Distributive Conjugal Transfer in Mycobacteria Generates Progeny with Meiotic-Like Genome-Wide Mosaicism, Allowing Mapping of a Mating Identity Locus

Todd A. Gray; Janet A. Krywy; Jessica Harold; Michael J. Palumbo; Keith M. Derbyshire

doi:10.1371/journal.pbio.1001602

Abstract

Horizontal gene transfer (HGT) in bacteria generates variation and drives evolution, and conjugation is considered a major contributor as it can mediate transfer of large segments of DNA between strains and species. We previously described a novel form of chromosomal conjugation in mycobacteria that does not conform to classic oriT-based conjugation models, and whose potential evolutionary significance has not been evaluated. Here, we determined the genome sequences of 22 F1-generation transconjugants, providing the first genome-wide view of conjugal HGT in bacteria at the nucleotide level. Remarkably, mycobacterial recipients acquired multiple, large, unlinked segments of donor DNA, far exceeding expectations for any bacterial HGT event. Consequently, conjugal DNA transfer created extensive genome-wide mosaicism within individual transconjugants, which generated large-scale sibling diversity approaching that seen in meiotic recombination. We exploited these attributes to perform genome-wide mapping and introgression analyses to map a locus that determines conjugal mating identity in M. smegmatis. Distributive conjugal transfer offers a plausible mechanism for the predicted HGT events that created the genome mosaicism observed among extant Mycobacterium tuberculosis and Mycobacterium canettii species. Mycobacterial distributive conjugal transfer permits innovative genetic approaches to map phenotypic traits and confers the evolutionary benefits of sexual reproduction in an asexual organism.

Author Summary

Bacteria reproduce by binary fission, generating two clones of the original; this restricts the genomic diversity of the population, which brings with it inherent evolutionary drawbacks. This problem can be eased by conjugation, which transfers DNA from a donor to a recipient bacterium. Understanding the potential of conjugal DNA transfer for generating genetic diversity is necessary for estimating gene flow through populations and for predicting rates of bacterial evolution. The influence of chromosomal conjugal DNA transfer on mycobacterial diversity has not been previously addressed. Here, we determine and compare the complete genome sequences of independent progeny from bacterial matings between defined donor and recipient strains of Mycobacterium smegmatis. We find the resulting hybrid bacteria to be extremely diverse blends of the parental strains, reminiscent of the genetic mixing that occurs through meiotic recombination in sexual organisms. This novel mechanism of conjugation can create genome-wide mosaicism in a single event, generating segments of donor DNA that range from small (∼0.05 kb) to large (∼250 kb), widely distributed around the recipient chromosome. We exploit this mixing by using genetic tools originally developed for finding mammalian disease genes to locate the genes that confer a donor phenotype in M. smegmatis. We speculate that similar genomic mosaicism observed in pathogenic mycobacteria arose from conjugation between ancestral progenitor strains.

Citation: Gray TA, Krywy JA, Harold J, Palumbo MJ, Derbyshire KM (2013) Distributive Conjugal Transfer in Mycobacteria Generates Progeny with Meiotic-Like Genome-Wide Mosaicism, Allowing Mapping of a Mating Identity Locus. PLoS Biol 11(7): e1001602. https://doi.org/10.1371/journal.pbio.1001602

Academic Editor: Jonathan A. Eisen, University of California Davis, United States of America

Received: April 25, 2012; Accepted: May 24, 2013; Published: July 9, 2013

Copyright: © 2013 Gray et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Funding: This work was supported by funds from the Wadsworth Center and grants AI042308, R56AI080694 to K.M.D. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Competing interests: The authors have declared that no competing interests exist.

Abbreviations: DCT, distributive conjugal transfer; HGT, horizontal gene transfer; oriT, origin of transfer

Introduction

Sexual reproduction in eukaryotes promotes genetic diversity by increasing gene flow through a population, permitting both the loss of mutant genes and the acquisition of functionally distinct gene alleles. The diversifying potential is further enhanced by crossover events that create new mosaic recombinant meiotic products, which in turn may impart new functionalities not present in either parent. In contrast, bacterial fission provides rapid clonal expansion to fill an environmental niche, but lacks the evolutionary advantages of sexual reproduction. Horizontal gene transfer (HGT) mitigates the diversification constraints of asexual reproduction by mediating limited gene flow through the population. The fundamental forms of HGT include transformation, transduction, and conjugation. Conjugation is considered a major contributor to HGT, as it can transfer more extensive segments of DNA between different species and even kingdoms [1]–[4].

Conjugation describes the unidirectional transfer of DNA from a donor to a recipient, and requires cell–cell contact. Conjugal processes are traditionally plasmid encoded, or encoded by a discrete genetic element integrated into the chromosome. Transfer proteins are generally classified into those that establish and maintain mating-pair formation or those responsible for DNA transfer [5],[6]. These latter proteins recognize and nick the unique origin of transfer (oriT) on the plasmid and guide the DNA into the recipient cell. oriT is cis-acting, and thus, when recombined into the chromosome, it can mediate transfer of chromosomal DNA, as first described for E. coli Hfr strains [7]. DNA transfer in M. smegmatis displays all of the hallmarks of conjugation: it requires stable and extended contact between a donor and a recipient strain, it is DNase resistant, and the transferred DNA segments are incorporated into the recipient chromosome by homologous recombination [8]. While the process clearly meets the traditional definition of conjugation, the similarities with the classical E. coli Hfr system end there [9]–[13]. Mycobacterial conjugation is chromosome—not plasmid—based, and bioinformatic and genetic studies have yet to identify a genetic element that might mediate transfer [14],[15]. In E. coli, Hfr transfer always initiates at the sole plasmid-encoded oriT site, and the DNA is transferred in a 5′ to 3′ direction, such that only genes proximal and 3′ to oriT are inherited at high frequencies [10],[16]. By contrast, in M. smegmatis, all regions of the chromosome are transferred with comparable efficiencies as demonstrated by equivalent transfer of a kanamycin-resistance marker regardless of its chromosomal location [11]. This position independence is consistent with the presence of multiple, but ill-defined, initiation sites [17].

Transposon mutagenesis screens provided initial insights into the genetic requirements of transfer [14],[15]. These studies established a prominent role for the Type VII secretion apparatus, ESX-1, in both donor and recipient activity. ESX-1 clearly plays different roles in each cell type. ESX-1 donor mutants are hyperconjugative, suggesting secretion plays a role in negatively regulating transfer activity [15]. By contrast, recipient strain ESX-1 mutants do not receive donor DNA [14]. Although these studies provided novel insights into the functional roles of ESX-1, they did not provide insights on the transfer mechanism, or define what determines the mating type of a cell (either donor or recipient).

Here, as an alternative approach, we examined the products of DNA transfer to better understand this process and its contributions to mycobacterial evolution. We used next-generation sequencing to determine the parental inheritance profiles in transconjugant M. smegmatis progeny. The genomic sequence of each of the M. smegmatis parental strains has been determined, and the abundant single nucleotide polymorphisms between the two strains indicated that the transferred segments comprising the transconjugant genomes could be mapped with precision. We found that the parental contributions to the transconjugants were much more complex than expected, indicating a surprisingly major role for conjugal DNA transfer in generating genomic diversity. The blending of the parental genomes is reminiscent of that seen in the meiotic products of sexual reproduction. This comparison is validated by our use here of genomic approaches previously developed and applied in sexual reproduction systems to define candidate genes for conjugal mating identity.

Results

Transconjugant Genomes Are Highly Mosaic

To provide a selectable marker for chromosomal DNA transfer, a kanamycin resistance gene (Km^r) was integrated in the chromosome of mc²155, the standard laboratory and conjugal donor strain of M. smegmatis. Donor mc²155 derivatives that differed in their Km^r insertion site were mated to an apramycin-resistant (Ap^r) recipient strain, mc²874 (Figure 1A). mc²874 is an independent isolate of M. smegmatis that we have used as a standard recipient strain [8],[18]. Apramycin resistance was episomally encoded to avoid inheritance biases caused by selecting for this gene on the recipient chromosome. From matings between these strains, 12 independent Km^rAp^r F1 progeny were isolated, and the DNA sequences of their genomes were determined (sequence data deposited in the EBI/ENA database at http://www.ebi.ac.uk/ena/data/view/ERP002619). Our comparative sequence analyses of the parental strains had shown that the circular mc²155 and mc²874 genomes are collinear, and that they contained abundant single nucleotide polymorphisms (SNPs; averaging one per 56 bp) providing a clear distinction between parental DNA origins (Figures 1A and S1). Individual sequence reads from each transconjugant were aligned with the donor strain genome to identify all transferred donor segments. When evaluating transconjugant sequences, we conservatively required the presence or absence of two consecutive recipient SNPs to define a boundary between recipient and donor sequence tracts, respectively (Figure S2). Donor segments replaced the corresponding recipient sequences, as evidenced by a concomitant localized loss of recipient-specific SNPs in transconjugants. Unique segments of transferred donor DNA, predicted by alignment analyses in transconjugants, were confirmed by conventional PCR and Sanger sequencing (Table S1). Two transconjugants had 11 regions that were merodiploid (approximately equal contributions of donor and recipient SNPs). As this was a resequencing and not a de novo sequencing strategy, we cannot determine the precise architecture and location of these regions. These regions did not contain repetitive elements, though it is possible that integration occurred at nonsynonymous sites via microhomology or through mechanisms not requiring homology.

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Figure 1. Mycobacterial transconjugant genomes are complex mosaics of their parental strains.

(A) Conjugation and genome comparison protocol. Sequence reads for each transconjugant were aligned with the reference donor genome and viewed with IGV. Columns of colored nucleotides mark informative SNPs between the recipient and donor strains, while random colored nucleotides indicate sequence errors. (B) A Circos plot depicts the mosaic nature of 12 M. smegmatis transconjugant genomes. mc²155 donor DNA segments (alternating blue and magenta, or green) replaced homologous recipient sequences (yellow). Positions of integrated kanamycin genes (Km) are shown around the periphery (green arrows), and transferred donor DNA segments containing the Km gene are shown in green. Strain nomenclature is based on the genomic location of the Km gene in Mb, thus Km0.1 is inserted at coordinate 0.1 Mb in mc²155. Strains are from outer to inner circle, respectively: Km6.9e, Km0.1f, Km6.9d, Km3.2, Km6.9c, Km0.1e, Km3.8, Km4.5b, Km2.2a, Km0.1d, Km0.1c, and Km6.4a. The innermost circle is a compilation of all segments of mc²155 DNA, showing that almost all regions of the donor chromosome were transferred despite the small sample size. (C) Microcomplexity of parental SNP profiles at some transconjugant recombination sites. Compiled sequence read landscapes are shown for mc²874 and one transconjugant (Km6.9e) aligned to the mc²155 sequence (top) for a 1 kb segment of the genome (see Table S2, coordinates 470,385–471,385). The presence of informative SNPs (each color represents a different base) indicates recipient sequences, while segments lacking SNPs define donor sequence. Accordingly, parental genotype segments are shown in the schematic below with recipient (yellow) and donor (blue and magenta) genotypes interspersed throughout this 1 kb region. Note that rare cases of isolated recipient SNPs in our designated donor segments are excluded by our stringent criterion requiring two consecutive SNPs to conclusively establish parental origin. The lower panel shows the same sequences aligned to the mc²874 sequence, in which the SNPs now indicate donor sequence. This reciprocal alignment confirms the assignment of donor and recipient sequences in the schematic map.

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The most striking observation from an alignment of our initial set of 12 transconjugant genomes with the parental genomes was that the transconjugant genomes were broadly mosaic, containing at least two, and as many as 21, separate tracts of cotransferred mc²155 DNA embedded in an mc²874 background (Figure 1B and Table S2). These separate segments of DNA were acquired in a single cell–cell transfer event, as determined in earlier studies [11]. To our knowledge, this degree of genome-wide diversity is unprecedented in genetic transfer events between bacteria. This contrasts directly with the iconic plasmid-transfer systems in which a single segment of donor DNA linked to oriT is inherited [10],[19]. Therefore, we refer to mycobacterial conjugation as distributive conjugal transfer to distinguish it from oriT-mediated transfer.

As expected, all transconjugant progeny acquired the selected Km^r gene, along with variable amounts of flanking mc²155 DNA (Figure 1B, Km^r, green segments embedded in yellow recipient DNA). Surprisingly, 5-fold more mc²155 DNA was co-inherited in segments that were not selected, and these segments were distributed around the genome with no obvious regional biases (Figure 1B, alternating blue and magenta improve visual discrimination between adjacent tracts; Table S2). The 12 transconjugant genomes analyzed contained from 57 kb to 679 kb (of 6.9 Mb) of mc²155-derived sequence. The sizes of the donor segments varied >1,000-fold, ranging from 59 bp to 226 kb (Figure S3 and Table S2), with an average size of 33.8 kb, and a mean of 10 tracts per genome (Table 1).

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Table 1. Total contributions of donor-derived DNA in transconjugants.

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Some regions showed intricate microcomplexity of multiple inherited segments separated by short intervals of recipient DNA (Figure 1C and highlighted in Table S2). Note that the single-nucleotide discrepancies (colored SNPs) derive from parental inheritance, not de novo mutation (see reciprocal parental reference sequence alignments in Figure 1C). These likely resulted from a combination of repair and recombination events occurring between the recipient chromosome and a single molecule of introduced donor DNA, as some segments are separated by only a few base pairs. Regardless of the mechanism, the net effect was to create a localized composite blend of parental contributions at the nucleotide level.

DCT Facilitates a Genome-Wide Mapping Approach That Identifies a Mating Identity (Mid) Locus

The image in Figure 1B shows the extent of mc²155 DNA transferred to recipients when selecting for a single event: acquisition of the gene encoding Km^r. Based on the distributive nature of transfer, we reasoned that we could employ secondary screens of the transconjugants to map any additional genetic trait regardless of its linkage to the Km^r gene. Tracking parental SNPs within a group of individual transconjugants exhibiting a given phenotype should identify those shared SNPs (and parental genes) associated with that phenotype. We have previously observed that a subset of transconjugants become donors, suggesting that these progeny acquired a donor-conferring locus [11]. We hypothesized that an unbiased genome-wide mapping approach would identify a shared segment of mc²155 DNA among those progeny encoding this trait. Transconjugants derived from crosses of the differentially marked donor strains were screened for donor ability, and 10 independent donor-proficient transconjugants were identified. We note that mating identity is a mutually exclusive phenotype, and transconjugants exhibit transfer efficiencies comparable to parental strains ([11] and Table S3). Genomic DNA from each donor-proficient transconjugant was prepared and its sequence determined. Comparative sequence analysis showed that all donor-proficient transconjugants, regardless of the location of the Km^r gene in the parent, shared only one segment of mc²155 DNA (Figure 2A and Table S4), with the smallest region of overlap encompassing coordinates 74,522 to 119,788 bp (Figure 2B). This result is consistent with transfer of a single 45 kb locus (mid) that is sufficient to switch mating identity from recipient to donor in these transconjugants.

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Figure 2. Exploiting DCT to identify esx1 as a determinant of donor-recipient function.

(A) A Circos plot depicts the fragmented genotype of 10 donor-proficient transconjugant genomes. Color key is the same as Figure 1. Strains are from outer to inner circle, respectively: Km4.5a, 2.2b, 0,8, 0.1a, 5.7, 6.9b, 6.9a, 6.4b, 1.5, and 0.1b. (B) An expanded map of the region inherited by all donor-proficient progeny, which includes a single contiguous segment of mc²155 DNA encompassing the esx1 locus (black). Clones are in the same order, outside-to-inside as in (A), and are labeled to indicate the location of the Km^r gene used in selection. Colored bars indicate the extent of DNA inherited from mc²155 in the recipient genome (yellow). The esx1 locus extends from 74,600 to 107,334 bp in mc²155.

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This region is not simply a hot spot for integration of acquired DNA, since the 12 recipient-proficient (i.e., did not become donors) transconjugants in Figure 1B were not similarly enriched for this segment of mc²155 DNA (compare Figures 1B and 2A, and see below). Closer examination of the region acquired by donor-proficient transconjugants established that they all had inherited a minimal segment of DNA encompassing the mc²155 esx1 locus (Figure 2B, 74,600–107,334 bp, esx1_D, where the subscript differentiates donor or recipient origin). The esx1 locus encodes a Type VII secretion system [20],[21]. The encoded ESX-1 apparatus assembles in the cell membrane and secretes a specific set of proteins, which, in M. tuberculosis, are essential for pathogenicity [22]–[24]. Proteins secreted by ESX-1 lack a signal peptide that would aid in their identification, and the most notable substrate is a heterodimer of two small proteins, EsxB and EsxA. Other proteins encoded within the esx1 locus and elsewhere in the genome are also secreted through ESX-1, some of which are co-dependent on EsxBA secretion. The functions of most of the proteins encoded by esx1 genes are unknown, but the overall composition of the esx1 loci between the parental mc²155 and mc²874 strains are similar (see below). Although our previous transposon mutagenesis studies have shown that ESX-1 plays an important role in the process of DNA transfer in both donor and recipient strains, mating-type identity is not reversed in ESX-1 mutants [14],[15]. Therefore, the role of ESX-1 in determining mating identity was quite unexpected, and underscores the utility of a “change-of-function” mapping approach.

While all of the donor-proficient transconjugants inherited an intact esx1_D locus, none of the recipient-proficient F1 strains did. Notably, four of the F1 recipient-proficient strains were derived from the Km0.1 parent, in which only 15 kb separate esx1_D and the selected Km^r gene. Despite this tight linkage, distributive conjugal transfer readily segregated the Km^r gene and intact esx1_D locus when appropriately screened, thereby augmenting the mapping resolution (Figure 1B, Table S2, and below). Helpfully, one of these recipient-proficient transconjugants (Km0.1c) inherited parts of esx1_D, excluding these esx1 genes from mid candidacy (0064–0068 and 0077–0083, Table S2). These negative correlations affirm the functional dependence of the donor trait on the mid genes of esx1_D and demonstrate the robust nature of distributive conjugal transfer in generating the level of genetic diversity necessary for our mapping analyses.

Fine Mapping of the Mid Locus by a Backcrossing Analysis

In classical genetic studies, fine mapping of a genetic determinant can be achieved by performing successive backcross introgression analyses to genetically purify a locus in a recipient background. We reasoned a similar strategy would achieve two goals: (1) discard mc²155 parental genes not required for the donor transfer trait and (2) further narrow the key conjugal mid gene region. Six F1 donor recombinants were backcrossed with mc²874 recipient derivatives that were marked with a different episomally encoded antibiotic resistance gene (Hyg^r or Apy^r) in successive generations. Introgression entailed co-selection for Km^r transfer and the recipient marker to identify transconjugants at each generation (N_x), and then screening progeny for donor proficiency (Figure 3). Comparative analyses of genomes of three donor-proficient strains showed a purifying selection of the donor-conferring locus and Km^r genes in an otherwise recipient genome (Figure 4, Table S4). In each case, the majority of the F1 mc²155 DNA was lost. For example, the F1 parent of Km0.1BCb contained 19 mc²155 segments totaling over 869 kb, yet following six backcross generations this DNA was trimmed to three segments totaling 110 kb, most of which encompassed the selected mid and Km^r genes (79 kb, Table S4).

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Figure 3. A pedigree showing the backcross introgression strategy.

To generate the initial F1 progeny, a kanamycin-resistant (Kan) mc²155 donor strain (blue square) was crossed with an apramycin-resistant (Apy) mc²874 recipient (yellow circle). The doubly resistant F1 transconjugants (K/A) were screened to identify donor-proficient progeny (green squares; see Figure 2). Donor-proficient F1 derivatives were then backcrossed with a derivative of the original mc²874 recipient strain that was marked with a plasmid encoding hygromycin resistance (Hyg). Doubly resistant transconjugants (K/H) were selected to create the N1 generation of transconjugants. As for the F1 stage, the N1 transconjugants were screened to identify donor-proficient progeny (squares) before backcrossing to the apramycin-resistant mc²874 recipient to generate the N2 generation. This process was reiterated to genetically purify the donor-determining genes in the mc²874 recipient background. Donor-proficient (square) or recipient-proficient (circle) progeny were isolated at either the N3 or the N6 stage, and their genomic DNA was isolated and the sequence determined (see Figures 4 and 5, respectively). The progressive purifying selection of the Km^r and mating identity genes is depicted by the reduced portion of the mc²155 DNA (blue sector) through each generation in the mc²874 genome (yellow circle) at right, and by the gradual conversion of the progeny background from green to yellow.

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Figure 4. Backcross introgression refines esx1 as a mating-identity locus in donor-proficient transconjugants.

Circos plots of donor-proficient backcross transconjugants showing F1 parental (outer ring) and backcross progeny (inner ring) for each strain pair. Km1.4BC was isolated from N3 progeny and Km0.1BCb from N6 progeny. Backcross (BC) strain names are based on their parent; thus, Km0.1BCb is the second (b), independent transconjugant derived from parent Km0.1. The expanded arc focuses on the esx1 locus (black). Color key is the same as Figure 1.

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As expected, backcross matings also resulted in recipient-proficient progeny, several of which were also sequenced (Figure 3). Coincident with a reversal of mating identity, the esx1_D locus failed to transfer. One recipient strain, Km0.8BC, retained only 75 kb of mc²155 DNA of the 920 kb originally present in the F1 parent (Figure 5, Table S4). Analyses of two recipient-proficient strains derived from independent F1 Km6.9 parents further refined the region of interest. Km6.9BCa included donor genes 0055D–0067D and 0079D–0083D and Km6.9BCb contained genes 0072–0075D (Figures 5 and 6, Table S4). Thus, these esx1_D genes are insufficient to confer a donor phenotype. Taken together, the mapping data identify esx1 genes in 0068D–0071D and/or 0076D–0078D as being critical for determining mating identity. Ongoing studies requiring multiple, precise, targeted gene swaps will identify the key gene(s).

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Figure 5. Backcross introgression excludes regions of esx1 as insufficient for mating identity in recipient-proficient transconjugants.

Circos plots of recipient-proficient backcross transconjugants showing F1 parental (outer ring) and backcross progeny (inner ring) for each strain pair. In the third backcross step, none (Km0.8BC) or part (Km6.9BC) of esx1 was transferred to the isolates shown, coincident with reversion to a recipient phenotype. The part of mc²155 esx1 present in Km 6.9BC indicates that these mc²155 genes are insufficient to confer donor identity. Nomenclature and color codes are the same as in Figure 4.

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Figure 6. The mid locus within esx1, as defined by the F1 association mapping and backcross introgression analyses.

A schematic guide encompassing 73 kb to 122 kb of the mc²155 reference genome, including the esx1_D locus genes (black filled, ms0055 at 74.6 kb through ms0083 at 107.3 kb). A repetitive IS element cluster absent in the recipient (ms0072–0074) is gray-filled. Below are key clones from crosses that progressively defined the mid gene candidates. Donor-proficient transconjugant clones had inherited mc²155 sequences sufficient to convey the donor phenotype. Recipient-proficient transconjugants inherited mc²155 sequences that were insufficient to impart the donor phenotype. Considered together, the key mid candidate regions span 6,923 bp of mc²155 DNA, from 90,697 to 94,949 and from 100,295 to 102,966. These regions span esx1_ms genes ms0069–0071 and ms0076–0078 as shown in the expansion at the bottom. The amino acid identities between the encoded proteins of mc²155 and mc²874 are notably low for the left region, consistent with functional disparity.

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While most esx1 gene products are highly conserved among mycobacterial species, M. smegmatis proteins 0069, 0070, and the N-terminal two-thirds of 0071 have notably low amino acid identity between donor and recipient orthologs (Figure 6 and Figure S4) [14] and are therefore good candidates for switching mating identity. The proteins encoded from this region are not predicted to contain an obvious motif or domain that would provide mechanistic insight into their role in conjugation. However, the location of the mid genes within esx1 suggests that the encoded proteins modify ESX-1 structure or function, to perhaps affect cell–cell communication or physically mediate DNA transfer.

Discussion

We used next-generation sequencing to examine transconjugant genomes and found that mycobacterial conjugation generates highly mosaic genomes created by a robust distributive conjugal transfer process. Transconjugants acquired large amounts of donor DNA (some exceeding one-fourth of the transconjugant genome; Table S4, Km4.5a), in varied segment sizes (spanning four orders of magnitude) that were distributed around the genome. We exploited these characteristics of distributive conjugal transfer (DCT) to map mating identity genes of M. smegmatis.

Hfr transfer in E. coli is initiated from the unique oriT and results in transfer of a single segment of the donor chromosome [9],[19],[25]. Thus, while the recipient acquires new genetic information, that new information is limited to DNA immediately adjacent and 3′ to oriT (Figure 7, left). Genetic analyses and an understanding of the RecBCD recombination machinery suggest that a single segment is integrated into the recipient chromosome via a recombination event occurring at each end of the transferred DNA molecule [16]. To our knowledge, whole genome sequencing has not been reported for Hfr– transconjugants, preventing a detailed comparison of the two conjugation systems. Thus, our study provides the first genome-wide analysis of bacterial conjugal transfer. In contrast to oriT-mediated transfer, the complex inheritance profiles exhibited by mycobacterial transconjugants suggest stochastic co-transfer from multiple origins, as previously predicted [17]. Based on our genome sequence data, we speculate that random chromosomal DNA fragments are generated in the donor, some of which are co-transferred into the recipient strain where they replace recipient sequences through homologous recombination. An alternative scenario is that a single large DNA molecule is transferred, which is processed into smaller segments before their integration into the recipient chromosome by homologous recombination. This scenario seems less likely as we would have expected to identify some transconjugant progeny containing exceedingly large chunks of donor DNA (3–4 Mb) integrated into the chromosome. These would have resulted from recombination close to the ends of the transferred molecule, before creation of small segments. This latter scenario is also less consistent with our previous observations, which indicated that the donor chromosome contained multiple initiation sites and that the efficiency of gene transfer was location-independent. We have considered examining boundary sequences to determine whether they provide insight on the mechanism of conjugation. However, there are multiple factors influencing boundary regions, which together prevent a unifying mechanistic insight. For example, the actual breakpoints generated by conjugation are almost certainly lost as the boundaries are driven by the requirement for homology and by different recombination mechanisms mediating integration, as evidenced by inheritance of both regions of microheterogeneity and single large integration events.

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Figure 7. Graphic summary of the evolutionary and gene mapping potential of distributive conjugal transfer in comparison to oriT-mediated transfer.

The parental donor and recipient strains are schematically shown at the top, with their native chromosomes (blue and yellow circles, respectively) that confer different phenotypes (pink and blue backgrounds, respectively). Co-incubation of the donor and recipient strains on solid media (agar plates) or in a biofilm, permits conjugation. For oriT-mediated transfer (left), all transferred segments of DNA are linked to oriT, which limits the extent of genetic diversity among the transconjugants. This contrasts with distributive conjugal transfer (DCT), wherein random segments of the donor chromosome are transferred to the recipient, generating unique transconjugants. Each transconjugant has a novel genotype that confers a unique phenotypic profile (different colored background). Importantly, multiple rounds of oriT-mediated transfer events with different donors would be required to approach the variation observed from a single DCT event. Under certain conditions, any transconjugant phenotype may have a growth advantage over other transconjugants and the parental strains. Such evolutionary selection can give rise to emergent strains or species. Transconjugants that share a specific phenotypic trait can be sequenced to identify SNPs that mark a shared genomic region associated with that trait. An F1 transconjugant with a specific donor-derived trait can be repetitively backcrossed with the recipient strain to introgress the functional donor gene into the recipient background.

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Mycobacteria encode multiple nonredundant recombination pathways (RecBCD, AdnAB, and nonhomologous end-joining), but are not known to encode a mismatch repair system [26],[27]. We postulate that homologous recombination mediated by AdnAB is likely responsible for the simple crossover events, which is consistent with the absolute requirement for RecA in DCT [17]. However, this form of homologous recombination alone seems insufficient to explain regions of microcomplexity. The clustered proximity of recombinant tracks indicates that an imported donor segment initially encompassed the entire region, but the mechanism underlying the internal mosaicism is unclear. Characterization of the mechanism and the enzymes behind this process will require careful directed approaches using defined recombination mutants.

Every facet of the transfer process contributes to the genetic complexity of the transconjugants (Figure 7). The large number and distributive character of the transferred segments, combined with the microcomplexity in some tracts, makes each transconjugant uniquely different from the others, as well as from the parental strains. The widely varied sizes of the transferred segments allows transconjugants to acquire both major changes, potentially bringing in entire operons encoding biological pathways, and minor nucleotide substitutions that provide subtle diversity, which could, for example, modify the activity or interaction specificity of an enzyme. Multiple pan-genomic changes that typically accompany evolution of bacteria are assumed to be a serial accrual of HGT and spontaneous mutation events (Figure 7). By contrast, a single step DCT event between two single cells generates a transconjugant strain that is a mosaic blend of the parental genomes, and not merely an incrementally altered derivative. Thus, distributive conjugal transfer provides an unparalleled mechanism for quickly generating tremendous genetic diversity, which rivals that seen in sexual reproduction [28].

Recent genome-wide studies of naturally competent strains provide an interesting contrast between the progeny of transformation and conjugation [29]–[32]. In these studies, nonselected segments of DNA were also observed around the recipient chromosome and thus contribute to variation. Microcomplexity in these segments suggested that, as for DCT, integration of transformed DNA was mediated by both recombination and/or repair machinery. However, the nonselected segments were significantly smaller (1–4 kb, depending on the species) than those described here, which average 49 kb and can be as large as 249 kb (Table S4, Km4.5b: 6,942,375–202,798). The limitation on recombination sizes in pneumococci correlated with an underrepresentation of large insertions, which together argued that transformation led to genome reduction and was unlikely to act as a mechanism for uptake of accessory loci [29]. The large DNA segments acquired via DCT, in contrast, facilitates inheritance of novel operons and genes. For example, one large recombination tract introduced a contiguous stretch of ∼55 kb of nonhomologous donor-derived DNA into the transconjugant chromosome (Km6.9b). Perhaps an example more functionally pertinent to our work was an insertion–deletion exchange observed in the divergent mid candidate region of esx1 in transconjugants switched to donors (Figure S5).

We have demonstrated conjugal DNA transfer in additional naturally derived M. smegmatis strains [8], indicating a broader presence for mycobacterial distributive conjugal transfer. The rough-colony morphology members of the Mycobacterium tuberculosis complex (MTBC) exhibit extremely low genetic variation, suggesting that they do not undergo HGT, are evolutionary young, and resulted from a recent clonal expansion [33]. However, there is now convincing evidence for HGT among M. canettii, and other smooth-colony MTBC strains, which display genome-wide mosaicism, although the precise mechanism(s) of HGT are unknown [34],[35]. Based on sequence comparisons, it was proposed that M. canettii strains are extant members of a genetically diverse MTBC progenitor species, M. prototuberculosis, whose members underwent frequent HGT [34],[36],[37]. The unspecified HGT process underlying that mosaicism is presumed to result from a series of sequential transfer events. However, based on our studies, distributive conjugal transfer involving the ancestral M. prototuberculosis offers a plausible and parsimonious explanation for the remarkably similar mosaicism observed among the extant M. canettii. We could envision that distributive conjugal transfer in M. prototuberculosis rapidly incorporated the necessary blend of parental genotypes that drove the emergence of the pathogenic, rough-colony morphology species, like M. tuberculosis, allowing their subsequent clonal expansion. Moreover, if DCT drove these postulated HGT events, the evolutionary clock for M. tuberculosis is likely much shorter because of the capacity of DCT to generate genome-wide mosaicism in a single step. Given the widespread nature of conjugation, we speculate that distributive conjugal transfer also occurs in other bacteria, conferring similar evolutionary benefits.

The characteristics of mycobacterial distributive conjugation suggested to us that tools developed for mammalian genetics could be applied here. Using a eukaryotic-style genome-wide association mapping approach, we mapped the mating identity locus (mid) for mycobacterial conjugation (Figure 7). Similarly, we applied a backcross introgression strategy to refine the mapping and to purge extraneous mc²155 sequence (Figure 7). The purifying selection of successive backcross generations effectively introgressed the mc²155 mid locus into the mc²874 background; this created a strain that was nearly isogenic to the mc²874 parent strain, but which now functioned as a conjugal donor. We note that the hybrid esx1 loci produced by distributive conjugal transfer have not been disabled (as in transposon mutagenesis screens), and still encode functional ESX-1 secretory apparatuses that secrete the major ESX-1 substrates (Figure S6). The un-annotated theoretical proteins encoded by the mid candidate genes bear no overt resemblance to those known to be involved in conjugation in other bacteria. Their association with the esx1 locus suggests that Mid proteins modify the ESX-1 secretion system, are secreted by ESX-1, or interact with other ESX-1–secreted substrates. The next step in their functional assessment will likely result from an extension of this work to identify which protein(s) or protein motifs are necessary and sufficient to impart conjugal sex identity. Interestingly, orthologs for the mid candidate genes are found in the sequenced genomes of other environmental mycobacteria, suggesting a possible ongoing role for distributive conjugal transfer in gene flow between mycobacteria. Orthologs of these mid candidates are not apparent in the esx1 locus of M. tuberculosis, consistent with our speculative model that the MTBC represents a clonally expanded product of distributive conjugal transfer, not necessarily an active participant in this process. Nevertheless, recent evidence from genome sequencing comparisons indicates that some form of genetic exchange has occurred between M. tuberculosis and M. canettii [35].

While we applied DCT to map mid genes, in principle any genetic trait that differs between the parental strains can be mapped using this genome-wide mapping strategy. For example, mc²155 and mc²874 grossly differ in colony morphology, biofilm formation, and phage susceptibility, any of which could have been scored as a change of function in the recipient and mapped by DCT. Similarly, biochemical differences between these strains could be discerned through simple, high-throughput assays. We recognize that more traditional approaches for mutagenic loss-of-function mapping [38],[39] will remain important in mycobacterial studies, but this new application of conjugation now allows any phenotype that differs between a mating pair to be unambiguously mapped.

Our analysis of distributive conjugal transfer (DCT) in M. smegmatis has practical and conceptual ramifications. It brings new tools to mycobacteriology, including those traditionally used exclusively in eukaryotic genetics. It also shows how bacterial evolutionary time scales can be compressed by generating incredible genetic diversity in a single step. Identifying the necessary components, such as esx1 and mid, will help to elucidate the mechanism, to allow modification of the system, and to computationally identify bacteria that actively participate in DCT—or engineer them to do so. Our previous finding of DCT in a mixed biofilm [40] underscores the importance of predicting how prevalent DCT may be in nature, for a more accurate interpretation of metagenomic datasets and to model gene flow through bacterial populations. Regardless of these secondary ramifications, our primary finding of the tremendous genomic variation generated by DCT takes a significant step toward bringing the evolutionary benefits of sexual reproduction to bacteria.

Materials and Methods

Mycobacterial Strains and Conjugation

M. smegmatis donor strains were derivatives of the laboratory strain, mc²155 [41]. Each derivative has a Km^R gene inserted at a unique location in the chromosome [11], which was mapped by DNA sequencing the flanking DNA and alignment to the mc²155 genome sequence (http://cmr.jcvi.org/tigr-scripts/CMR/GenomePage.cgi?org=gms), or the draft genome of the recipient (GenBank CM001762). The recipient strain mc²874 [18],[42] was transformed with a plasmid encoding either apramycin or hygromycin resistance to allow counterselection against the donor. M. smegmatis strains were cultured at 37°C in Trypticase Soy Broth with 0.05% Tween80, or on Trypticase Soy Agar (TSA) plates. Antibiotics were added at 100 µg/ml (apramycin), 100 µg/ml (hygromycin), and 10 µg/ml (kanamycin). DNA transfer experiments were carried out as described previously selecting for dual-resistant transconjugants [8]. To allow selection in the reiterative backcrosses, the recipient strain was alternated between that encoding either apramycin or hygromycin resistance. Each independent transconjugant was assayed in subsequent mating experiments to determine whether they were donor or recipient, in parallel with positive controls. As we have observed previously [8], this phenotype was mutually exclusive. Donor transfer frequencies were determined based on the average of three, independent mating experiments as described previously [8]. Zero transconjugants were obtained with recipient strains, below the sensitivity threshold of one event per 10⁸ cells [8].

Genomic Sequencing and Analysis

Transconjugants were colony purified, and genomic DNA was prepared and then subjected to whole-genome DNA sequence analysis at the Institute for Genome Sciences (IGS), U. Maryland, using paired-end Illumina technology. The sequence coverage for each genome was between 50-fold for F1 progeny and ∼1,000-fold for backcross strains. Sequence reads were mapped to the mc²155 reference sequence by IGS. Single nucleotide polymorphisms (SNPs) or sequence gaps were identified using the Integrative Genomics Viewer (IGV) sequence viewer [43] to define genomic regions of different parental origins. Boundaries of recipient- and donor-derived segments were recorded as the last recipient SNP observed with a minimum of two consecutive SNPs defining parental identity (Figure S2). A donor segment unique to each transconjugant was identified to confirm accuracy of the aligned sequence reads. Primers were designed to specifically amplify these segments, and the amplified products were cloned and sequenced (Table S1) to confirm that donor SNPs had been inherited by the recipient. A compilation of the donor and recipient segments from each transconjugant was projected onto the circular mycobacterial donor chromosome reference sequence, arranged as concentric circles of a Circos plot [44], with color optimization guided by ColorBrewer (Cynthia Brewer, The Pennsylvania State University). Collinearity of the donor and recipient genome was determined using Mauve, a program that was also used to identify SNPs and in/dels [45],[46]. All sequence data have been deposited at the European Nucleotide Archive at http://www.ebi.ac.uk/ena/data/view/ERP002619.

Supporting Information

Figure S1.

Genome collinearity of the parental strains, mc²155 (donor) and mc²874 (recipient). The circular genomes of the parental strains are depicted in linear form and aligned. Genome sequences for mc²874 were obtained by combining reads from one Illumina and two 454 paired-end libraries (GenBank CM001762). Sequence data are deposited in the EBI/ENA database at http://www.ebi.ac.uk/ena/data/view/ERP002619. A de novo build was assembled into a scaffold, and this nucleotide sequence was aligned (Mauve 2.3.1) with the GenBank/JCVI sequence for mc²155 (CP000480.1) [45],[46]. This figure shows the alignment viewed at Mauve's default, highest stringency setting, thereby displaying even small interruptions. Locally Collinear Blocks (LCBs) are independently colored, with the largest five LCBs comprising nearly all of each genome, and maintaining their order and orientation. The crossed lines between each map indicate modest rearrangements. The sequence data identified 122,186 SNPs (∼1 every 56 bp) between the donor and recipient sequences allowing for easy discrimination between donor and recipient DNA in the transconjugants (see also Figures 1A and S2).

https://doi.org/10.1371/journal.pbio.1001602.s001

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Figure S2.

IGV image illustrating donor/recipient junction assignment in a transconjugant. Sequence reads from the recipient strain mc²874 and a transconjugant are shown aligned to the mc²155 reference sequence. A gray bar indicates an individual Illumina sequence read, with the arrow indicating the direction of each read. For simplicity, a depth of 10 reads is shown here, but the average read depth was approximately 50- to 1,000-fold. Gray sequence indicates identity between the sequenced clone and the mc²155 reference genome. Single nucleotide polymorphisms (SNPs) present in sequenced strains appear as colored bases in each read that align vertically with the corresponding polymorphic mc²155 nucleotide. The total SNP content in this 649 bp region is revealed upon mc²874 recipient alignment with the mc²155 reference. Recipient sequence in the transconjugant is conservatively defined by the presence of two consecutive SNPs, and is indicated by the yellow bars below. The left boundary of the replacement donor sequence tract lies between the last recipient SNP present (green) and the next missing SNP (red); as intervening regions match the reference sequence (gray coloration), the donor segment is designated to extend from SNP to SNP, as indicated by the blue bar below. Note that to more clearly discern closely localized donor tracts on the lower resolution Circos plots, successive donor tracts were alternately colored blue or magenta.

https://doi.org/10.1371/journal.pbio.1001602.s002

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Figure S3.

Distribution of donor tract sizes identified in transconjugant genomes. The calculated donor-derived tract sizes for the initial 12 transconjugants are graphically displayed (blue bar represents donor segment length).

https://doi.org/10.1371/journal.pbio.1001602.s003

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Figure S4.

Pairwise alignments of Mid candidate protein sequences between donor and recipient strains of M. smegmatis. A conceptual translation of the six open reading frames comprising the mid candidate regions defined by the combined mapping approaches were globally aligned using a Needleman-Wunsch algorithm (http://www.ebi.ac.uk/Tools/services/web_emboss_needle/). Immediately below each protein identifier (bold text) are input parameters and output statistics. In each alignment, the upper sequence represents the mc²155 (donor) sequence and the bottom is the mc²874 (recipient) sequence. The degree of amino acid conservation is indicated between paired residues: vertical line (identical), dots (similar), or nothing (dissimilar). Horizontal lines represent gaps created by the algorithm to maintain alignment. Similarity statistics for the divergent N-terminus and conserved C-terminus of Msmeg_0071 are listed separately following the full-length alignment of this protein.

https://doi.org/10.1371/journal.pbio.1001602.s004

(DOCX)

Figure S5.

In/dels are transferred in DCT. Whole genome alignment analysis of the mc²155 and mc²874 parental strains by Mauve identified 694 in/dels of >18 bp. The 3′ end of the esx1 locus was identified by Mauve as having insertions in mc²155 (i.e., deleted or divergent in mc²874, indicated by red bars above). Sequence reads aligned to the donor reference viewed in IGV verified that no sequence reads from mc²874 (top alignment, yellow background) mapped to the mc²155 reference sequence in this region, consistent with in/del status. This ∼9 kb region includes donor genes Ms0069 through Ms0071 and a cluster of defective IS elements (Ms0072–0075), displayed at the bottom of the IGV window. Donor sequences from a donor-proficient transconjugant (middle alignment, blue background) have replaced this recipient in/del region, showing that novel sequences can be acquired and incorporated by DCT. Note that reads spanning IS elements in this transconjugant have a lower mapping score (light-shaded reads) because they could map to multiple sites in the genome. Recombination events can occur close to in/del regions, as illustrated by the donor reads in Ms0068 derived from the recipient-proficient transconjugant at the bottom.

https://doi.org/10.1371/journal.pbio.1001602.s005

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Figure S6.

A Western analysis shows that hybrid transconjugants, like their parents, still secrete EsxAB. Culture filtrates and cell pellets were collected as described previously [47]. Following concentration, equivalent cell volumes of each sample were loaded and separated on a 4–12% gradient SDS-PAGE gel. Proteins were transferred to a PVDF membrane and then probed with polyclonal antibodies to detect EsxB. EsxB is secreted by the wild-type strain MKD8 and is therefore detected in both the supernatant (2) and cell pellet (3). In a strain containing a transposon insertion in Ms0062, EsxB is not secreted (4) and is found exclusively in the pellet (5). In transconjugant Km0.1c (Table S2), which contains a mosaic esx1 region, EsxB is found in the supernatant (6) and the pellet (7) as for wild-type. Protein standards are shown in lane 1 and are listed in kilodaltons.

https://doi.org/10.1371/journal.pbio.1001602.s006

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Table S1.

Primers used to verify transferred donor SNPs in transconjugant genomes. The primers, their genome coordinates, used for each transconjugant are listed. Sanger sequencing of the PCR product verified the presence of uniquely transferred donor SNPs in transconjugant genomes. Multiple informative SNPs present in each amplicon to facilitated unambiguous parental origin identification. Two PCR clones were sequenced from each transconjugant strain to avoid potential complications from PCR errors.

https://doi.org/10.1371/journal.pbio.1001602.s007

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Table S2.

Donor and recipient boundary addresses as mapped to the reference sequence. Transconjugant clone name appears along the left margin. Strain nomenclature is based on the genomic location of the Km gene insertion (in Mb); thus, Km0.1 represents the mc²155 derivative with an insertion at coordinate 114 kb. A lower case subscript indicates transconjugants derived from independent crosses using the same parental donor. Donor segments are mapped as where the last consecutive recipient SNP is present (donor begin) to where the next consecutive recipient SNP is detected (donor end). The length of the intervening donor tract (donor size), the total amount of donor DNA in each transconjugant (total donor), and the length of recipient DNA separating adjacent donor tracts are shown (separation). The segments containing the selected kanamycin resistance gene are highlighted in green. Totals for the cohort appear at the bottom. Note that donor regions separated by less than 1 kb are boxed in blue highlights to indicate they may be due to multiple, internal recombination events of a larger transferred segment, or a single recombination modified by mismatch repair.

https://doi.org/10.1371/journal.pbio.1001602.s008

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Table S3.

Transfer frequencies of F1 transconjugants. Transfer frequencies are the number of transconjugants divided by the number of donor cells. These frequencies are the average of at least two independent matings, which were carried out in parallel with a positive control (MKD6 and MKD8, [8]). The threshold of detection is ∼1 transfer event per 10⁸ donor or recipient parental cells.

https://doi.org/10.1371/journal.pbio.1001602.s009

(DOCX)

Table S4.

Donor and recipient boundary addresses as mapped to the reference sequence for donor-proficient F1 strains and their recipient-proficient backcross derivatives. Transconjugant strain nomenclature, and column headings are the same as in Figure S2, with added columns in the F1 analysis for the number of donor segments (donor #), and the percentage of donor DNA transconjugant (% Donor). Backcross (BC) strain names are based on their parent; thus, Km0.1BC is derived from parent Km0.1. Six F1 derivatives were used for the backcross analysis, shown in the far right columns, adjacent to their parental strains. To emphasize the introgression, F1 segments of DNA that were transferred in the backcrosses are alternately colored blue or red. The same colors are used in the final backcross strain to indicate their origin. As above, the length, size, and percent of donor DNA in BC derivatives are indicated. The segment of DNA encoding the Km gene is also indicated (green shading), and a column listing the esx1 genes, if present in the BC strains, has been added.

https://doi.org/10.1371/journal.pbio.1001602.s010

(XLS)

Acknowledgments

We are grateful to Nigel Grindley, Joe Wade, and Paul Masters for critical comments; to the Wadsworth Genetics and Computational cores for their services; and to Luke Tallon and Ivette Santana-Cruz at the Institute for Genome Sciences, University of Maryland, for input on sequence determination and analysis.

Author Contributions

The author(s) have made the following declarations about their contributions: Conceived and designed the experiments: TAG KMD. Performed the experiments: JAK JRH TAG KMD. Analyzed the data: MP TAG KMD JAK. Wrote the paper: TAG KMD. All authors discussed the results and commented on the manuscript.

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