded to the pyruvate oxidase gene, spxB, which is one of the more abundant polypeptides of the transparent variants of S. pneumoniae (Overweg et al., 2000
). This enzyme is also essential for infection (Spellerberg et al., 1996
), and produces, in the presence of oxygen, acetyl-phosphate and hydrogen peroxide. The latter is an important pneumococcal virulence factor (Duane et al., 2000
), which additionally could cause an inhibitory effect on the growth of competitive microbes in the upper respiratory tract (Pericone et al., 2000
).
Genes expressed at low levels
Low CAI values were calculated for genes with a putative regulatory function, which included 27 genes of two-component systems (TCS) (Fig. 2B) and 62 general regulators, with mean CAI values of 0·247 and 0·281, respectively. Additionally, low CAI values were also calculated for the 35 genes involved in prosthetic group/cofactor biosynthesis and the 19 genes of aromatic amino-acid biosynthesis with mean CAI values of 0·292 and 0·294, respectively. Some of these gene groups also had low median fluorescence values: regulators (914 FU, n=50), TCS (1399 FU, n=26) (Fig. 4B
) and cofactor-vitamin biosynthesis (1542 FU, n=34).
Low CAI values were also calculated for 24 competence genes (mean CAI of 0·269; Fig. 2B), and most also had low fluorescence values (median 868 FU, n=21) (Fig. 4B
). These genes localized in the central part of the COA plot, with the exception of comD, comE and comF, which localized in the right horn, and had G+C contents of 32·0 %, 30·7 % and 36·2 %, respectively. Consequently, they could be recently acquired genes. It is worth emphasizing that S. pneumoniae becomes naturally competent for only a few minutes, resulting in rapid changes in its protein profile (Morrison & Baker, 1979
), and that constitutive activation of the competence regulon could be deleterious for the cell (Martin et al., 2000
). Thus it is possible that the presence of rare codons in competence genes could be a mechanism that limits translation, thereby minimizing adverse physiological stresses prior to induction of competence-gene expression, as suggested in the case of some E. coli regulatory genes (Kronigsberg & Codson, 1983
). In accordance with this hypothesis, other mechanisms negatively controlling expression of competence involve the cleavage of competence factors by the ClpP protease (Chastanet et al., 2001
), and the action of the inhibitor of the competence-stimulator peptide (Berge et al., 2001
). In contrast, the recA gene had a moderately high CAI (0·489) and a high fluorescence value (8286 FU), being the only competence gene that appears in the left horn of in the COA, probably because it is involved in multiple cellular processes.
Virulence factors
Virulence factors include capsule and cell-wall biosynthesis enzymes, pneumolysin, autolysin, neuraminidase, IgA1 protease, and some surface proteins (Paton et al., 1993). Nearly all these genes had CAI values of 0·250 to 0·350, and could be considered medium-expressed genes. Nevertheless, psaA was PHE. Most genes of capsule biosynthesis, as well as nanB, pspA, iga, genes of choline-binding proteins (cbpC and cbpF), and lytB appear in the right horn (Fig. 1C
) of the COA, suggesting a recent acquisition by horizontal transfer. In agreement with this idea, the G+C contents of the cps4EFGH capsular genes, nanB and pspA were 27·8 % to 33·5 %, 33·4 %, and 35·0 %, respectively, which is lower than that of the bulk of the genome coding sequences (39·7 %).
Apparently there are two mechanisms that determine the persistence/virulence of S. pneumoniae, operating on different time scales. One is the optimization of codon usage, as detected by CAI analysis for sugar-transporter and oxidative-metabolism genes, possibly reflecting a long-term progressive adaptation to persistence in carrier hosts. The other is the recent acquisition of new virulence factors by horizontal transfer, as detected by COA and G+C content.
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ACKNOWLEDGEMENTS |
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Received 13 February 2004;
revised 26 April 2004;
accepted 28 April 2004.
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