Direct and inverted repeats elicit genetic instability by both exploiting and eluding DNA double-strand break repair systems in mycobacteria.

Repetitive DNA sequences with the potential to form alternative DNA conformations, such as slipped structures and cruciforms, can induce genetic instability by promoting replication errors and by serving as a substrate for DNA repair proteins, which may lead to DNA double-strand breaks (DSBs). However, the contribution of each of the DSB repair pathways, homologous recombination (HR), non-homologous end-joining (NHEJ) and single-strand annealing (SSA), to this sort of genetic instability is not fully understood. Herein, we assessed the genome-wide distribution of repetitive DNA sequences in the Mycobacterium smegmatis, Mycobacterium tuberculosis and Escherichia coli genomes, and determined the types and frequencies of genetic instability induced by direct and inverted repeats, both in the presence and in the absence of HR, NHEJ, and SSA. All three genomes are strongly enriched in direct repeats and modestly enriched in inverted repeats. When using chromosomally integrated constructs in M. smegmatis, direct repeats induced the perfect deletion of their intervening sequences ~1,000-fold above background. Absence of HR further enhanced these perfect deletions, whereas absence of NHEJ or SSA had no influence, suggesting compromised replication fidelity. In contrast, inverted repeats induced perfect deletions only in the absence of SSA. Both direct and inverted repeats stimulated excision of the constructs from the attB integration sites independently of HR, NHEJ, or SSA. With episomal constructs, direct and inverted repeats triggered DNA instability by activating nucleolytic activity, and absence of the DSB repair pathways (in the order NHEJ>HR>SSA) exacerbated this instability. Thus, direct and inverted repeats may elicit genetic instability in mycobacteria by 1) directly interfering with replication fidelity, 2) stimulating the three main DSB repair pathways, and 3) enticing L5 site-specific recombination.

Introduction

The first genome of a Mycobacterium tuberculosis strain was sequenced in 1998 [1] and since then additional strains, including other species of the Mycobacterium genus have been sequenced, with 24 M. tuberculosis complete genomes currently available (http://www.ncbi.nlm.nih.gov/genome/genomes/166) [2]–[4]. Sequence analyses of these genomes revealed considerable conservation overall, with as much as 99.95% identity between M. tuberculosis and M. bovis [4], the main difference being the presence and distribution of repeat elements, including insertion sequences (IS), direct repeats (DR) and mycobacterial interspersed repetitive units, a locus containing variable numbers of tandem repeats (MIRU-VNTR). Indeed, because of the high variability in location and sequence, these and other repetitive elements have served as a tool for molecular typing of M. tuberculosis in human isolates [5], [6].

Simple sequence repeats (SSRs), a subset of DNA motifs comprising short tandem repeats of 1–6 nucleotide units, are distributed throughout the mycobacterial genomes at an average of 220–230 tracts per kb [7]. SSRs have been shown to exhibit higher mutation rates than genome-wide average, in both eukaryotes and prokaryotes [8]–[14]. This distinct property has in part been associated with the ability of SSRs to adopt alternative DNA conformations (non-B DNA), in addition to the canonical right-handed B-form [15]–[19], and to promote slipped misalignment and other replication errors during DNA synthesis [20], [21].

Studies over the past few decades have revealed that various types of DNA sequences, in addition of SSRs, may adopt non-B DNA conformations, including DRs (which can form slipped/hairpin structures), inverted repeats (IRs, cruciform structures), polypurine•polypyrimidine tracts with mirror symmetry (triplex conformations), alternating purine-pyrimidine tracts (left-handed Z-DNA) and four closely-spaced runs of 3–5 guanines (G-quadruplexes) [15], [22]–[28]. In addition to a regulatory role during transcription [29]–[32], non-B DNA structures have been implicated in causing genetic instability, including deletions, translocations, and single base substitutions, associated with human disease etiology [16], [22], [33].

The molecular mechanisms underlying the genetic instability induced by repetitive DNA sequences remain to be fully elucidated; however, proteins involved in replication, transcription, and DNA repair pathways have been implicated, by either generating or processing strand breaks in proximity of the repeats [16], [34]–[41]. DNA double-strand breaks (DSBs) lead to cell death if left unrepaired, and homologous recombination (HR) and non-homologous end-joining (NHEJ) are considered the two main pathways for processing DSBs. Thus, the detection of microhomologies at breakpoints of deletions and translocations induced by repetitive DNA has prompted speculation that NHEJ serves as the major pathway for the repair of repetitive DNA-dependent genetic instabilities [30], [42].

Little is known of the genome-wide distribution of repetitive DNA motifs in mycobacteria and their processing by DNA repair systems. We and others have shown that, in addition to HR, mycobacteria possess a prototypical NHEJ apparatus encoded by evolutionarily conserved ku and ligD genes [41], [43]–[48], as well as a single-strand annealing (SSA) pathway [49]. Herein, we conducted genome-wide in silico investigations in M. smegmatis, M. tuberculosis, and E. coli to identify potential non-B DNA-forming repeats, and report that both mycobacterial species are strongly enriched in DRs and IRs. M. smegmatis and E. coli were used as model systems to investigate the roles of DRs and IRs in inducing deletions, both in wild-type strains and in strains deficient in the common HR pathway or the mycobacterial-specific NHEJ and SSA functions, using both integrated and episomal systems. In M. smegmatis, DRs elicited deletions of the intervening sequence even in the absence of functional HR, NHEJ or SSA, whereas both types of repeat induced large deletions, particularly in the DSB repair-deficient strains, in the order ΔNHEJ>ΔHR>ΔSSA. In addition, both DRs and IRs stimulated L5 site-specific recombination at the attB site, causing loss of the integrated constructs at much higher frequencies than the non-repeat-containing constructs (which did not carry DR or IR sequences). In E. coli, DRs were inert, whereas IRs induced negative supercoiling-dependent and HR-dependent deletions, suggesting a role for non-B DNA structure formation and replication, respectively.

We conclude that, on the one hand, repetitive DNA motifs may pose a challenge to genome stability in mycobacteria, which respond by employing their DSB repair functions. On the other hand, by acting upon a large pool of repetitive sequences, DNA repair may contribute to genomic diversity and adaptation.

Materials and Methods

Bacterial strains and cell culture conditions

The bacterial strains are listed in Table S1. Mycobacterial strains were cultured in 8 g/L NB (Nutrient Broth, Difco) and 10 g/L glucose. As required, further additions included: 0.2% Tween-80 (pH 6.0–6.2), 50 µg/mL hygromycin (Hyg), 7.5 µg/mL gentamycin (Gm, 25 µg/mL if used together with kanamycin), and 25 µg/mL kanamycin (Km). E. coli strains were cultured in LB media (10 g/L trypton, 5 g/L yeast extract, 10 g/L NaCl, pH 7.0). As required, further additions included 100 µg/mL ampicillin (Amp), 200 µg/mL Hyg, 10 µg/mL Gm (50 µg/mL if used together with Km) and 50 µg/mL Km.

Cloning

Constructs were engineered on the basis of the pMV206Km E. coli/Mycobacterium shuttle vector and the pMV306Km mycobacterial integration vector (Figure S1). Specifically, the hph gene (HygR) was disrupted by cloning synthetic oligonucleotides, comprising either two pairs of IRs or two DR units, within the EcoRI site of the gene using standard protocols. DRs and IRs were further separated by cloning the aacC1 gene (GmR) in orientations A and B. This resulted in two pairs of IRs or one pair of DRs, on either side of the aacC1 gene. The disrupted hph was also flanked, 5′ and 3′ respectively, by the aph (KmR) and lacZ (conferring blue color) genes (Figure 1). This yielded two sets of plasmids: pDRIA, pDRIB, pIRIA, pIRIB and pDREA, pDREB, pIREA, pIREB (I, integrated; E episomal) (Table S2). The plasmid sequencing data have been deposited in GenBank with the following accession numbers: BankIt1574770 pDREA JX993915, BankIt1574770 pDREB JX993916, BankIt1574770 pDRIA JX993917, BankIt1574770 pDRIB JX993918, BankIt1574770 pIREA JX993919, BankIt1574770 pIREB JX993920, BankIt1574770 pIRIA JX993921, BankIt1574770 pIRIB JX993922.

Figure 1

Key features of integration and self-replicating constructs.

Panel A, OligoIR and OligoDR constructs. The hph (HygR, dark blue) gene was interrupted by two pairs of IRs (top) or one pair of DRs (bottom; black and maroon arrows over blue/red) flanking the aacC1 (GmR, green) gene in both orientations (A and B). These cassettes were further flanked by the aph (KmR, orange) gene on the left and the lacZ (blue color, light blue) gene on the right. Panel B, detailed DNA sequence of the IRs and DRs and the relevant restriction sites (EcoRI and ScaI) used during cloning. Note that because the sequence is given in the 5′→3′ direction with respect to the hph gene, the map is opposite to that shown in Panel A.

Constructs were used to engineer E. coli and mycobacterial strains. The plasmids, or chromosomal DNA, of mycobacterial transformants were recovered and analyzed as described [50]. To determine the extent to which the IR and DR sequences induced genetic instability, PCR analyses were performed to identify loss-of-function of the aacC1 and hph genes. In addition, PCR analyses and Southern blot hybridization were employed to assess the instabilities at the attB region of the mycobacterial genome. For the Southern blots, a hybridization probe was generated by PCR and labeled by a non-radioactive primer extension system (DIG-labeling system, Amersham). The primers used for PCR amplification are listed in Table S3.

To perform unmarked deletions of recBCD genes in M. smegmatis we used a suicidal recombination delivery vector based on p2NIL. The recombination vector carried the region upstream from recC together with its 5′ end and the region downstream of recD with its 3′ fragment cloned together (Figure S2). Finally, the PacI screening cassette from pGOAL17 was inserted into the constructs, resulting in the suicide delivery vector pMK212, which was then used to engineer the ΔrecBCD M. smegmatis strain (Table S1), as described previously [51], [52]. The resultant mutant strain was verified by PCR and Southern blot hybridization (Figure S2).

Protocol for assessing genetic instabilities caused by DR and IR sequences in M. smegmatis and E. coli

Constructs (Figures 1 and S1) were introduced into the appropriate M. smegmatis and E. coli strains and blue, KmR and GmR colonies were selected. Plasmid instability was determined on non-selective plates by overnight (E. coli) or 48 h (M. smegmatis) growth of KmR, GmR and blue colony-forming units (CFUs) on LB/NB agar plates, which were then washed-out and plated at the appropriate dilutions on LB/NB agar plates supplemented with either 5-bromo-4-chloro-3-indoxyl-beta-D-galactopyranoside (X-gal) or Hyg. CFUs from X-gal plates were further transferred by replica plating on four LB/NB agar plates that contained the following indicators: 1) Km plus Hyg; 2) Km plus Gm; 3) Km alone and 4) X-gal (Figure S3). The number of ensuing individual CFUs was counted and used for statistical analyses. The frequencies of mutations from 3–6 experiments were analyzed statistically using either the χ2 test on 2×2 contingency tables, the z-test or the pair-wise Holm-Sidak test. The Holm-Sidak test was used for the frequency data with standard deviations. In the case where the data were obtained from replica plating, the low numbers of CFUs per plate were cumulatively added (comparing to about 1,000 CFUs from the plates with no selection) and analyzed by the chi square test or the z-test, since these allow comparisons between observed and expected observations.

Identification of repeat elements in bacterial genomes

Putative non-B DNA-forming motifs, including tandem repeats, DRs, IRs, R•Y tracts and quadruplex-forming motifs were identified in the genomes of M. tuberculosis, M. smegmatis, and E. coli using the criteria reported in Table S4. In the case of IRs, the spacing between repeats was set to ≤20 bases, since cruciform formation tends to be discouraged by large loops (i.e. the bases separating the repeats). By contrast, no minimum loop size is known to prevent direct repeats from interacting; therefore, we allowed any space between DRs. The complete genome sequences of M. tuberculosis H37Rv (NC_000962), M. smegmatis str. mc2155 (NC_008596), and E. coli str. K-12 substr. MG1655 (NC_000913) were downloaded from the National Center for Biotechnology Information (NCBI) ftp server at ftp://ftp.ncbi.nih.gov/genomes/Bacteria/. Tandem repeats were analyzed by the mreps software [53], DRs were identified according to the repeat-match algorithm of the MUMmer package [54], IRs were screened with the palindrome program of the EMBOSS package [55] and the R•Y and quadruplex-forming motifs were identified using in-house Perl scripts. To determine whether the numbers and lengths of repeats were greater than expected by chance, we compared the observed distributions with those predicted by reshuffling the respective genome sequences 1,000 times using shuffleseq (EMBOSS).

Results

DRs and IRs are overrepresented in mycobacterial genomes

Repetitive DNA sequences, including tandem repeats, DRs, IRs, G-rich regions, and R•Y tracts with mirror symmetry are abundant in many genomes and have been implicated in inducing genomic instability, in part through the formation of DNA strand breaks triggered by the transient formation of non-B DNA conformations [14]–[17], [33], [38], [56]–[58]. To identify such structure-forming sequences in mycobacteria, we conducted in silico genome-wide searches for repetitive motifs (Table S4) in the reference genomes of M. smegmatis and M. tuberculosis, the causative agent of tuberculosis, and E. coli.

For each repeat type, we assessed if the numbers and lengths of repeats were greater than expected by chance alone. Hence, we compared the observed genome-wide distributions with those predicted by randomly reshuffling the chromosomal sequences, which generates Gaussian ensembles of repeat numbers as a function of length. Note that for sets of repeats, such as the set of >24 IS1096 elements in the M. smegmatis mc2155, each element was counted as one repeat. For DRs, the maximum lengths of the predicted sequences did not exceed ∼20–25 bases, whereas the observed length distributions showed the presence of repeats up to thousands of bp in all three genomes, with a gradual decline in the number of sequences as a function of length (Figure 2A, C and E). We found that 1,146,588 nt of DRs (33.58% of the total length of all DRs) accounted for 165 genes annotated to the PE, PE-PGRS, and PPE families in the M. tuberculosis genome, whereas only 12,575 nt of DRs (0.13% of the total length of all DRs) in 10 such annotated genes were found in the M. smegmatis genome. Thus, the PE and PPE gene families contribute to the distribution of DRs substantially more in M. tuberculosis than in M. smegmatis. Transposons also contributed to the high number of DRs, particularly in mycobacteria, although this is unlikely to fully account for the differences between mycobacteria and E. coli.

Figure 2

Direct and inverted repeats are overrepresented in mycobacterial and E. coli genomes.

Genome-wide distributions of DRs and IRs. Panels A and B, E. coli K12; panels C and D, M. smegmatis; panels E and F, M. tuberculosis; left panels, direct repeats (DR); right panels, inverted repeats (IR); x-axes, length of repeats in nucleotides; y-axes, number of repeats; open symbols, predicted random distributions; closed symbols, observed distributions.

IRs were found to be overrepresented in the three bacterial species (Figure 2B, D and F); however, both the difference between the predicted and observed maxima in bp lengths (Figure 2 and Table S5) and the maximum numbers of observed sequences (Figure 2, maximum y-axis values) were ∼3 orders of magnitude smaller for IRs than for DRs (maxima in bp lengths near y = 100 was ∼14 bp vs. ∼19–32 bp, i.e. ∼2-fold difference for IRs and ∼23 bp vs. ∼1,697–55,473 bp, i.e. ∼50–2,000-fold difference for DRs; max. y-axes = ∼250–460 bp for IRs and ∼40,000–400,000 bp for DRs).

Tandem repeats only accounted for a small proportion (9% in E. coli, 4% in M. tuberculosis, and 3% in M. smegmatis) of all DRs (Table S5), such that ∼60,000 (E. coli), ∼190,000 (M. tuberculosis) and ∼585,000 (M. smegmatis) non-tandem DRs exist in these genomes. Hence, the genome-wide potential for genomic instability due to DR interactions, such as during replication, is ∼3 to 10-fold higher in the two mycobacterial species than in E. coli. For G-quadruplex, Z-DNA, and triplex-forming sequences, no differences were observed between the predicted and observed distributions (data not shown). In summary, a significantly greater number of long DRs than expected by chance alone, along with a modest enrichment in IRs, are present in the three bacterial species, particularly in the mycobacterial genomes, which may serve as substrate for genomic instability.

DRs induce precise deletion of the intervening sequence in mycobacteria but not in E. coli

To assess the contribution of DRs and IRs to deletions in mycobacterial genomes, synthetic constructs were engineered and integrated in M. smegmatis by L5 site-specific recombination at the attB site [59]. Two pairs of IRs (OligoIR) (Figure 1A), each predicted to fold into a cruciform structure comprising a 16 and 18 bp stem with an EcoRI (GAATTC) site in the center (Figure 1B), or a 38-bp DR (OligoDR) (Figure 1), also containing an EcoRI site in the center, were cloned within the hph gene so as to abrogate the HygR phenotype (Figure 1). We reasoned that repair of DSBs or resumption of arrested replication forks within the IRs or DRs would be assisted by the homologous EcoRI single-stranded loop of cruciforms (OligoIR), or the 38-bp DR sequences, thereby leading to the precise deletion of the cloned inserts and reconstitution of the hph gene. The aacC1 gene conferring GmR was also cloned in both orientations between the DRs and IRs with the purpose of detecting imprecise deletions that would otherwise not confer HygR. OligoIR and OligoDR were further flanked by the aph (KmR) and lacZ genes to allow for scoring large deletions further away from the repeats through the loss of KmR and blue color (Figure 1A).

Selection for HygR CFUs indicating on precise deletion within repeated sequences yielded frequencies of 6.9±2.2 and 5.8±2.5×10−6 for pDRIA and pDRIB (superscript I stands for integrated), respectively, which harbored the OligoDR constructs and the aacC1 (GmR) gene in either orientation [A (pDRIA) or B (pDRIB); Figure 3A]. By contrast, no CFUs were obtained out of ∼8.5×109 plated cells when OligoIR was integrated in pIRIA (aacC1 in orientation A), pIRIB (aacC1 in orientation B) or in the control pCI, which is devoid of DR or IR sequences (Figure 3A). Thus, the 38-bp DR in OligoDR stimulated the rate of deletion of the intervening sequence (precise deletions) by at least 1,000-fold (p = 0,001 for pDRIA, p = 0,003 for pDRIB), regardless of the orientation of the internal aacC1 gene. The HygR phenotype was confirmed by PCR analyses using hph-specific primers (Figure S4 and Table S3).

Figure 3

OligoDR and OligoIR induce genetic instabilities in M. smegmatis and E. coli.

Panel A, reconstitution of hph (HygR) gene through the precise deletion of the aacC1 (GmR) is only detected with the integrated OligoDR, but not OligoIR, in M. smegmatis. x-axis, M. smegmatis mc2155 strains: pC, pMV306KmHyg::Gm (control); pIR, pMV306KmHyg::OligoIRGmA lacZ; pIR, pMV306KmHyg::OligoIRGmB lacZ; pDR, pMV306KmHyg::OligoDRGmA lacZ; pDR, pMV306KmHyg::OligoDRGmB lacZ; y-axis, frequencies of HygR CFUs: asterisks, p<0.05 (pair-wise Holm-Sidak test for pIRIA, pIRIB, pDRIA, pDRIB against pCI). Panel B, large deletions occur in both the integrated OligoDR and OligoIR constructs in M. smegmatis. x-axis, as in Panel A; y-axis, percent GmS (black bars), KmS (light grey bars), and white (dark grey bars) CFUs; IR, OligoIR; DR, OligoDR.; asterisks, p<0.05 (χ2 test of pIRIA, pIRIB, pDRIA, pDRIB against pCI, z-test of pIRIA against pIRIB and pDRIA against pDRIB). Panel C, OligoIR induces deletions in a supercoiling-dependent manner in E. coli. Percent GmS and KmS CFUs in E. coli strains containing various steady-state levels of negative supercoil density. x-axis, E. coli strains carrying the self-replicating OligoIR (pIREA) or OligoDR (pDREA) vectors: JTT1, wild-type; RS2, topA mutant, higher negative supercoil density than JTT1; SD2, topA and gyrB mutant, lower negative supercoil density than JTT1; y-axis, percent GmS and KmS CFUs, geometric mean (+/−SD) from 100 CFUs obtained from 3 independent experiments; black bars, OligoIR (pIREA); grey bars, OligoDR (pDREA); asterisks, p<0.05 (χ2 test of SD7 against RS2 and RS2 against JTT1).

Next, we investigated whether the OligoDR-stimulated precise deletions were specific to M. smegmatis. To address this, the control, direct (OligoDR) and inverted (OligoIR) repeat-containing inserts were transformed in both E. coli and M. smegmatis using a self-replicating episomal plasmid system (Figure S1 and Table S2). In M. smegmatis, both the control (pCE; superscript E, episomal) and the OligoIR-containing plasmids (pIREA and pIREB) yielded HygR CFUs at frequencies of 2.2±0.3 and 2.4±0.3×10−7, respectively (Figure S5). However, the OligoDR-containing plasmids in pDREA and pDREB led to an ∼1,000-fold increase (p = 0,001) in HygR CFUs to ∼2.0±0.7 and 2.5±1.0×10−4, respectively (Figure S5), in agreement with the data obtained from the integrated system. By contrast, no HygR CFUs were rescued in E. coli with any of the self-replicating plasmids. Hence, we conclude that 1) the ∼1,000-fold stimulation of precise deletions elicited by the 38-bp DRs was specific to M. smegmatis; and 2) both the integrated and episomal plasmid systems were concordant in revealing this type of mutational event.

IRs and DRs induce large deletions in both M. smegmatis and E. coli

The lack of HygR CFUs in the presence of OligoIR and the induction of precise deletions by OligoDR in M. smegmatis but not in E. coli raised the question as to whether the sequences were able to form the predicted cruciform and looped-out structures, or whether differences in the repair or replication systems between these two species (such as the presence of NHEJ in M. smegmatis) were involved. To address these possibilities, M. smegmatis carrying the integrated OligoIR (pIRIA and pIRIB) or OligoDR (pDRIA and pDRIB) constructs were screened for large deletions by the loss of KmR or blue phenotypes caused by the inactivation of the aph and lacZ genes, respectively (Figure 1). KmS CFUs were detected at approximately 0.8% in the control pCI (Figure 3B). However, a significant 3- to 4-fold increase in KmS and white CFUs was observed in the presence of either OligoIR or OligoDR (p = 0,0005 for pIRIA, p = 0,01 for pIRIB, p = 0,001 for pDRIA, p = 0,01 for pDRIB), depending on the orientation of the internal aacC1 (Figure 3B). Specifically, orientation A in pIRIA (OligoIR) and pDRIA (OligoDR), in which the hph and accC1 genes were transcribed from complementary strands, yielded greater instabilities (p = 0,03) than the alternative orientation B (Figures 1A and 3B). These results support the conclusion that both IRs and DRs were able to induce large deletions in M. smegmatis. Moreover, the greater instability observed by divergent transcription of the aacC1 and hph genes (orientation A, Figure 1A) was consistent with our expectation, since this enables the accumulation of greater negative supercoiling during RNA polymerase translocation than same-sense transcription, which should favor B-DNA to non-B DNA structural transitions [60], [61].

To assess whether the IRs and DRs were giving rise to non-B DNA structures, OligoIR (pIREA and pIREB) and OligoDR (pDREA and pDREB) were transformed as self-replicating plasmids into isogenic E. coli strains that, because of mutations in the gyrase and topoisomerase I genes (Table S1), contained different steady-state levels of negative supercoiling. The use of E. coli strains deficient in gyrase/topoisomerases is a convenient and well-documented tool to address the requirement of torsional stress on the transitions between B-DNA and non-B DNA structures [62], [63]. In the wild-type JTT1 strain, in the presence of OligoIR ∼2±1% CFUs were found to be GmS and KmS as a result of large deletions (Figure 3C). In the RS2 strain, which sustains higher levels of negative supercoil densities than JTT1, a significant increase (p = 0,02) in GmS and KmS (7±1%) CFUs was observed, whereas in the SD7 strain, which is characterized by low levels of negative supercoil densities, a significant reduction (p = 0,002) in deletions (as assessed by GmS and KmS (1±0%) CFUs) compared to RS2 was revealed (Figure 3C). Alternatively, no differences in the fractions of GmS and KmS CFUs were noted in these strains for the OligoDR-containing plasmids (Figure 3C).

These results are consistent with the conclusion that the IRs in OligoIR were able to fold into cruciform structures, which then served as substrates for the generation of large deletions, both in E. coli and M. smegmatis. The lack of induction of large deletions by OligoDR in E. coli suggests that the distant repeats were either prevented from interacting to give rise to slipped structures or, if DNA secondary structures were formed, they were resolved in an error-free manner. Alternatively, differences in DNA replication-dependent misalignment between the repeats might have been involved. In summary, DRs were substantially more mutagenic in M. smegmatis than in E. coli.

The precise deletions stimulated by DRs in M. smegmatis occur independently of NHEJ, HR and SSA

In addition to HR, a conserved pathway for the repair of DSBs in most organisms, M. tuberculosis and M. smegmatis (but not E. coli) also express an NHEJ activity that uses Ku and DNA ligase D (LigD) to process DSBs [44], [64], [65] without the need for large regions of sequence homology. Thus, we investigated whether the precise deletions induced by the chromosomally integrated OligoDR in M. smegmatis (Figure 3A) involved either the HR or the NHEJ pathways. To this end, we employed mutant strains (Table S1) in which either one or both DNA repair pathways were inactivated [45], [46]. Knocking out the NHEJ pathway in the Δ(ku ligD) M. smegmatis mutant did not significantly impair the ability of OligoDR [pDRIA (p = 0,5) and pDRIB (p = 0,2)] to stimulate precise deletions, as assessed by the number of HygR CFUs (Figure 4A).

Figure 4

Deletions occur independently of NHEJ and HR in M. smegmatis.

Panel A, precise deletions stimulated by DRs occur independently of NHEJ and are increased in the absence of RecA. x-axis, M. smegmatis strains: wt/pDR, wild-type/pMV306KmHyg::OligoDRGmA lacZ; Δku, Δku/pDRIA; Δ(ku ligD), ΔkuΔligD/pDRIA; ΔrecA, ΔrecA/pDRIA; Δ(recA ku ligD), ΔrecAΔkuΔligD/pDRIA; y-axis, frequencies of HygR CFUs; asterisks, p<0.05 (pair-wise Holm-Sidak test for mutant strains against wild-type). Panel B, large deletions are stimulated by HR (RecA) in E. coli. x-axis, E. coli strains carrying the self-replicating OligoIR vector pIREA; wt, KMBL1001; ΔrecA, Top10 mutant; asterisks, p<0.05 (χ2 test of mutant strains against wild-type). Panels C and D, large deletions occur independently of NHEJ and HR in M. smegmatis. x axis, M. smegmatis strains; y-axis, percent KmS (black bars) or GmS (grey bars) CFUs. Panel C, M. smegmatis strains: wt/pC, wild-type/pMV206KmHyg::Gm (control); wt/pIR, wild-type/pMV206KmHyg::OligoIRGmA lacZ; Δ(ku ligD), ΔkuΔligD/pIREA; ΔrecA, ΔrecA/pIREA. Panel D, M. smegmatis strains: wt/pC, as in Panel D; wt/pDR, wild-type/pMV306KmHyg::OligoDRGmA lacZ; Δ(ku ligD), ΔkuΔligD/pDREA; ΔrecA, ΔrecA/pDREA (asterisks, p<0.05 (χ2 test of mutant strains against wild-type).

RecA is a critical protein that facilitates the strand exchange reaction during HR [66]. In the absence of RecA (Δrec M. smegmatis), OligoDR-dependent precise deletions were significantly enhanced (∼5-fold; p = 0,0006 for pDRIA, p = 0,00001 for pDRIB) relative to the wild-type strain (Figure 4A). This indicates that strand invasion is not required for direct repeat recombination, but in fact may prevent these events. Similar findings have been reported in yeast and mammalian cells [67], [68]. In addition, the ΔrecA-dependent enhancement of precise deletions was not compromised in the absence of NHEJ in the Δ(recA ku ligD) M. smegmatis triple mutant. These results indicate that neither HR nor NHEJ were involved in the process(es) that deleted the sequences separating the distant DRs. Recently, a third DNA repair pathway based on single-strand annealing (SSA) has been reported in M. smegmatis [49], which complements HR and NHEJ in processing DSBs at short DRs, and which relies on a dedicated RecBCD complex for end-resection. The ΔrecBCD M. smegmatis mutant strains (ΔrecBCD/pDREA, aacC1 in orientation A, ΔrecBCD/pDREB, aacC1 in orientation B), in which the entire RecBCD operon was ablated, yielded precise deletions at frequencies that were indistinguishable from the wild-type strains (wt/pDREA and wt/pDREB), (Figure S6). This was in contrast with the results obtained with OligoIR (ΔrecBCD/pIREA and ΔrecBCD/pIREB), in which the fractions of precise deletions increased (p = 0,01) relative to the wild-type strains (wt/pIREA and wt/p IREB) ∼8- to 10-fold (Figure 5). Thus, we conclude that none of the three canonical DSB repair mechanisms, HR, NHEJ and SSA, was required for generating precise deletions between the distant DRs of OligoDR in M. smegmatis. In contrast, RecBCD was involved in preventing precise deletions between the distant pairs of IRs in OligoIR.

Figure 5

Precise deletions and SSA.

RecBCD deficiency increases the frequency of precise deletions between IRs. Panels A and B, x-axis, M. smegmatis strains; y-axis, frequencies of HygR CFUs; asterisks, p<0.05 (pair-wise Holm-Sidak test for ΔrecBCD M. smegmatis against wild-type). Panel A, wt/pC, wild-type/pMV206KmHyg::Gm (control); wt/pIR, wild-type/pMV206KmHyg::OligoIRGmA lacZ; ΔrecBCD/pIR, ΔrecBCD/pMV206KmHyg::OligoIRGmA lacZ. Panel B, wt/pC, as in Panel A; wt/pIR, wild-type/pMV206KmHyg::OligoIRGmB; ΔrecBCD/pIR, ΔrecBCD/pMV206KmHyg::OligoIRGmB.

IRs and DRs induced the excision of OligoIR and OligoDR by activating L5 site-specific recombination

In an effort to elucidate the potential mechanisms underlying the stimulation of large deletions by DRs and IRs in M. smegmatis (Figure 3B), we analyzed the attB loci of 118 white and KmS mutant CFUs by PCR, Southern hybridization, and DNA sequencing (Figure S7), including 3 CFUs from the control wt/pCI and 115 CFUs from strains harboring OligoDR (pDRIA and pDRIB) or OligoIR (pIRIA and pIRIB). These 115 CFUs comprised 31 wild-type, 38 Δku, 30 Δ(ku ligD), and 16 ΔrecA M. smegmatis strains. In all 118 cases, the entire integrated plasmid was deleted, whereas the attB sequences were precisely reconstituted. Integration of mycobacteriophage L5 is catalyzed primarily by the phage-encoded tyrosine integrase (Int-L5) and the host-encoded protein, mIHF, whereas the excision reaction during the prophage lytic cycle depends upon the recombination directionality factor (RDF), the product of phage gene 36 (Xis-L5) [69]. Our results suggest that DRs and IRs acted as stimulators of mycobacteriophage L5 site-specific recombination.

HR and NHEJ guard against DNA nucleolytic processing triggered by DR and IR sequences

Because of the stimulation of L5-dependent recombination by the DR and IR sequences, we used OligoIR (pIREA and pIREB) and OligoDR (pDREA and pDREB) as self-replicating plasmids, which uncouples the repeats from L5 site-specific recombination, to compare the interaction of DRs and IRs with the host DNA repair systems (M. smegmatis and E. coli). Thus, we determined the numbers of GmS, KmS and/or white CFUs in wild-type and mutant strains lacking components of HR (M. smegmatis and E. coli), NHEJ (M. smegmatis), or SSA (M. smegmatis). In the Top10 E. coli mutant strain (Table S1), absence of RecA significantly repressed the instabilities induced by OligoIR (pIRIA and pIRIB) ∼10-fold (p = 0,0008 and p = 0,00001, respectively) relative to the wild-type KMBL1001, from 2.8±1.0% to undetectable levels (Figure 4B). This implies that RecA, and thus HR (or other RecA dependent processes, such as the induction of an SOS response and/or the regulation of translesion DNA synthesis), was involved in IR-dependent deletions. The wild-type M. smegmatis strain mc2155 harboring the control vector (pCE, no DR or IR sequences) gave rise to spontaneous KmS or GmS colonies at frequencies of ∼20% (Figure 4C and D), 30- to 40-fold more frequently than pCI (the corresponding wild-type strain harboring the integrated control vector, Figure 3B), and ∼7-fold higher than in E. coli (Figure 4B). A 20% plasmid loss after 48 h culture on nonselective media was expected for this plasmid system, which is based on the pAL5000 origin from M. fortuitum. pAL5000-containing vectors are commonly used for growth in E. coli, mycobacteria, and for the expression of foreign antigens in recombinant BCG vaccines [70]–[74]. Plasmid DNA was not detectable by DNA isolation or by PCR analysis in white M. smegmatis mutant colonies sensitive to Km and Gm, implying that DNA was processed by nucleases and, thus, plasmid was lost. The presence of OligoIR (pIREA) significantly increased the fractions of KmS/GmS ∼3-fold (p = 0,00001) (Figure 4C), supporting the conclusion that, as in E. coli (Figure 3C), cruciform structures were extruded from the IRs and triggered instability through DSBs. Absence of RecA (ΔrecA M. smegmatis, Figure 4C) led to a further increase (to ∼67–79%, p = 0,00001) in the fraction of KmS/GmS colonies. Similarly, absence of Ku and LigD in Δ(ku ligD) M. smegmatis resulted in loss (p = 0,00001) of the Km/Gm resistance genes in the majority of the bacterial population. Thus, in contrast to E. coli, in which HR enhanced IR-induced instabilities, NHEJ and HR displayed a protective role in M. smegmatis.

The 38-bp DRs in the self-replicating OligoDR (pDREA) also stimulated (∼2-fold; p = 0,00001) short deletions that disrupted the aacC1 (GmR) gene in M. smegmatis (Figure 4D); however, no induction of large deletions into the flanking aph (KmR) gene (and therefore plasmid loss) was observed (Figure 4D). The number of GmS or KmS CFUs that lost plasmids increased significantly (to 66–93%; p = 0,00001) in the absence of either HR (ΔrecA M. smegmatis) or NHEJ (Δ (ku ligD) M. smegmatis). We postulate that DSBs, which were left unrepaired in strains defective in RecA or NHEJ proteins in M. smegmatis, may have been responsible for the increase in DNA processing and subsequent plasmid loss. In summary, we conclude that both NHEJ and HR served a critical role in repairing DSBs induced by slipped DNA-forming DRs and cruciform-forming IR sequences in M. smegmatis.

Discussion

Herein, we report that the reference genomes of two mycobacterial species, M. smegmatis and M. tuberculosis, are strongly enriched in DRs and IRs. By using two synthetic constructs harboring DRs and IRs, we addressed whether these repetitive motifs may elicit genomic instability in M. smegmatis, a model organism that carries all three (HR, NHEJ and SSA) DSB repair pathways. We also used E. coli strains, since these enable a direct relationship between repeat DNA-induced genetic instability and negative supercoiling, a topological state known to favor B-DNA to non-B-DNA structural transitions [62], [63], [75]. E. coli and M. smegmatis represent quite different model systems with regard to DNA metabolism and DNA repair mechanisms. Specifically, M. smegmatis, as well as other mycobacteria, are devoid of genes encoding the highly conserved mismatch repair (MMR) proteins MutS and MutL, suggesting a lack in postreplicative MMR [1], [2], [76], [77], whereas E. coli is devoid of genes encoding the conserved two-component core NHEJ enzymes, Ku and LigD, leaving the processing of incompatible DSBs to alternative mechanisms [78]–[80].

We report four findings. First, the 38-bp DRs in OligoDR strongly induced the precise deletion of their ∼1 kb intervening sequence even in the absence of functional DSB repair in M. smegmatis. Whereas RecA-independent slipped mispairing between tandem repeats is a well-recognized mechanism leading to replication errors [12], [81], the ability of the M. smegmatis replication apparatus to relocate at distant DRs unassisted by canonical DSB repair proteins has not been reported, to our knowledge. Absence of RecA, both alone or in combination with NHEJ deficiency, favored this process, suggesting that either HR prevented deletions or that binding of RecA to single-stranded DNA (either because of looping-out following DR interactions or because of arrested replication forks [82]), inhibited primer relocation. In contrast to OligoDR, precise deletions between the two IRs in OligoIR were considerably less abundant, being detected only upon loss of the RecBCD operon.

The only mechanism through which hph gene reconstitution could have occurred in OligoIR was by precisely rejoining the two EcoRI sites that separated the two halves of the gene (Figure 1). Based on the E. coli mutant data (Figure 3C), in which OligoIR-induced instabilities increased in a supercoiling-dependent manner, we speculate that both IRs were able to fold into cruciform structures; these then underwent strand breaks at the single-stranded EcoRI sequences, which were repaired by microhomology-mediated end-fusion between the two IRs. Because this type of event was stimulated in the absence of RecBCD, we propose that EcoRI-specific DSBs were processed through the SSA pathway in the wild-type strains and by the NHEJ machinery in the ΔSSA strains [41]. In E. coli, the absence of precise deletions in IR-containing constructs is consistent with the lack of canonical NHEJ. Thus, SSA would appear to compete effectively with NHEJ in processing repeat-induced strand-breaks in mycobacteria.

Second, both DRs and IRs incited int-L5 site-specific recombination in M. smegmatis. The instability of integrated constructs by L5 integrase activity has been reported [83]; we document a strong stimulation of this process by DRs and IRs. In M. smegmatis, the directionality of mycobacteriophage L5 integration and excision reactions is governed by the phage recombination directionality factor (RDF) Xis-L5, a small 56 amino acid helix-turn-helix peptide that bends Xis-L5 DNA recognition targets in proximity to attR [69]. Xis-L5 does not participate directly in the excision reaction, but instead acts as an architectural protein. We speculate that, if a role for Xis-L5 were to stabilize attR and attL site interaction leading to synapsis, then such interaction may be facilitated by flexible hinges along the DNA chain at local non-B DNA conformations, such as those formed by slipped and cruciform structures at DRs and IRs, respectively. Other mechanisms are possible, including bidirectional DNA nuclease activity from the DNA secondary structures into the site-specific recombination sites. Regardless of the mechanism involved, it is clear that DR and IR sequences strongly stimulate L5 site-specific recombination.

Third, absence of HR and NHEJ, (ΔNHEJ>ΔHR), resulted in extensive DNA processing and plasmid loss in M. smegmatis, indicating that both pathways play important roles in protecting genome integrity from the destabilizing effects of DRs and IRs. In this regard, a contrasting effect was observed between M. smegmatis and E. coli, since in the latter abrogation of the HR pathway in the ΔrecA strains led to greater genomic stability. The reasons for these differences remain to be clarified.

Fourth, DRs are the most abundant type of repetitive motif in the M. smegmatis and M. tuberculosis genomes. Short repetitive motifs are a hallmark of insertion sequence (IS) integration sites in mycobacteria. Duplications, deletions and genome shuffling play major roles in driving genomic diversity and evolution, and mycobacterial IS elements, such as IS1096 and IS6110, are believed to contribute to such rearrangements [84], [85]. We found 165 genes annotated to PE, PE-PGRS and PPE families in M. tuberculosis, for a maximum contribution to the total length of DRs of 8.2%. In M. smegmatis, only 10 such genes were found. The PE and PPE families of proteins confer pathogenic advantage to M. tuberculosis, and antigenic variation may result in part from the interactions between the PE/PPE proteins and the emergence of new or rare MHC alleles in the host genome [86]. Thus, it is possible that duplication of these gene families might have been exploited, and therefore maintained, through positive selection as a means to increase diversity through recombination, and perhaps avoid gene decay during evolutionary time in M. tuberculosis. A second class of genetic elements thought to generate mosaicism in mycobacteria is represented by mycobacteriophages; at least sixty-two different genomes of these obligate parasites known to infect M. smegmatis mc2155 have been sequenced [87]. Short repetitive motifs in the bacterial host, such as the 36 DR integration hotspot [88], represent common sites for the integration and excision of such elements, and both mycobacterial DNA repair proteins, such as LigD and Ku [89], and phage integrases may cooperate to carry out the insertion and excision reactions [90]. Mycobacteriophages are characterized by a substantial degree of mosaicism, including the occasional acquisition of mycobacterial sequences, such as the MetE gene in the Giles genome [91], [92]. Such mosaicism is thought to arise in part through lateral gene transfer (LGT). A comparison between the M. tuberculosis genome and its relatives M. marinum and M. avium subsp. paratuberculosis suggests that at least 80 distinct regions have been acquired by M. tuberculosis through LGT, along with genome downsizing, in the course of its adaptation from an environmental ancestor to a specialized human pathogen [93]. Our results raise the possibility that the abundant repetitive elements in mycobacteria might instigate recombination events between the host and mycobacteriophage genomes, contributing to LGT. In summary, we demonstrate that DR and IR sequences lead to genomic instability in M. smegmatis by eliciting a diverse repertoire of cellular responses, including interactions with DNA repair pathways (HR, NHEJ and SSA) and the mycobacteriphage L5 site-specific recombination apparatus. Thus, these results provide support for a much broader range of cellular responses to repetitive DNA sequences and their putative secondary structures than previously anticipated, and suggest future studies aimed at addressing the evolutionary aspects and origins of repetitive sequences.

Cloning strategy. The hph gene (HygR) in the pMV206Km and pMV306Km vectors was disrupted by introducing synthetic oligonucleotides, comprising either two pairs of inverted repeats (IRs) or two direct repeat (DR) units, within an internal EcoRI site of the gene. DRs and IRs were further separated by cloning the aacC1 (GmR) gene in orientations A and B. This resulted in two pairs of IRs and one pair of DRs, on either side of the aacC1. The disrupted hph was also flanked, 5′ and 3′ respectively, by the aph (KmR) and lacZ (blue color) genes. Pag85, promoter for the lacZ gene.

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Construction of ΔrecBCD strain by replacement of the wild-type recBCD operon with a mutant sequence. Panel A, the chromosomal location of recBCD is represented by arrows. The restriction sites (BamHI and ClaI) used for cleaving chromosomal DNA are shown. The restriction DNA fragment and the size of the internal deletion in the mutated copies are shown by thin black arrows. The probe used for Southern blot hybridization is displayed by a grey rectangle. Panel B, Southern blot hybridization. Lane 1, M. smegmatis mc2155; lane 2, M. smegmatis recBCD and ΔrecBCD; lanes 3, 4, M. smegmatis ΔrecBCD. Arrows, DNA restriction fragments expected for the M. smegmatis wild-type recBCD (982 bp) and ΔrecBCD (1601 bp) strains.

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Protocol for assessing genetic instabilities caused by the Oligo and . From the top, competent cells were transformed with OligoDR (pDRIA, pDRIB, pDREA, pDREB) or OligoIR (pIRIA, pIRIB, pIREA, pIREB) vectors and plated on LB (E. coli) or NB (M. smegmatis) media containing gentamycin (Gm), kanamycin (Km) and X-gal. CFUs were harvested, plated on non-selective media and grown for 24 h (E. coli) or 48 h (M. smegmatis) to select for mutants. Cells were then washed and plated at the appropriate dilutions on LB/NB agar plates supplemented with either 5-bromo-4-chloro-3-indoxyl-beta-D-galactopyranoside (X-gal) or hygromycin (Hyg). Colonies from X-gal plates were transferred by replica plating on four LB/NB agar plates, as follows: 1) Km plus Hyg, 2) Km plus Gm, 3) Km and 4) X-gal.

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Oligo gene (Hyg Agarose gel electrophoresis of PCR products using hph specific primers on DNA isolated from HygR colonies. Lane 1, 1-kb DNA ladder; lane 2, M. smegmatis carrying pDRIA (HygS, GmR); lanes 3–12, selected HygR and GmS M. smegmatis mutant CFUs harboring pDRIA or pDRIB.

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Reconstitution of (Hyg . x-axis, M. smegmatis mc strains: pC, pMV206KmHyg::Gm (control); pIR, pMV206KmHyg::OligoIRGmA lacZ; pIR, pMV206KmHyg::OligoIRGmB lacZ; pDR, pMV206KmHyg::OligoDRGmA lacZ; pDR, pMV206KmHyg::OligoDRGmB; y-axis, frequencies of HygR CFUs; asterisks, P<0.05 (pair-wise Holm-Sidak test of pIREA, pIREB, pDREA, pDREB against pCE).

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Precise deletions and SSA. M. smegmatis ΔRecBCD strains process precise deletions between DRs with similar efficiencies as the wild-type strain. Panel A and B, x-axis, M. smegmatis strains; y-axis, frequencies of HygR CFUs. Panel A, x-axis, wt/pC, wild-type/pMV206KmHyg::Gm (control); wt/pDR, wild-type/pMV206KmHyg::OligoDRGmA lacZ; ΔrecBCD/pDR, ΔrecBCD/pMV206KmHyg::OligoDRGmA lacZ. Panel B, x-axis, wt/pC, as in Panel A; wt/pDR, wild-type/pMV206KmHyg::OligoDRGmB lacZ; ΔrecBCD/pDR, ΔrecBCD/pMV206KmHyg::OligoDRGmB lacZ.

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The bacteriophage L5 integrase excises the DR- and IR-containing constructs integrated at the sites. Analysis of the attB region of selected mutants using Southern blot hybridization. Panel A, scheme of the plasmids integrated at the attB site of M. smegmatis mc2155. SalI, restriction sites used for DNA cleavage showing the 1,883 bp SalI fragment detectable by the Southern blot hybridization probe in the wild-type strain and the DNA fragments (grey arrows) generated by SalI cleavage in the integrated plasmid. Panel B, Southern blot hybridization. Lane 1, M. smegmatis mc2155; lane 2, M. smegmatis mc2155/pDRIA (pMV306KmHyg::OligoDRGmA lacZ); lanes 3, 4, 6, 9–17, KmS, GmS and white mutant CFUs from M. smegmatis mc2155/pDRIA; lanes 5, 7–8, KmR, GmS and blue mutant CFUs from M. smegmatis carrying pDRIA. Red arrows, DNA restriction fragments expected for the wild-type strain (1,883 bp) and for M. smegmatis mc2155/pDRIA (4,698 bp and 1,185 bp).

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Bacterial strains, sources and genetic features.

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List of plasmids, general description, genetic markers and sources/references.

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Primer sequences used for PCR amplification.

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Criteria used for in silico analyses of repetitive elements in bacterial genomes.

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Statistics of in silico searches of repeats genome-wide.

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