The yefM-yoeB Toxin-Antitoxin Systems of Escherichia coli and Streptococcus pneumoniae: Functional and Structural Correlation

Abstract

Toxin-antitoxin loci belonging to the yefM-yoeB family are located in the chromosome or in some plasmids of several bacteria. We cloned the yefM-yoeB locus of Streptococcus pneumoniae, and these genes encode bona fide antitoxin (YefM_Spn) and toxin (YoeB_Spn) products. We showed that overproduction of YoeB_Spn is toxic to Escherichia coli cells, leading to severe inhibition of cell growth and to a reduction in cell viability; this toxicity was more pronounced in an E. coli B strain than in two E. coli K-12 strains. The YoeB_Spn-mediated toxicity could be reversed by the cognate antitoxin, YefM_Spn, but not by overproduction of the E. coli YefM antitoxin. The pneumococcal proteins were purified and were shown to interact with each other both in vitro and in vivo. Far-UV circular dichroism analyses indicated that the pneumococcal antitoxin was partially, but not totally, unfolded and was different than its E. coli counterpart. Molecular modeling showed that the toxins belonging to the family were homologous, whereas the antitoxins appeared to be specifically designed for each bacterial locus; thus, the toxin-antitoxin interactions were adapted to the different bacterial environmental conditions. Both structural features, folding and the molecular modeled structure, could explain the lack of cross-complementation between the pneumococcal and E. coli antitoxins.

The gram-positive, spherical bacterium Streptococcus pneumoniae (pneumococcus) is the cause of many human diseases, such as pneumonia, bacterial blood poisoning (bacteremia), inflammation of the membranes surrounding the brain and spinal cord (meningitis), middle-ear infection (otitis media), osteomyelitis, septic arthritis, endocarditis, peritonitis, pericarditis, and sinusitis; pneumonia is the most severe disease (15, 28). Although the pneumococcus can normally be found in the noses and throats of healthy individuals, it can grow and cause infection when the immune system is weakened. The people who are most at risk of developing pneumococcal pneumonia have a weakened immune system. These people include the elderly, infants, cancer patients, AIDS patients, postoperative patients, alcoholics, and people with diabetes. The global rate of mortality is more than 1,000,000 people per year, and this figure represents about 15 to 20% of the people infected. Epidemiological studies of community-acquired pneumonia have shown that S. pneumoniae is still one of the most significant etiologic agents in all age groups in developing and industrialized countries (28). A recently published analysis estimated that 1.6 to 2.2 million children die from acute respiratory infection worldwide each year and that about 30% of the deaths are in Southeast Asia (52). Historically, the treatment for pneumococcal pneumonia has been penicillin. However, an increasing number of pneumococcal strains are partially or completely resistant not only to penicillin but also to macrolides, trimethoprim-sulfamethoxazole, and cephalosporins, making it increasingly difficult to treat this disease (3, 50). Vaccination is an available solution, but unfortunately, the people for whom vaccination is most recommended are the people who are least likely to respond favorably to it. Therefore, the overall effectiveness of a vaccine remains questionable, and the need for novel drugs is increasing (51).

Seeking new approaches and finding new targets for pneumococci comprise an important field. In this sense, chromosomally encoded proteic toxin-antitoxin (TA) systems can be considered suitable targets for antibiotics (17). Originally, these systems were discovered in bacterial plasmids, but they are also abundant in the chromosomes of bacteria and archaea (37). They consist of two proteins that form a harmless complex in which the unstable antitoxin neutralizes the toxicity of the cognate stable toxin. When cells encounter nutritional or environmental stresses, cellular proteases (Lon or Clp) activate the toxins by actively degrading their antitoxin counterparts (1, 10, 11). However, the toxin activity does not necessarily lead to cell death provided that within a certain window of time synthesis of the antitoxin is resumed (16, 36, 38). The chromosomal TA systems seem to operate by modulating the global level of translation, with the toxins functioning as specific endoribonucleases (12, 20) that cleave either free mRNA, like YoeB or MazF (26, 55), or mRNA associated with actively translating ribosomes, like RelE (39). Thus, the bacterial toxins are potentially interesting as new antibiotics (17, 20, 36). Ideally, an inhibitor that mimics the most relevant toxin residues and their interactions with the antitoxin, leading to a new complex (compound-antitoxin) that frees the toxin to cause bacterial damage, would be an excellent antimicrobial agent.

In the chromosome of S. pneumoniae R6 (24), at least three TA loci have been identified. Two of these loci, relBE1_Spn and relBE2_Spn, exhibit homology with the relBE genes of Escherichia coli (19), whereas the third locus, yefM-yoeB_Spn, is homologous to the yefM-yoeB (also designated relBE3) genes of E. coli (5). A similar locus has been reported to be present in plasmid pRUM of Enterococcus faecium (22). DNA fragments containing the putative toxin genes relE1_Spn and relE2_Spn were cloned in an E. coli expression vector. Overproduction of both toxins showed that RelE2_Spn was toxic to E. coli, whereas RelE1_Spn was innocuous, indicating that relE2_Spn is a toxin gene (36). The relB2_Spn and relE2_Spn genes were shown to be organized in a single operon. Overexpression of the relE2_Spn toxin gene both in S. pneumoniae and in E. coli led to cell growth arrest and a concomitant reduction in the number of viable cells, which could be reversed by expression of the cognate antitoxin (36).

The yefM-yoeB TA locus was first identified on the basis of its similarity to the axe-txe TA system of plasmid pRUM (22). Later, the E. coli yefM-yoeB locus was analyzed, and the chromosomal proteins YefM and YoeB were characterized in detail. The YefM antitoxin of E. coli was shown to be unfolded in its native state (5), although the YoeB toxin was folded and formed a physical complex with the unfolded YefM antitoxin (6). YoeB exhibited endogenous endoribonuclease activity, and its interaction with YefM induced a conformational change in the toxin around the putative active site, leading to inhibition of the RNase activity of YoeB (26). Although the antitoxins associated more efficiently with their cognate toxins, effective cross-complementation between Axe and YoeB and, to lesser extent, between YefM and Txe has been shown to occur in vivo (22), demonstrating the broad specificity of the TA of the two bacterial species and suggesting that there is a common mechanism of toxin-antitoxin interaction.

In this paper, we describe cloning, characterization, and analysis of the yefM-yoeB_Spn pneumococcal TA system. We analyzed the cross-complementation between the two YefM antitoxins from E. coli and S. pneumoniae with the corresponding heterologous YoeB toxins. Unlike the interaction of Axe and YefM_Eco, the YefM_Spn antitoxin was able to interact only with its cognate toxin, indicating that there are some structural differences between the antitoxins which could hinder heterologous TA interactions. Far-UV circular dichroism (CD) and molecular modeling analyses indicated that even though the toxins of E. coli and S. pneumoniae exhibited a high level of similarity, the YefM antitoxin counterparts seemed to be structurally different, thus explaining the lack of cross-complementation. Therefore, similar TA systems harbored by different bacteria may have specifically evolved to respond to different environmental conditions, thereby optimizing the TA interactions in their hosts.

MATERIALS AND METHODS

Bacterial strains and growth conditions.

The E. coli strains used were TOP-10 [F⁻ mcrA Δ(mrr-hsdRMS-mcrBC) φ80lacZΔM15 ΔlacX74 recA1 deoR araD139 Δ(ara-leu)7697 galU galK rpsL(Str^r) endA1 nupG] (Invitrogen), BL21 [F⁻ ompT gal (dcm) (lon) hsdS_B(r_B m_B⁻)] (an E. coli B strain) (47), BL21(DE3)(pLysS) (Novagen), MG1655 (wild-type E. coli) (53), and two isogenic derivatives of MG1655, SC36 (MG1655ΔyefM-yoeB) (7) (provided by K. Gerdes) and MG1655lon (a gift from L. van Melderen). For bacterial two-hybrid assays, E. coli XL-Blue MRF′ Km (Stratagene) was used as the host during construction of the recombinant bait and target vectors. The recombinant bait and target pairs were then cotransformed into competent cells of the Bacteriomatch II E. coli validation reporter (Stratagene), a derivative of E. coli XL1-Blue MRF′ [Δ(mcrA)183 Δ(mcrCB-hsdSMR-mrr)173 endA1 hisB supE44 thi-1 recA1 gyrA96 relA1 lac (F′ lacI^q his-3 aadA Kan^r)], which allowed detection of protein-protein interactions through transcriptional activation of the His reporter gene. All cultures were grown in TY medium (33), which was supplemented with 100 μg/ml ampicillin or with 50 μg/ml kanamycin. All cultures were grown at 37°C. The source of S. pneumoniae chromosomal DNA was strain R61, which was grown as reported previously (29) and which is a derivative of the R6 sequenced strain (24). The growth conditions and details concerning induction of synthesis of the pneumococcal toxin and its cognate antitoxin in E. coli have been described elsewhere (36); briefly, the procedures included measuring the turbidity of the cultures by monitoring the optical density at 600 nm (OD₆₀₀) and determining the number of CFU by plating suitable dilutions of the cultures.

Plasmids used.

Plasmids used in this work were constructed as follows.

(i) pYBS2.

The yoeB_Spn gene with its own Shine-Dalgarno sequence was amplified by PCR from chromosomal DNA (prepared from S. pneumoniae R61) using primers yoeB_N2 (5′-CTGGAATTCCGCAGGTCCATGTGATTGAGGAGT-3′) and yoeB_C2 (5′-CGCGGATCCGGTAGAGACTTGAGAAAAAGCCTA-3′). The resulting 338-bp PCR fragment was doubly digested with EcoRI and BamHI and ligated into plasmid pFUS2 (31) digested with EcoRI and BglII (compatible ends with BamHI sites). This construction placed the yoeB_Spn gene under control of the arabinose-inducible P_BAD promoter. Thus, when cells were grown in arabinose-containing medium, AraC was active and promoted transcription from the P_BAD promoter, whereas when cells were grown in the presence of glucose, AraC was inactive and transcription from P_BAD was switched off (54).

(ii) pYFS10.

A DNA fragment encompassing the yefM_Spn gene with its putative Shine-Dalgarno sequence was amplified by PCR from pneumococcal chromosomal DNA using primers yefM_N (5′-CGCGGATCCGCTTGTACAAGTTCCTGACAATTTC-3′) and yefM_c (5′-CTGGAATTCCGTTTTGCCAGTAGCAATAATCTGC-3′). The 403-bp PCR fragment was digested with BamHI and EcoRI before ligation into the equivalent sites of plasmid pNM220, placing yefM_Spn under control of the isopropyl-β-d-1-thiogalactopyranoside (IPTG)-inducible P_lac promoter (21).

(iii) pFYBE.

The yoeB_Eco gene was amplified from E. coli genomic DNA by PCR using primers yoeB_NE (5′-CTGGAATTCCTGAAATCAGGCAAAGGAACGGAAA-3′) and yoeB_CE (5′-CGCGATCCGTATCAAAACTGACAATTCATT-3′). The resulting 350-bp PCR product was digested with EcoRI and BamHI before ligation into the EcoRI and BglII sites of pFUS2, as described above.

(iv) pNMYE.

The yefM_Eco gene was amplified from E. coli genomic DNA by PCR using primers yefM_NE (5′-CGCGGATCCGTTAATTAACGCTCATCATTGAT-3′) and yefM_CE (5′-CTGGAATTCCTCAGACCAGATTAGTTTCA-3′). The resulting 341-bp product was digested with EcoRI and BamHI before ligation into the equivalent sites of pNM220.

(v) pRES2.

A PCR DNA fragment obtained from the chromosome of S. pneumoniae containing the relE2_Spn gene with its own Shine-Dalgarno sequence was generated using primers relE2_N (5′-GCGAATTCGATGCATGATTTAGGCTTGAAG-3′) and relE2_C (5′-CGGGATCCGAATGAAAATTTACTTGAAAAAAGT-3′). The 325-bp DNA fragment was digested with BamHI and EcoRI and ligated into pFUS2 digested with EcoRI and BglII.

(vi) pEMH10.

The yefM_Spn gene from the S. pneumoniae chromosome was amplified by PCR using primers yefM_NHis (5′-GCTCTAGAATGGTTATGGAAGCAGTCCTT-3′) and yefMc (5′-CTGGAATTCCGTTTTGCCAGTAGCAATAATCTGC-3′). The resulting 337-bp PCR fragment was doubly digested with XbaI and EcoRI and inserted into plasmid pET28a digested with NheI (compatible with XbaI) and EcoRI. This construction yielded a His-tagged YefM_Spn protein.

(vii) pEMBH13.

A DNA fragment from the pneumococcal chromosome spanning both the yefM_Spn and yoeB_Spn genes was PCR amplified using primers yefM_NHis (5′-GCTCTAGAATGGTTATGGAAGCAGTCCTT-3′) and yoeB_CHis (5′-GAACTCGAGGTAATGATCTTTAAAGGACAAG-3′). The resulting 535-bp fragment was digested with XbaI and AvaI and ligated into plasmid pET24b digested with NheI and XhoI. This construction yielded His-tagged pneumococcal toxin-antitoxin proteins.

(viii) pBT-YefM_Spn.

A DNA fragment containing the coding sequence of the yefM_Spn gene was obtained by PCR using the chromosomal DNA of S. pneumoniae as the template and primers yefM1Spn-F (5′-GAATCCGGTGTATAATAGTGGAAAAGAGCTAAAAC-3′) and yefMSpn-R (5′-CTCGAGTCACTCCTCAATCACATGG-3′). The resulting 262-bp PCR fragment was digested with EcoRI and XhoI and ligated into the equivalent sites of pBT, generating pBT-YefM_Spn, which expressed YefM_Spn as a fusion protein with λcI at the N terminus.

(ix) pBT-YoeB_Spn.

The yoeB_Spn gene was amplified by PCR from chromosomal DNA of S. pneumoniae using primers yoeB1Spn-F (5′-GAATCCAATGCTACTCAAGTTTACAG-3′) and yoeBSpn-R (5′-CTCGAGTTAGTAATGATCTTTAAAGG-3′). The resulting 257-bp PCR fragment was digested with EcoRI and XhoI and ligated into similarly digested pBT, yielding pBT-YoeB_Spn, which produced YoeB_Spn as a fusion protein with λcI at the N erminus.

(x) pTRG-YefM_Spn.

The yefM_Spn gene from the S. pneumoniae chromosome was amplified by PCR using primers yefM2Spn-F (5′-GAATCCGGGTGTATAATAGTGGAAAAGAGC-3′) and yefMSpn-R (5′-CTCGAGTCACTCCTCAATCACATGG-3′). The resulting 263-bp fragment was digested with EcoRI and XhoI prior to ligation into EcoRI- and XhoI-digested pTRG to generate the pTRG-YefM_Spn recombinant, which expressed YefM_Spn as an N-terminal fusion protein with the RNA polymerase α subunit (RNAPα).

(xi) pTRG-YoeB_Spn.

A DNA fragment encompassing the yoeB_Spn gene was PCR amplified from DNA of the S. pneumoniae chromosome using primers yoeB2Spn-F (5′-GAATCCATATGCTACTCAAGTTTACAG-3′) and yoeBSpn-R (5′-CTCGAGTTAGTAATGATCTTTAAAGG-3′). The resulting 258-bp fragment was digested with EcoRI and XhoI and then ligated with similarly digested pTRG to obtain the pTRG-YoeB_Spn recombinant, which expressed YoeB_Spn as a fusion protein with RNAPα at its N terminus.

Purification of S. pneumoniae His-YefM antitoxin and the YefM-YoeB-His antitoxin-toxin pair.

The pEMH10 vector, containing the coding sequence of yefM_Spn, and the pEMBH13 vector, containing the coding sequences of yefM-yoeB_Spn, were transformed into E. coli BL21(DE3)(pLysS). Transformed bacteria were grown in 2YT broth at 37°C and 200 rpm to an OD₆₀₀ of 0.4. Protein expression was induced by addition of 1 mM IPTG at 30°C. After 3 h, cells were harvested and resuspended in buffer A (300 mM NaCl, 20 mM NaH₂PO4; pH 8.0) to which 1 ml protease inhibitor cocktail (Sigma) and 0.5 mM phenylmethylsulfonyl fluoride were added. Cells were disrupted by sonication (four 20-s pulses; 0°C; 1-min breaks between pulses). The insoluble material was removed by centrifugation at 4°C and 20,000 × g for 20 min, followed by filtration (pore size, 0.45 μm), and the supernatant was applied to an XK 16/20 fast protein liquid chromatography column (GE Healthcare) packed with Ni-CAM HC affinity resin (Sigma) and preequilibrated with buffer A. Following extensive washing, the bound proteins were eluted from the column in a single broad peak using buffer A containing 500 mM imidazole. Fractions containing the His-YefM_Spn protein or the coeluted YoeB_Spn-His and YefM_Spn proteins were identified by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) analyses, combined, and dialyzed against phosphate-buffered saline (PBS) (pH 7.4) (10 mM Na₂HPO₄, 1.8 mM KH₂PO₄, 140 mM NaCl, 2.7 mM KCl). The identities of the His-YefM_Spn protein and the (YefM-YoeB)_Spn-His complex were verified by mass spectrometry analysis.

The fractions were then pooled, concentrated, and exchanged with buffer B (50 mM sodium phosphate [pH 7.2], 150 mM NaCl) using a spin column concentrator (Vivaspin). The identity of the expressed His-YefM_Spn protein was verified by Western hybridization using anti-His antibodies. Protein concentrations were calculated using extinction coefficients at 280 nm of 1,197 M⁻¹ cm⁻¹ for a single tyrosine and 5,559 M⁻¹ cm⁻¹ for a single tryptophan under neutral conditions, as described by Mihalyi (35). The protein solution was then applied to a HiPrep 16/60 Sephacryl S-100 high-resolution size exclusion column (GE Healthcare) which had a molecular weight (M_r) separation range of 1 × 10³ to 1 × 10⁵ and which was preequilibrated with buffer B. Albumin (M_r, 67,000), ovalbumin (M_r, 43,000), chymotrypsinogen A (M_r, 25,000), and RNase A (M_r, 13,700) were used as molecular weight standards to plot a calibration curve for log M_r against mean K_av values, which were determined as follows: K_av = (V_e − V₀)/(V_t − V₀), where V_e is the elution volume for the target protein, V₀ is the column void volume (i.e., elution of Blue Dextran 2000), and V_t is the total bed volume (120 ml for the HiPrep 16/60 Sephacryl S-100 column) (44). The target proteins were eluted from the column in a single peak using buffer B containing 150 mM NaCl, and 0.5-ml fractions were collected. The desired fractions were pooled and concentrated prior to SDS-PAGE analysis. The target protein was then stored at −20°C. For the E. coli YefM-YoeB-His complex, the size exclusion column used was a Superdex 75 10/300 column (GE Healthcare). The column was preequilibrated with PBS (pH 7.3), and the complex was eluted at a flow rate of 1 ml/min at the ambient temperature. Ovalbumin (M_r, 44,000), myoglobin (M_r, 17,000), and vitamin B₁₂ (M_r, 1,350) were used as the molecular weight standards (Bio-Rad) to plot a calibration curve as described above. The column void volume was determined using Blue Dextran 2000, and the total bed volume was 24 ml. The elution spectrum was deconvoluted into Gaussian-shaped peaks, and peaks values were determined using the PeakFit analysis software (Seasolve).

Detection of protein-protein interactions using a bacterial two-hybrid system.

A BacterioMatch II two-hybrid system vector kit (Stratagene) was employed to investigate whether there were any interactions between the YefM_Spn antitoxin and its cognate YoeB_Spn toxin. This system uses a new HIS3-aadA reporter cassette, and detection of protein-protein interactions is based on transcriptional activation of the HIS3 reporter gene, which allows growth in the presence of 3-amino-1,2,4-triazole (3-AT), a competitive inhibitor of the His3 enzyme. The DNA fragments encoding the bait proteins (yefM_Spn as well as yoeB_Spn) were amplified and cloned in frame with the λcI repressor of the pBT bait vector via the EcoRI and XhoI restriction sites. The corresponding DNA fragments that encoded the target proteins (yoeB_Spn and yefM_Spn) were similarly cloned in frame with the RNAPα reading frame of the pTRG target vector via the EcoRI and XhoI sites. Each of the recombinant bait and target pairs (i.e., the pBT-yefM_Spn-pTRG-yoeB_Spn pair or the pBT-yoeB_Spn-pTRG-yefM_Spn pair) was cotransformed into the E. coli reporter strain provided by the supplier. A positive interaction between the λcI fusion protein produced by the recombinant pBT plasmid and the RNAPα fusion protein produced by the recombinant pTRG plasmid resulted in growth of the reporter strain cotransformants on the selective medium containing 5 mM 3-AT.

Circular dichroism.

CD spectra were obtained using an AVIV 202 spectropolarimeter equipped with a temperature-controlled sample holder and a 10-mm-path-length cuvette. The mean residual ellipticity ([θ]) was calculated as follows: [θ] = (100 × θ × m)/(c × L), where θ is the observed ellipticity, m is the mean residual weight, c is the concentration (in mg/ml), and L is the path length (in cm). All experiments were performed in PBS (pH 7.3) using a protein concentration of 2 μM. Prior to analysis, all protein samples were dialyzed against PBS (pH 7.3) at 4°C and centrifuged for 10 min at 12,000 × g to remove insoluble protein aggregates. The protein concentration used was approximately 2 μM. Evaluation of the secondary structure composition based on the far-UV CD spectra obtained was facilitated by use of the Selcon3, ContiLL, and CDsstr programs (25, 41, 45) included in the CDpro software package (46) and the K2d program (2) on the K2d server (http://www.embl-heidelberg.de/∼andrade/k2d/).

Model construction.

Three-dimensional models for the sequences of YefM_Spn, YoeB_Spn, Axe, and Txe were constructed using a knowledge-based protein modeling method based on the given pairwise sequence-template alignments for the sequences extracted from the multiple alignments of members of the YefM and YoeB protein families (5) and the 2.05-Å-resolution X-ray crystallographic structure of the E. coli YefM-YoeB heterotrimeric complex as the template (PDB code 2a6q) (26). The homology modeling program Nest (40) was used to build and refine by energy minimization the final structures of the models. Computations were carried out using an SGI Octane R10000 workstation. Calculations and surface mapping of the electrostatic potentials for all the structures, as well as the graphic display, were performed with the Swiss-PdbViewer v3.7 computer program (23). Potentials were computed using a Poisson-Boltzmann interaction, with the protein structure simulated at pH 7.0, with the default protonation state for all residues, and taking into account only charged residues (i.e., Arg, Lys, Glu, and Asp). For superposition of each model on the structure of the corresponding toxin and antitoxin templates (E. coli YoeB and YefM, respectively) in order to perform an accurate comparative analysis of the surface electrostatic potentials, we used a combinatorial extension algorithm for calculating each pairwise structure alignment (43).

RESULTS

Chromosomal location of the yefM-yoeB_Spn operon.

Genome analyses showed that the two sequenced pneumococcal strains, TIGR4 and R6, harbor homologs of the E. coli yefM-yoeB and E. faecium plasmid pRUM-encoded axe-txe TA systems (5, 22, 37). By PCR amplification of chromosomal DNA of the R6 pneumococcal strain, we were able to clone the region spanning the yefM-yoeB locus in a pneumococcal plasmid vector and show that (i) the genes constitute an operon and (ii) the toxin was able to stop the growth of pneumococcal cells (unpublished results). The antitoxins exhibited more sequence divergence than the toxins; YefM_Eco exhibited 24% identity with YefM_Spn and 27% identity with Axe. For the toxin interaction domains, the levels of similarity were higher, 67% for YefM_Spn and YefM_Eco and 56% for Axe and YefM_Eco.

Overproduction of YoeB_Spn inhibits cell growth and colony formation in different strains of E. coli.

The yoeB_Spn gene was amplified by PCR from the pneumococcal chromosome and cloned in a plasmid vector, pFUS2 (31), which placed the toxin gene under control of the arabinose-inducible P_BAD promoter of the araBAD operon and the araC gene for its transcriptional activator. Plasmid pYBS2, harboring the pneumococcal toxin gene, was transferred into E. coli strain BL21, MG1655, or TOP-10, and transformants were selected in TY medium plates containing 0.4% glucose to minimize toxin expression. When the toxicity of YoeB_Spn was tested, normal cell growth was observed when the E. coli cells were grown in glucose-containing medium (Fig. 1A) (note that for these conditions only the results for strain MG1655 are shown) or when antitoxin expression was induced by addition of IPTG in E. coli cells containing plasmid pYFS2 (yefM_Spn). However, total arrest of cell growth and a great reduction in the number of viable cells were observed for the three E. coli strains (BL21, MG1655, and TOP-10) harboring pYBS2 when the cultures were shifted to arabinose-containing medium. The reduction in the number of CFU depended on the strain tested, but at the end of the 6-h exposure to YoeB_Spn, the differences between the viability and the viability of the control cultures decreased about 8 and 4 to 5 logarithmic units for BL21 and the other two strains, respectively (Fig. 1B), demonstrating that YoeB_Spn is a potent toxin against E. coli cells. Furthermore, when the pneumococcal yefM-yoeB_Spn genes were cloned into a segregationally unstable mini-F replicon and the rate of plasmid loss was calculated, it was apparent that there was an increase in plasmid stability (not shown).

FIG. 1.

Effect of yoeB_Spn expression in E. coli strains. (A) Cell growth arrest after induction of yoeB_Spn expression in strains MG1655 (○ and •), TOP-10 (▪), and BL21 (▴) harboring pYBS2 (yoeB_Spn). Cells were grown exponentially in medium containing 0.2% glucose (repression conditions) and kanamycin to an OD₆₀₀ of 0.03 to 0.04. Cultures were divided in two. One half of each culture was grown in the presence of glucose (open symbols; for clarity, only the data for strain MG1655 are shown), and the other half was induced by addition of 0.2% arabinose (solid symbols). Growth was monitored by determining the OD₆₀₀ of the cultures. (B) At the times indicated, the numbers of CFU in the cultures were determined by plating appropriate dilutions on TY agar supplemented with 0.4% glucose and kanamycin and incubating the preparations overnight at 37°C. Neither cell growth arrest nor a reduction in the number of CFU was observed for E. coli TOP-10 cultures containing the pYFS2 plasmid (YefM_Spn) (□) after induction of antitoxin synthesis by addition of 2 mM IPTG. This culture was grown and plated as described above but using ampicillin instead of kanamycin for selection. All experiments were performed at least in duplicate.

Cytotoxic effect of YoeB_Spn is alleviated only by its cognate antitoxin, YefM_Spn.

In addition to the chromosomal yefM-yoeB of E. coli (5-7), another yefM-yoeB analog, axe-txe, has been studied in some detail (22). Overproduction of the Txe toxin in E. coli severely impaired bacterial growth, but no reduction in the number of viable cells was observed. The toxic effect of the Txe toxin was alleviated by expression of the cognate antitoxin gene (axe) or was partially alleviated by expression of the heterologous E. coli yefM gene. Likewise, synthesis of the Axe antitoxin alleviated the toxic effect of YoeB_Eco, showing the capacity of the two TA systems to interact with each other in vivo (22). When a similar experiment was performed with the pneumococcal yefM-yoeB TA, it was apparent that overproduction of YoeB_Spn or YoeB_Eco in E. coli cultures not only resulted in growth inhibition but also led to a reduction in the number of viable cells (Fig. 2). It is interesting that after 6 h of YoeB_Eco synthesis about 27% of the bacteria were still able to form colonies (Fig. 2D). This could have been due to neutralization of the toxin by the endogenous levels of the antitoxin encoded by the E. coli chromosomal copy of the yefM-yoeB locus, in agreement with previous results (7, 36). To test whether there was cross-complementation between yoeB_Spn and yefM_Eco, E. coli TOP-10 cells were transformed with DNA of plasmids pYBS2 (yoeB_Spn) and pYFS10 (yefM_Spn) or with DNA of plasmids pYBS2 (yoeB_Spn) and pNMYE (yefM_Eco). Whereas synthesis of the pneumococcal toxin was inducible by arabinose, the genes encoding the antitoxins (either the pneumococcal antitoxin or the E. coli antitoxin) were inducible by IPTG. E. coli cultures containing only pYBS2 (yoeB_Spn) were used as toxicity controls. Coinduction of both the pneumococcal yefM and yoeB genes (by addition of arabinose and IPTG) resulted in a normal rate of cell growth (Fig. 2A), indicating that the toxic effect of YoeB_Spn was neutralized by coexpression of the yefM_Spn antitoxin gene. However, coinduction of yoeB_Spn and the noncognate yefM_Eco antitoxin gene did not neutralize the YoeB_Spn toxicity, and the reduction in the number of CFU was similar to that observed after arabinose addition in control cultures harboring only plasmid pYBS2 (yoeB_Spn) (Fig. 2A and B). To determine whether the toxicity of E. coli YoeB could be counterbalanced by coexpression of the pneumococcal antitoxin, a similar approach was used with E. coli cells that harbored different pairs of plasmids, either pFYBE (yoeB_Eco) and pNMYE (yefM_Eco) or pFYBE (yoeB_Eco) and pYFS10 (yefM_Spn). E. coli cells harboring only plasmid pFYBE (yoeB_Eco) were used as a toxicity control. The results (Fig. 2C and D) confirmed that as in the previous experiment, there was no interaction between the noncognate toxin and the antitoxin proteins.

FIG. 2.

Toxicity of YoeB_Spn is neutralized only by combined expression of the cognate antitoxin in E. coli. (A and B) E. coli TOP-10 strains harboring pYBS2 (yoeB_Spn) (○), pYBS2 (yoeB_Spn), pYFS10 (yefM_Spn) (•), or pYBS2 (yoeB_Spn) and pNMYE (yefM_Eco) (▴) were grown exponentially in TY medium containing 0.2% glucose, kanamycin, and ampicillin to an OD₆₀₀ of 0.03 to 0.04. Then 0.2% arabinose (toxin synthesis induction) and 1 mM IPTG (antitoxin synthesis induction) were added. (A) Absorbance at 600 nm was used to monitor the growth of the cultures. (B) At the times indicated, samples were diluted and plated on TY agar containing 0.4% glucose, kanamycin, and ampicillin and incubated overnight at 37°C. (C and D) E. coli TOP-10 strains harboring pFYBE (yoeB_Eco) (○), pFYBE (yoeB_Eco) and pNMYE (yefM_Eco) (•), or pFYBE (yoeB_Eco) and pYFS10 (yefM_Spn) (▴) were grown and treated as described above. (C) Absorbance at 600 nm was used to monitor the growth of the cultures. (D) At the times indicated, samples were diluted and plated on TY agar containing 0.4% glucose, kanamycin, and ampicillin and incubated overnight at 37°C. All the experiments were performed at least in duplicate.

Recovery of cell viability after induction of YefM_Spn antitoxin synthesis in cultures treated with the YoeB_Spn toxin.

To determine whether the toxicity of the YoeB_Spn pneumococcal toxin in E. coli could be eliminated by the cognate antitoxin YefM_Spn, E. coli cells harboring plasmids pYBS2 (yoeB_Spn) and pYFS10 (yefM_Spn) were grown in the presence of 0.2% arabinose to induce toxin synthesis. Bacterial growth was measured by monitoring the optical densities of the cultures, and the number of CFU was determined by plating samples on glucose-containing medium (repressed conditions for the toxin) supplemented or not supplemented with IPTG (to induce antitoxin synthesis). The number of CFU was plotted as a function of the time of toxin induction, and the results indicated the fraction of surviving cells (Fig. 3). It was apparent that the number of viable cells decreased after induction of toxin expression, although the reduction was more dramatic when there was no induction of the antitoxin (plates without IPTG). After 6 h of toxin overproduction, plates with IPTG contained 3.5% of the original number of E. coli CFU, compared with the 0.3% survivors when the cells were grown in IPTG-free plates.

FIG. 3.

Recovery of cell viability due to antitoxin synthesis after overproduction of YoeB_Spn. E. coli TOP-10 cells harboring plasmids pYBS2 (yoeB_Spn) and pYFS10 (yefM_Spn) were grown in TY medium without glucose containing kanamycin and ampicillin. When the culture reached an OD₆₀₀ of 0.13, 0.2% arabinose was added. Absorbance data were obtained for 7 h after induction of toxin synthesis (inset). At different times, samples were plated on TY agar containing 0.4% glucose, kanamycin, and ampicillin supplemented (•) or not supplemented (○) with IPTG.

Effect of YoeB_Spn overproduction in lon⁺ and lon E. coli strains.

Overproduction of the Lon protease in E. coli triggers bacterial growth inhibition mediated by YoeB_Eco (7). Furthermore, indirect results obtained with a strain in which lon was deleted suggested that this strain was less sensitive to YoeB_Eco overproduction, indicating that antitoxin degradation could be involved in Lon-dependent YoeB_Eco-mediated lethality (7). For pneumococcal YoeB_Spn, overproduction in E. coli resulted in a reduction in bacterial growth, and this effect could not be alleviated by expression of the host yefM_Eco gene (Fig. 2). In addition, when E. coli strain SC36, which lacked the yefM-yoeB locus (7), was tested to determine the toxicity of pneumococcal YoeB_Spn, we found no differences between this strain and strain MG1655, which is wild type for the yefM-yoeB locus (not shown). Both sets of results suggested that degradation of the YefM_Eco host antitoxin by the Lon protease was not necessary for YoeB_Spn activity. To test directly whether the Lon protease has a role in YoeB_Spn toxicity in E. coli, two isogenic strains that were defective and not defective for the lon gene (MG1655 and MG1655lon, respectively) were transformed with the yoeB_Spn-containing plasmid pYBS2 (yoeB_Spn). Cells were treated identically by growing them under toxin induction conditions (with arabinose), and the effect of pneumococcal toxin overproduction was determined by measuring cell growth and CFU counting. The results showed that synthesis of the pneumococcal toxins led to growth arrest in both strains (Fig. 4A), indicating that inhibition of growth by YoeB_Spn does not seem to require lon expression. However, plotting the percentages of surviving cells of the lon⁺ and lon strains showed that there were differences between the Lon-proficient strain and the mutant. After 1 h of toxin synthesis, about 85% of the lon mutant bacteria were able to form colonies, but only 25% of the wild-type bacteria were able to form colonies (Fig. 4B). This result could be explained by a direct effect of the lon mutation, although at present we cannot rule out the possibilities that the two strains had different growth rates and that there were different levels of expression in the two strains. However, these possibilities seem unlikely since (i) the two strains had similar doubling times and at time zero the numbers of CFU were almost identical for the two strains (around 10⁷ CFU/ml) and (ii) expression of the relE2_Spn gene (encoding the pneumococcal toxin RelE2_Spn), using the same expression vector, resulted in up to a 5% reduction in the number of viable cells of a lon strain after 1 h of toxin overproduction (36).

FIG. 4.

Differences in YoeB_Spn and RelE2_Spn toxicity in E. coli lon⁺ and lon strains. (A) Inhibition of cell growth by overproduction of the pneumococcal toxins YoeB_Spn (○ and •) and RelE2_Spn (▴ and ▵) in E. coli strain MG1655 (lon⁺) (solid symbols) or in the lon isogenic mutant MG1655lon (open symbols). E. coli MG1655 (• and ▴) or MG1655lon (○) was grown in TY medium supplemented with kanamycin and 0.2% glucose (▪) or arabinose (•, ○, ▴, and ▵). Absorbance data were obtained at different times after the addition of arabinose. (B) To determine the number of CFU, samples were removed at various times and spread on TY agar plates containing 0.4% glucose and kanamycin. The percentages of viable cells were calculated by comparison of the numbers of CFU in the induced cultures to the numbers of CFU in the noninduced cultures at time zero.

Purification of YefM_Spn and of the (YefM-YoeB)_Spn complex.

A DNA fragment spanning the pneumococcal region that included either the (yefM-yoeB)_Spn genes or only the yefM_Spn gene was cloned in two different pET vectors (see Materials and Methods). The pneumococcal genes were placed under control of promoter φ10 of phage T7 (47), so IPTG induction led to synthesis of a His-tagged toxin-antitoxin complex or only a His-tagged antitoxin. The YefM_Spn antitoxin (9,953 Da) coprecipitated with the His-tagged YoeB_Spn toxin (11,467 Da) and eluted in a single broad peak (Fig. 5A). The proteinaceous yield of the purified complex was relatively high, as a considerable amount of complex (>15 mg) could be obtained from 2 liters of a bacterial culture. Compared to the yield of the complex, the proteinaceous yield of the His-tagged YefM_Spn antitoxin (12,457 Da) was lower (Fig. 5B). This was unexpected since the YefM_Eco antitoxin exhibited high solubility on the one hand and should not have provoked transcriptional or translational inhibition on the other hand, which may have led to such poor yields. However, we speculated that susceptibility of the antitoxin to proteases (due to partial unfolding [see below]) without an available cognate partner to stabilize it could have been the reason for the results observed.

FIG. 5.

Purification of (YefM-YoeB-His)_Spn complex and His-YefM_Spn antitoxin and indications of YefM-YoeB_Spn interaction. (A and B) Chromatograms showing the elution pattern of proteins from the nickel affinity column. Note that although the yield of the YefM_Spn protein (B) was poor, an increase in the absorbance was evident. However, no peak was observed, most likely because of the small amount of protein which was masked by the increase in the imidazole background absorbance. The results of SDS-PAGE analyses of eluted fractions are shown in the insets. RT, retention time; mAu, milli-absorbance units. (C) Elution profile of the YefM-YoeB_Spn protein complex from a 16/60 Sephacryl S-100 HR gel filtration column, showing a void volume of 45.89. The 45.89-ml peak with a K_av value of 0.1351 corresponds to an M_r of approximately 49,500. (D) E. coli two-hybrid indicator strain (Stratagene) (derived from XL-1 Blue MRF′) harboring plasmids pBT-LGF2 and pTRG-Gal11^P (positive control) (streak 1), pBT-yefM_Spn and pTRG (streak 2), pBT and pTRG-yoeB_Spn (streak 3), pBT and pTRG-Gal11^P (streak 4), pBT-yefM_Spn and pTRG-yoeB_Spn (streak 5), or pBT-yoeB_Spn and pTRG-yefM_Spn (streak 6) was streaked on selective medium containing 3-AT and incubated overnight at 37°C. Cotransformants in streaks 2, 3, and 4 were used as negative controls.

Analysis of YefM_Spn and YoeB_Spn interactions.

Crude lysates of E. coli cells overproducing the pneumococcal toxin and antitoxin were loaded onto a nickel affinity column under native conditions. Two distinct protein bands were observed during an SDS-PAGE analysis following elution with 500 mM imidazole, and the positions of these bands corresponded to the expected sizes of YefM_Spn and YoeB-His_Spn, indicating that under native conditions the two proteins copurified (Fig. 5A). This, in turn, suggests that the YefM_Spn protein may have formed a tight complex with its toxin counterpart. This inference was validated when the purified proteins were subjected to size exclusion chromatography. A single peak at 49.5 kDa was detected, suggesting that YefM_Spn and YoeB_Spn generated a protein complex with an apparent stoichiometry of (YefM_Spn)₂(YoeB_Spn)₂ (Fig. 5C). This finding agrees with the 2:2 stoichiometry observed for the E. coli YefM-YoeB complex based on size exclusion chromatography of approximately 0.2 mg/ml of the YefM-YoeB-His complex, although 2:1 and 2:4 stoichiometries were also observed, but with fewer occurrences (I. Cherny and E. Gazit, unpublished). In the case of the Kis-Kid proteins, 1:2, 2:2, and 2:1 stoichiometries were also found, although the results depended on the relative protein concentrations (27). Subsequent Western hybridization using an anti-His₆ antibody confirmed the identity of the protein.

To detect whether the two proteins interacted in vivo, a two-hybrid system was employed. To this end, the yefM_Spn and yoeB_Spn reading frames were cloned into both the pBT bait and pTRG target vectors for the two-hybrid assay as described in Materials and Methods. Positive protein-protein interactions, which were indicated by growth of the indicator strain harboring both the bait and target recombinants on the selection medium containing 5 mM 3-AT, were detected for both the positive control pBT-LGF2 and pTRG-Gal11^P (Fig. 5D, streak 1) and for the pBT-yoeB_Spn-pTRG-yefM_Spn pair (Fig. 5D, streak 6). However, when the interaction pair was changed (i.e., pBT-yefM_Spn and pTRG-yoeB_Spn instead of pBT-yoeB_Spn and pTRG-yefM_Spn), there was sparser growth of the indicator strain harboring both plasmids on the 3-AT-containing selective medium (Fig. 5D, streak 5).

Far-UV CD analyses of YefM_Spn and the (YefM-YoeB)_Spn complex.

The CD spectra of His-YefM_Spn at 4°C, 37°C, and 60°C included two negative bands at 217 nm and 208 nm (Fig. 6A). The first minimum corresponded to the presence of beta structures, whereas the second minimum, which was significantly lower, could be attributed to the presence of both α-helices and random coil conformations. Since the presence of α-helices contributed to the CD signals at both 208 nm and 222 nm (although it contributed more to the latter), the major negative band at 208 nm should be ascribed to the presence of considerable amounts of unstructured or flexible conformations. This is in agreement with the calculations for the secondary structure content using different deconvolution programs (Table 1), which estimated that 55 to 57% of the YefM_Spn conformations were unordered at 4°C. Intriguingly, despite having a large disordered content, the YefM_Spn antitoxin did not exhibit complete unfolding at elevated temperatures, even at 90°C (data not shown), like YefM or Phd homologues antitoxins exhibit (5, 18). The CD spectrum of the YefM-YoeB-His_Spn complex (Fig. 6B) at 4°C is compatible with an elevated occurrence of α-helices (47% α-helices, 10% β-strands, and 43% coils) (Table 1). With a temperature increase, part of the helical structures was lost in favor of β structures and, to some extent, in favor of an unordered conformation, as the CD minimum signals were weakened at both 221 and 208 nm and shifted to 218 and 207 nm.

FIG. 6.

Far-UV CD spectra of His-YefM_Spn (A) and (YefM-YoeB-His)_Spn complex (B) at 4°C (solid line), 37°C (dashed line), and 60°C (dotted line). (C) CD ellipticity of His-YefM_Spn (▴) and (YefM-YoeB-His)_Spn (○) was measured at 220 nm at various temperatures to estimate the thermal stability. The values were normalized between 0 and 1 and are expressed as fractional changes. (D) SDS-PAGE analysis of (YefM-YoeB-His)_Spn sample that was examined by CD analysis before and after exposure to 85°C. Lane M, marker; lane 1, before treatment (sample at room temperature); lane 2, after treatment (soluble fraction after exposure to 85°C).

TABLE 1.

Secondary structure contents determined from CD spectra

Protein(s)	Methoda	% in:
		α-Helices				β-Strands				Coilsb
		4°C	37°C	60°C	65°C	4°C	37°C	60°C	65°C	4°C	37°C	60°C	65°C
YefM	K2d	26	27	25		17	21	20		57	52	55
	Selcon3	26	24	19		19	20	23		55	56	58
	ContinLL	27	25	20		18	20	22		55	55	58
	CDsstr	25	23	17		19	19	24		56	58	59
	Avg	26	24.75	20.25		18.25	20	22.25		55.75	55.25	57.5
YefM-YoeB	K2d	55	37		28	9	15		15	36	50		57
	Selcon3	50	32		30	8	13		14	42	55		56
	ContinLL	38	39		34	6	11		14	56	50		52
	CDsstr	45	42		38	17	15		24	38	43		38
	Avg	47	37.5		32.5	10	13.5		16.75	43	49.5		50.75

^aK2d, K2d program developed by Andrade et al. (2); Selcon3, method developed by Sreerama and Woody (46); ContinLL, method developed by Provencher and Glockner (41); CDsstr, method developed by Johnson (25).

^bCoils consist of random conformations and turns.

The thermal stabilities of the antitoxin and the complex were estimated by monitoring the ellipticity at 220 nm (Fig. 6C) at various temperatures between 4 and 90°C. Both the antitoxin and the complex seemed to undergo unfolding when the temperature increased. However, two noteworthy differences were observed: (i) the unfolding rate of the antitoxin was higher than that of the complex (the difference in the melting temperatures was greater than 10°C, as estimated from the inflection points of the two melting curves), and (ii) following thermal melting the sample containing the complex became turbid, indicating that YoeB-His_Spn aggregation occurred during the melting. SDS-PAGE analysis of the soluble fraction which remained after heating (Fig. 6D) showed that the aggregation was predominantly related to the toxin, while the antitoxin remained soluble.

Molecular modeling of YoeB-YefM-like protein structures.

To shed some light on the structural basis of the interactions between members of the YefM and YoeB families of proteins, we constructed structural models for YefM_Spn, YoeB_Spn, Axe, and Txe (Fig. 7), based on the previously determined crystal structure of the E. coli YefM₂-YoeB heterotrimeric complex (26). Because in this complex the C-terminal segment of the YefM monomer, which docks mainly with YoeB, folds into an ordered structure, we used this major monomer as the antitoxin template (YefM-ordered monomer). In spite of an intricate atomic interaction network supporting the E. coli YefM₂-YoeB complex, recognition of the YoeB_Eco monomer is due to two sites of the YefM_Eco-ordered monomer; one site is composed of the H3 and H4 helices, and the other site is composed of an extended β-strand (26). For the toxin models, we used the YoeB_Eco monomer that belongs to the complex (YefM-bound YoeB). The levels of pairwise sequence identity for the alignments between the YoeB-like proteins (YoeB_Spn and Txe) and the template (51% and 52%, respectively) made it possible to construct reliable homology models for the YoeB_Spn and Txe toxins. On the other hand, the levels of pairwise sequence identity for the alignments between the YefM-like proteins (YefM_Spn and Axe) and the template (24% and 27%, respectively) are in the so-called “twilight zone” for reliable homology modeling, although the levels of sequence similarity for the residues encompassing the two sites for recognition of YoeB by YefM are 67% and 56%, respectively. Additionally, the intrinsic qualities of the YefM_Spn and Axe models were probed and confirmed by using several specific programs (WHAT_CHECK, PROCHECK, and Verify 3D). Thus, the aim of this modeling study was to perform a comparative analysis of some structural features of the interaction domains of the YefM-like and YoeB-like proteins.

FIG. 7.

Surface electrostatic potentials of the interaction domains of the antitoxins YefM_Eco (A), YefM_Spn model (C), and Axe model (E) with their cognate YoeB toxins and surface electrostatic potentials of the toxins YoeB_Eco (B), YoeB_Spn model (D), and Txe model (F). All the surfaces are oriented facing the interacting side and in equivalent positions (by superposition with the CE algorithm). Positive potentials are blue, and negative potentials are red.

With all the considerations described above, we focused on the interaction domain of YefM-YoeB, and we performed an analysis of the surface electrostatic potentials of the structural models. The positively charged hindrance defined by the YefM_Eco R72 residue in the neutral H4 helix was shown to be the main part of the electrostatic interaction with the negatively charged pocket on the interface of YoeB_Eco (26); the equivalent residue is K64 in the pneumococcal antitoxin. This positively charged moiety seems to be also exposed in the Axe model but not in the YefM_Spn model (Fig. 7A, B, and C), and there are no other apparent differences between the surface electrostatic potentials of the antitoxins. The change in the distribution of charges in the residues that configure this region in the pneumococcal antitoxin could indicate that single amino acid substitutions may not necessarily lead to a total loss of antitoxin activity. The lack of this positively charged patch in the YefM_Spn antitoxin could explain its failure to neutralize the heterologous YoeB_Eco toxic effect; in addition, it suggests that interaction of the pneumococcal TA could involve other residues. A detailed mutational analysis of this region should clarify this possibility. When the models of the toxins were examined, an analysis of the surface electrostatic potentials showed that there were no significant differences (Fig. 7D, E, and F). However, a quantitative analysis of the solvation energies of the surface areas calculated with the program GETAREA (http://www.scsb.utmb.edu/getarea/) proved that the YoeB_Spn structural model has a larger exposed surface (7% larger polar area) than the other two toxins as a result of 9 surface atoms more than the YoeB_Eco-ordered monomer and 18 buried atoms less than the YoeB_Eco-ordered monomer. This structural feature of YoeB_Spn increases the potential interaction surface and influences a wider range of protein interactions, leading to a likely explanation for the ineffectiveness of the YefM_Eco antitoxin for counteracting the toxic effect of the pneumococcal toxin. Definite insights into the structural interface of the pneumococcal YefM-YoeB complex, however, await X-ray crystallographic resolution data for this TA system.

DISCUSSION

The yefM-yoeB_Spn locus has been identified as a new chromosomal TA system of S. pneumoniae. Overproduction of the pneumococcal YoeB_Spn toxin in E. coli cells resulted in cytotoxic effects commonly linked to toxin activity. However, the size of the negative effect mediated by YoeB_Spn depended on the strain used; whereas in the K-12 strains used, TOP-10 and MG1655, the reductions in the number of CFU were more than 10⁴- to 10⁵-fold, respectively, in the E. coli B strain (BL21) the reductions in the number of CFU were more than 10⁸-fold (Fig. 1). This influence of the type of strain used on the YoeB toxicity could explain the previous inability to obtain transformants from plasmid DNA harboring the yoeB_Eco gene in an E. coli B strain (26). The differences in the reduction in the number of viable cells for the E. coli strains used could have been due to different levels of expression of yoeB_Spn or to different sensitivities of the genetic backgrounds. The yefM-yoeB_Spn cassette functions as an antitoxin-toxin module both in S. pneumoniae (unpublished results) and in E. coli (Fig. 1 to 4), and it seems likely that degradation of the pneumococcal antitoxin by a Lon-type protease could trigger the YoeB_Spn toxic activity in S. pneumoniae. In the case of E. coli, it has been shown that Lon overproduction stimulates the toxic activity of YoeB_Eco and that a Δlon strain is less sensitive to YoeB_Eco overproduction than a lon⁺ strain is, indicating that the Lon protease could be responsible for antitoxin degradation and the subsequent activation of YoeB_Eco (7). Our results (Fig. 4) suggested that the activity of YoeB_Spn did not require degradation of the E. coli antitoxin. We hypothesized that Lon could mediate the toxicity of YoeB-like proteins by antitoxin degradation and/or by an antitoxin degradation-independent mechanism.

Overproduction of YoeB_Spn resulted in cessation of cell growth and a substantial decrease in the number of CFU, which then increased gradually as the time of toxin synthesis increased (Fig. 1 and 2). The reduction in cell viability was alleviated by antitoxin expression for almost 2 h, so that at this time the number of CFU was reduced only 60%. After 4 h of exposure to the toxin, neutralization by the antitoxin resulted in 4% viability, compared to the 0.4% viability in the absence of antitoxin synthesis (Fig. 3). The YoeB_Spn toxin could inhibit protein synthesis by mRNA degradation like its E. coli homolog (7, 26). Overproduction of the pneumococcal toxin for extended periods of time could lead to very low levels of translation, thus favoring the senescence processes and finally leading to cell death. We believe that the function of the YoeB_Spn toxin is to promote cell growth arrest under stress conditions; in a physiological situation, the amount of free toxin could be enough to reduce cell growth but permit a residual level of protein synthesis, so that the cells could be protected from irreversible damage and the metabolism could adapt to the unfavorable conditions.

The toxic effect of YoeB_Spn could be neutralized by its cognate antitoxin, YefM_Spn, but not by the E. coli counterpart (Fig. 2). This behavior is different from that of the YoeB_Eco toxin, whose activity was counteracted by both the cognate YefM_Eco antitoxin and antitoxin Axe encoded by the axe-txe locus of plasmid pRUM (22). The lack of cross-complementation suggested that there is not a favorable interaction between the two heterologous proteins, namely, YoeB_Spn and YefM_Eco. Far-UV CD analysis of the YefM_Spn protein and of the (YefM-YoeB)_Spn complex indicated that unlike YefM_Eco, YefM_Spn does not seem to be an unfolded protein in its native state, although this does not necessarily mean that is a well-structured protein. It may include exposed regions that are not available for proteases in its bound form (in a complex with the toxin). This hypothesis is supported both by its lower thermal stability (melting temperature, ∼45°C) compared to that of the complex (melting temperature, ∼70°C) and by its resistance to heat (at least 85°C) (Fig. 6D). The latter property also suggests that YefM_Spn lacks a significant hydrophobic core, which in turn may be important to keep it proteolytically unstable. The difference between the YefM proteins was also detectable in the analysis of their amino acid sequences; alignment of the proteins revealed that their C-terminal portions (the region that binds the YoeB toxin) are different and cannot be aligned.

The fact that there is a considerable unstructured region in YefM_Eco may explain the structural difference between the two proteins and may also explain the lack of complementation between the toxins and the heterologous antitoxins, which was apparent from the molecular modeling of the proteins (Fig. 7). This in turn may indicate that the specific interactions of a toxin with its cognate antitoxin could be related to the mechanism of survival in the different niches that the bacteria colonize (e.g., the gut for E. coli and the nasopharynx for pneumococci). In the case of strain R6 of S. pneumoniae (24), two different functional TA loci, namely relBE2_Spn and yefM-yoeB_Spn, the residual nonfunctional relBE1_Spn genes (36), and a putative homolog of omega-epsilon-zeta (13; J. C. Alonso, personal communication) are present in the chromosome. In the case of virulent strain TIGR4 (48), in addition to these three loci, there are two more putative TA loci (37), one locus homologous to P1 phage phd/doc (30) and the other homologous to Rts1 plasmid higBA (49). YoeB and RelE toxins have similar toxic activities, but they have different mRNA cleavage patterns and sets of features that could enable the two TA systems to play different roles. First, RelE cleaves at UAG, UAA, UGA, UCG, and CAG sequences with preference for the stop codon UAG (39), and a similar pattern has been observed for pneumococcal RelE2_Spn (9); cleavage of mRNA by YoeB_Eco occurs predominantly at the 3′ end of adenine or guanine residues (26). Second, RelE-dependent cleavage occurs only in the ribosome (39), whereas YoeB_Eco has an intrinsic RNase activity and is able to cleave RNA in the absence of ribosomes (26). Third, structure-based comparisons (26) revealed that the residues involved in the RNase activity of YoeB_Eco (D46, H83, and Y84) are not conserved in RelE, with the exception of R65, suggesting that RelE could be an incomplete RNase which lacks the essential residues for catalytic activity. Finally, the signal that triggers mRNA cleavage could be different, since RelE activity in E. coli is induced by amino acid starvation (10), whereas the Lon protease triggers YoeB_Eco-dependent RNA cleavage (7). Thus, either TA systems could act through independent mechanisms or they could work together under stress conditions (i.e., amino acid starvation), as has recently been suggested for RelE and MazF (12). The combined action of the two toxins with RNase activity (namely, YoeB_Eco with free mRNA and RelE with mRNA bound to ribosomes) could lead to significant depletion of mRNA and an effective, but not total, block of translation, leaving low levels of antitoxin synthesis which could result in toxin-mediated arrest of cell growth but not in induction of a bacterial death response.

Even though TA loci appear to be nonessential, it is curious that in many bacterial species more than one TA locus is conserved in the chromosome and in plasmids. The role of the TA systems in the extrachromosomal elements is related to stable inheritance, or the TA systems may be triggered when a plasmid cannot replicate (4, 14). Furthermore, all E. coli TA loci can be deleted without causing significant growth differences in the wild-type strains (7, 8, 36, 38). However, antibiotics that inhibit transcription and/or translation in E. coli and induce mazEF-dependent cell death do not reduce cell viability in mazEF mutants (42). Mutations affecting both MazF and RelE activities in Streptococcus mutans resulted in cells whose acid tolerance and growth in glucose-based medium were affected (32). In the case of Neisseria gonorrhoeae workers have identified a mutant with a mutation in a putative TA system (designated FitAB for fast intracellular trafficking; function unknown) which grows normally extracellularly but has a higher rate of intracellular replication, and there is a concomitant increase in the rate at which this mutant traverses a monolayer of polarized epithelial cells (34).

Taking into account the complexity of the “biological niches” of S. pneumoniae and other pathogenic bacteria, it is very simplistic to attempt to ascertain the function of the TA system when cells are growing in a culture medium. Bacteria grow in communities with other living cells and surely compete with each other for the surrounding nutrients. In these bacterial environments the levels of nutrients are not as high as those used in laboratory conditions. For S. pneumoniae, the mucosal epithelium of the nasopharynx is the primary site of colonization, where it does not cause any symptoms of illness. Occasionally, bacteria can switch from colonization to infection in the lungs, blood, and other tissues, and many times they traverse the blood-brain barrier and infect the meninges. Consequently, S. pneumoniae has to adapt to different situations, and perhaps in these different situations the TA systems play an important role in survival when the bacteria are exposed to host defenses.