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Distributive Conjugal Transfer: New Insights into Horizontal Gene Transfer and Genetic Exchange in Mycobacteria

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  • Authors: Keith M. Derbyshire1, Todd A. Gray2
  • Editors: Graham F. Hatfull3, William R. Jacobs Jr.4
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    Affiliations: 1: Division of Genetics, Wadsworth Center, New York State Department of Health, and Department of Biomedical Sciences, University at Albany, Albany, NY 12201; 2: Division of Genetics, Wadsworth Center, New York State Department of Health, and Department of Biomedical Sciences, University at Albany, Albany, NY 12201; 3: University of Pittsburgh, Pittsburgh, PA; 4: Howard Hughes Medical Institute, Albert Einstein College of Medicine, Bronx, NY
    • Source: microbiolspec January 2014 vol. 2 no. 1 doi:10.1128/microbiolspec.MGM2-0022-2013
  • Received 22 August 2013 Accepted 03 September 2013 Published 17 January 2014
  • Correspondence: Keith M. Derbyshire, [email protected]
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  • Abstract:

    The past decade has seen an explosion in the application of genomic tools across all biological disciplines. This is also true for mycobacteria, where whole-genome sequences are now available for pathogens and nonpathogens alike. Genomes within the complex (MTBC) bear the hallmarks of horizontal gene transfer (HGT). Conjugation is the form of HGT with the highest potential capacity and evolutionary influence. Donor and recipient strains of actively conjugate upon coculturing in biofilms and on solid media. Whole-genome sequencing of the transconjugant progeny demonstrated the incredible scale and range of genomic variation that conjugation generates. Transconjugant genomes are complex mosaics of the parental strains. Some transconjugant genomes are up to one-quarter donor-derived, distributed over 30 segments. Transferred segments range from ∼50 bp to ∼225,000 bp in length and are exchanged with their recipient orthologs all around the genome. This unpredictable genome-wide infusion of DNA sequences is called distributive conjugal transfer (DCT), to distinguish it from traditional -based conjugation. The mosaicism generated in a single transfer event resembles that seen from meiotic recombination in sexually reproducing organisms and contrasts with traditional models of HGT. This similarity allowed the application of a genome-wide association study approach to map the donor genes that confer a donor mating identity phenotype. The mating identity genes map to the locus, expanding the central role of ESX-1 function in conjugation. The potential for DCT to instantaneously blend genomes will affect how we view mycobacterial evolution and provide new tools for the facile manipulation of mycobacterial genomes.

  • Citation: Derbyshire K, Gray T. 2014. Distributive Conjugal Transfer: New Insights into Horizontal Gene Transfer and Genetic Exchange in Mycobacteria. Microbiol Spectrum 2(1):MGM2-0022-2013. doi:10.1128/microbiolspec.MGM2-0022-2013.

References

1. Frost LS, Leplae R, Summers AO, Toussaint A. 2005. Mobile genetic elements: the agents of open source evolution. Nat Rev Microbiol 3:722–732. [PubMed][CrossRef]
2. Thomas CM, Nielsen KM. 2005. Mechanisms of, and barriers to, horizontal gene transfer between bacteria. Nat Rev Microbiol 3:711–721. [PubMed][CrossRef]
3. Gogarten JP, Townsend JP. 2005. Horizontal gene transfer, genome innovation and evolution. Nat Rev Microbiol 3:679–687. [PubMed][CrossRef]
4. McDaniel LD, Young E, Delaney J, Ruhnau F, Ritchie KB, Paul JH. 2010. High frequency of horizontal gene transfer in the oceans. Science 330:50. [PubMed][CrossRef]
5. Nakamura Y, Itoh T, Matsuda H, Gojobori T. 2004. Biased biological functions of horizontally transferred genes in prokaryotic genomes. Nat Genet 36:760–766. [PubMed][CrossRef]
6. Ochman H, Lawrence JG, Groisman EA. 2000. Lateral gene transfer and the nature of bacterial innovation. Nature 405:299–304. [PubMed][CrossRef]
7. Wiedenbeck J, Cohan FM. 2011. Origins of bacterial diversity through horizontal genetic transfer and adaptation to new ecological niches. FEMS Microbiol Rev 35:957–976. [PubMed][CrossRef]
8. Smith NH, Dale J, Inwald J, Palmer S, Gordon SV, Hewinson RG, Smith JM. 2003. The population structure of Mycobacterium bovis in Great Britain: clonal expansion. Proc Natl Acad Sci USA 100:15271–15275. [PubMed][CrossRef]
9. Smith NH, Gordon SV, de la Rua-Domenech R, Clifton-Hadley RS, Hewinson RG. 2006. Bottlenecks and broomsticks: the molecular evolution of Mycobacterium bovis. Nat Rev Microbiol 4:670–681. [PubMed][CrossRef]
10. Sreevatsan S, Pan X, Stockbauer KE, Connell ND, Kreiswirth BN, Whittam TS, Musser JM. 1997. Restricted structural gene polymorphism in the Mycobacterium tuberculosis complex indicates evolutionarily recent global dissemination. Proc Natl Acad Sci USA 94:9869–9874. [PubMed]
11. Supply P, Warren RM, Banuls AL, Lesjean S, Van Der Spuy GD, Lewis LA, Tibayrenc M, Van Helden PD, Locht C. 2003. Linkage disequilibrium between minisatellite loci supports clonal evolution of Mycobacterium tuberculosis in a high tuberculosis incidence area. Mol Microbiol 47:529–538. [PubMed]
12. Brosch R. 2002. A new evolutionary scenario for the Mycobacterium tuberculosis complex. Proc Natl Acad Sci USA 99:3684–3689. [PubMed][CrossRef]
13. Guttierrez MC, Brisse S, Brosch R, Fabre M, Omais B, Marmiesse M, Supply P, Vincent V. 2005. Ancient origin and gene mosaicism of the progenitor of Mycobacterium tuberculosis. PLoS Pathog 1:1–7. [PubMed][CrossRef]
14. Supply P, Marceau M, Mangenot S, Roche D, Rouanet C, Khanna V, Majlessi L, Criscuolo A, Tap J, Pawlik A, Fiette L, Orgeur M, Fabre M, Parmentier C, Frigui W, Simeone R, Boritsch EC, Debrie AS, Willery E, Walker D, Quail MA, Ma L, Bouchier C, Salvignol G, Sayes F, Cascioferro A, Seemann T, Barbe V, Locht C, Gutierrez MC, Leclerc C, Bentley SD, Stinear TP, Brisse S, Medigue C, Parkhill J, Cruveiller S, Brosch R. 2013. Genomic analysis of smooth tubercle bacilli provides insights into ancestry and pathoadaptation of Mycobacterium tuberculosis. Nat Genet 45:172–179. [PubMed][CrossRef]
15. 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:e1001602. [PubMed][CrossRef]
16. de la Cruz F, Frost LS, Meyer RJ, Zechner EL. 2010. Conjugative DNA metabolism in Gram-negative bacteria. FEMS Microbiol Rev 34:18–40. [PubMed][CrossRef]
17. Firth N, Ippen-Ihler K, Skurray RA. 1996. Structure and function of the F factor and mechanism of conjugation, p 2377–2401. In Neidhardt FC (ed), Escherichia coli and Salmonella : Cellular and Molecular Biology, 2nd ed, vol. 2. ASM Press, Washington, DC.
18. Wozniak RA, Waldor MK. 2010. Integrative and conjugative elements: mosaic mobile genetic elements enabling dynamic lateral gene flow. Nat Rev Microbiol 8:552–563. [PubMed][CrossRef]
19. Guglielmini J, Quintais L, Garcillan-Barcia MP, de la Cruz F, Rocha EP. 2011. The repertoire of ICE in prokaryotes underscores the unity, diversity, and ubiquity of conjugation. PLoS Genet 7:e1002222. [PubMed][CrossRef]
20. Christie PJ, Atmakuri K, Krishnamoorthy V, Jakubowski S, Cascales E. 2005. Biogenesis, architecture and function of bacterial type IV secretion systems. Annu Rev Microbiol 59:451–485. [PubMed][CrossRef]
21. Bhatty M, Laverde Gomez JA, Christie PJ. 2013. The expanding bacterial type IV secretion lexicon. Res Microbiol 164:620–639. [PubMed][CrossRef]
22. Grohmann E, Muth G, Espinosa M. 2003. Conjugative plasmid transfer in Gram-positive bacteria. Microbiol Mol Biol Rev 67:277–301. [PubMed]
23. Alvarez-Martinez CE, Christie PJ. 2009. Biological diversity of prokaryotic type IV secretion systems. Microbiol Mol Biol Rev 73:775–808. [PubMed]
24. Dunny GM. 2007. The peptide pheromone-inducible conjugation system of Enterococcus faecalis plasmid pCF10: cell-cell signaling, gene transfer, complexity and evolution. Philos Trans R Soc Lond B Biol Sci 362:1185–1193. [PubMed][CrossRef]
25. Lederberg J, Tatum EL. 1946. Gene recombination in E. coli. Nature 158:558. [PubMed]
26. Wollman EL, Jacob F, Hayes W. 1956. Conjugation and genetic recombination in Escherichia coli K-12. Cold Spring Harb Symp Quant Biol 21:141–162. [PubMed]
27. Crawford JT, Falkinham JO. 1990. Plasmids of the Mycobacterium avium complex, p 97–120. In McFadden J (ed), Molecular Biology of the Mycobacteria. Academic Press, San Diego, CA.
28. Movahedzadeh F, Bitter W. 2009. Ins and outs of mycobacterial plasmids. Methods Mol Biol 465:217–228. [PubMed][CrossRef]
29. Pashley C, Stoker NG. 2000. Plasmids in mycobacteria, p 55–67. In Hatfull GF, Jacobs WR Jr (ed), Molecular Genetics of Mycobacteria. ASM Press, Washington DC.
30. Jucker MT, Falkingham JO. 1990. Epidemiology of infection by nontuberculous mycobacteria. Am Rev Respir Dis 142:858–862. [PubMed]
31. Kirby C, Waring A, Griffin TJ, Falkinham JO, 3rd, Grindley ND, Derbyshire KM. 2002. Cryptic plasmids of Mycobacterium avium: Tn552 to the rescue. Mol Microbiol 43:173–186. [PubMed]
32. Picardeau M, Le Dantec C, Vincent V. 2000. Analysis of the internal replication region of a mycobacterial linear plasmid. Microbiology 146:305–313. [PubMed]
33. Le Dantec C, Winter N, Gicquel B, Vincent V, Picardeau M. 2001. Genomic sequence and transcriptional analysis of a 23-kilobase mycobacterial linear plasmid: evidence for horizontal transfer and identification of plasmid maintenance systems. J Bacteriol 183:2151–2164. [PubMed][CrossRef]
34. Rauzier J, Moniz-Pereira J, Gicquel-Sanzey B. 1988. Complete nucleotide sequence of pAl5000, a plasmid from Mycobacterium fortuitum. Gene 71:315–321. [PubMed]
35. Stinear TP, Mve-Obiang A, Small PL, Frigui W, Pryor MJ, Brosch R, Jenkin GA, Johnson PD, Davies JK, Lee RE, Adusumilli S, Garnier T, Haydock SF, Leadlay PF, Cole ST. 2004. Giant plasmid-encoded polyketide synthases produce the macrolide toxin of Mycobacterium ulcerans. Proc Natl Acad Sci USA 101:1345–1349. [PubMed][CrossRef]
36. Stinear TP, Pryor MJ, Porter JL, Cole ST. 2005. Functional analysis and annotation of the virulence plasmid pMUM001 from Mycobacterium ulcerans.Microbiology 151:683–692. [PubMed][CrossRef]
37. Wang J, Parsons LM, Derbyshire KM. 2003. Unconventional conjugal DNA transfer in mycobacteria. Nat Genet 34:80–84. [PubMed][CrossRef]
38. Leao SC, Matsumoto CK, Carneiro A, Ramos RT, Nogueira CL, Lima JD, Jr, Lima KV, Lopes ML, Schneider H, Azevedo VA, da Costa da Silva A. 2013. The detection and sequencing of a broad-host-range conjugative IncP-1beta plasmid in an epidemic strain of Mycobacterium abscessus subsp. bolletii. PLoS One 8:e60746. [PubMed]
39. Gormley EP, Davies J. 1991. Transfer of plasmid RSF1010 by conjugation from Escherichia coli to Streptomyces lividans and Mycobacterium smegmatis. J Bacteriol 173:6705–6708. [PubMed]
40. Parsons LM, Jankowski CS, Derbyshire KM. 1998. Conjugal transfer of chromosomal DNA in Mycobacterium smegmatis. Mol Microbiol 28:571–582. [PubMed]
41. Mizuguchi Y, Suga K, Tokunaga T. 1976. Multiple mating types of Mycobacterium smegmatis. Jpn J Microbiol 20:435–443. [PubMed]
42. Mizuguchi Y, Tokunaga T. 1971. Recombination between Mycobacterium smegmatis strains Jucho and Lacticola. Jpn J Microbiol 15:359–366. [PubMed]
43. Derbyshire KM, Willetts NS. 1987. Mobilization of the non-conjugative plasmid RSF1010: a genetic analysis of its origin of transfer. Mol Gen Genet 206:154–160 (Erratum, 209:411). [PubMed]
44. Everett R, Willetts NS. 1982. Cloning, mutation and location of the origin of conjugal transfer. EMBO J 1:747–753. [PubMed]
45. Wang J, Derbyshire KM. 2004. Plasmid DNA transfer in Mycobacterium smegmatis involves novel DNA rearrangements in the recipient, which can be exploited for molecular genetic studies. Mol Microbiol 53:1233–1241. [PubMed][CrossRef]
46. Wang J, Karnati PK, Takacs CM, Kowalski JC, Derbyshire KM. 2005. Chromosomal DNA transfer in Mycobacterium smegmatis is mechanistically different from classical Hfr chromosomal DNA transfer. Mol Microbiol 58:280–288. [PubMed][CrossRef]
47. Daffe M, Reyrat JM. 2008. The Mycobacterial Cell Envelope. ASM Press, Washington, DC.
48. Flint JL, Kowalski JC, Karnati PK, Derbyshire KM. 2004. The RD1 virulence locus of Mycobacterium tuberculosis regulates DNA transfer in Mycobacterium smegmatis. Proc Natl Acad Sci USA 101:12598–12603. [PubMed][CrossRef]
49. Coros A, Callahan B, Battaglioli E, Derbyshire KM. 2008. The specialized secretory apparatus ESX-1 is essential for DNA transfer in Mycobacterium smegmatis. Mol Microbiol 69:794–808. [PubMed][CrossRef]
50. Abdallah AM, Gey van Pittius NC, DiGiuseppe Champion PA, Cox J, Luirink J, Vandenbroucke-Grauls CMJE, Appelmelk BJ, Bitter W. 2007. Type VII secretion: mycobacteria show the way. Nat Rev Microbiol 5:883–891. [PubMed][CrossRef]
51. Bitter W, Houben EN, Bottai D, Brodin P, Brown EJ, Cox J, Derbyshire KM, Fortune SM, Gao LY, Liu J, Gey van Pittius NC, Pym AS, Rubin EJ, Sherman DR, Cole ST, Brosch R. 2009. Systematic genetic nomenclature for type VII secretion systems. PLoS Pathog 5:e1000507. [PubMed][CrossRef]
52. Converse SE, Cox JS. 2005. A protein secretion pathway critical for Mycobacterium tuberculosis virulence is conserved and functional in Mycobacterium smegmatis. J Bacteriol 187:1238–1245. [PubMed][CrossRef]
53. Smith GR. 1991. Conjugational recombination in E. coli: myths and mechanisms. Cell 64:19–27. [PubMed]
54. Taylor AF, Smith GR. 1992. RecBCD enzyme is altered upon cutting DNA at a chi recombination hotspot. Proc Natl Acad Sci USA 89:5226–5230. [PubMed]
55. Sinha KM, Unciuleac MC, Glickman MS, Shuman S. 2009. AdnAB: a new DSB-resecting motor-nuclease from mycobacteria. Genes Dev 23:1423–1437. [PubMed][CrossRef]
56. Gupta R, Barkan D, Redelman-Sidi G, Shuman S, Glickman MS. 2011. Mycobacteria exploit three genetically distinct DNA double-strand break repair pathways. Mol Microbiol 79:316–330. [PubMed][CrossRef]
57. Warner DF, Mizrahi V. 2011. Making ends meet in mycobacteria. Mol Microbiol 79:283–287. [PubMed][CrossRef]
58. Rayssiguier C, Thaler DS, Radman M. 1989. The barrier to recombination between Escherichia coli and Salmonella typhimurium is disrupted in mismatch-repair mutants. Nature 342:396–401. [PubMed][CrossRef]
59. Springer B, Sander P, Sedlacek L, Hardt WD, Mizrahi V, Schar P, Bottger EC. 2004. Lack of mismatch correction facilitates genome evolution in mycobacteria. Mol Microbiol 53:1601–1609. [PubMed][CrossRef]
60. Shuman S, Glickman MS. 2007. Bacterial DNA repair by nonhomologous end joining. Nat Rev Microbiol 5:852–861. [PubMed][CrossRef]
61. Possoz C, Ribard C, Gagnat J, Pernodet JL, Guerineau M. 2001. The integrative element pSAM2 from Streptomyces: kinetics and mode of conjugal transfer. Mol Microbiol 42:159–166. [PubMed]
62. Vogelmann J, Ammelburg M, Finger C, Guezguez J, Linke D, Flotenmeyer M, Stierhof YD, Wohlleben W, Muth G. 2011. Conjugal plasmid transfer in Streptomyces resembles bacterial chromosome segregation by FtsK/SpoIIIE. EMBO J 30:2246–2254. [PubMed][CrossRef]
63. Lee JY, Finkelstein IJ, Crozat E, Sherratt DJ, Greene EC. 2012. Single-molecule imaging of DNA curtains reveals mechanisms of KOPS sequence targeting by the DNA translocase FtsK. Proc Natl Acad Sci USA 109:6531–6536. [PubMed][CrossRef]
64. Reuther J, Gekeler C, Tiffert Y, Wohlleben W, Muth G. 2006. Unique conjugation mechanism in mycelial streptomycetes: a DNA-binding ATPase translocates unprocessed plasmid DNA at the hyphal tip. Mol Microbiol 61:436–446. [PubMed][CrossRef]
65. Sepulveda E, Vogelmann J, Muth G. 2011. A septal chromosome segregator protein evolved into a conjugative DNA-translocator protein. Mob Genet Elements 1:225–229. [PubMed][CrossRef]
66. Namouchi A, Didelot X, Schock U, Gicquel B, Rocha EP. 2012. After the bottleneck: genome-wide diversification of the Mycobacterium tuberculosis complex by mutation, recombination, and natural selection. Genome Res 22:721–734. [PubMed][CrossRef]
67. Krzywinska E, Krzywinski J, Schorey JS. 2004. Naturally occurring horizontal gene transfer and homologous recombination in Mycobacterium. Microbiology 150:1707–1712. [PubMed][CrossRef]
68. Wang J, Fan HC, Behr B, Quake SR. 2012. Genome-wide single-cell analysis of recombination activity and de novo mutation rates in human sperm. Cell 150:402–412. [PubMed][CrossRef]
69. McLaughlin B, Chon JS, MacGurn JA, Carlsson F, Cheng TL, Cox JS, Brown EJ. 2007. A mycobacterium ESX-1–secreted virulence factor with unique requirements for export. PLOS Pathog 3:e105. [PubMed][CrossRef]
70. Xu J, Laine O, Masciocchi M, Manoranjan J, Smith J, Du SJ, Edwards N, Zhu X, Fenselau C, Gao L-Y. 2007. A unique mycobacterium ESX-1 protein co-secretes with CFP-10/ESAT-6 and is necessary for inhibiting phagosome maturation. Mol Microbiol 66:787–800. [PubMed][CrossRef]
71. Bottai B, Stinear TP, Supply P, Brosch B. 2014. Mycobacterial pathogenomics and evolution. Microbiol Spectrum 2(1) :MGM2-0025-2013. doi:10.1128/microbiolspec.MGM2-0025-2013.
72. Derbyshire KM, Bardarov S. 2000. DNA transfer in mycobacteria: conjugation and transduction, p 93-107. In Hatfull GF, Jacobs WR Jr (ed), Molecular Genetics of Mycobacteria. ASM Press, Washington, DC.
73. Hatfull GF. Molecular genetics of mycobacteriophages. In Hatfull GF, Jacobs WR Jr (ed), Molecular Genetics of Mycobacteria, 2nd ed. ASM Press, Washington, DC, in press.
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2014-01-17
2020-02-26

Abstract:

The past decade has seen an explosion in the application of genomic tools across all biological disciplines. This is also true for mycobacteria, where whole-genome sequences are now available for pathogens and nonpathogens alike. Genomes within the complex (MTBC) bear the hallmarks of horizontal gene transfer (HGT). Conjugation is the form of HGT with the highest potential capacity and evolutionary influence. Donor and recipient strains of actively conjugate upon coculturing in biofilms and on solid media. Whole-genome sequencing of the transconjugant progeny demonstrated the incredible scale and range of genomic variation that conjugation generates. Transconjugant genomes are complex mosaics of the parental strains. Some transconjugant genomes are up to one-quarter donor-derived, distributed over 30 segments. Transferred segments range from ∼50 bp to ∼225,000 bp in length and are exchanged with their recipient orthologs all around the genome. This unpredictable genome-wide infusion of DNA sequences is called distributive conjugal transfer (DCT), to distinguish it from traditional -based conjugation. The mosaicism generated in a single transfer event resembles that seen from meiotic recombination in sexually reproducing organisms and contrasts with traditional models of HGT. This similarity allowed the application of a genome-wide association study approach to map the donor genes that confer a donor mating identity phenotype. The mating identity genes map to the locus, expanding the central role of ESX-1 function in conjugation. The potential for DCT to instantaneously blend genomes will affect how we view mycobacterial evolution and provide new tools for the facile manipulation of mycobacterial genomes.

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Distributive Conjugal Transfer: New Insights into Horizontal Gene Transfer and Genetic Exchange in Mycobacteria
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Citation: Derbyshire K, Gray T. 2014. Distributive conjugal transfer: new insights into horizontal gene transfer and genetic exchange in mycobacteria. microbiolspec 2(1): doi:10.1128/microbiolspec.MGM2-0022-2013
/content/microbiolspec/10.1128/microbiolspec.MGM2-0022-2013.fig1
FIGURE 1
directs both plasmid and chromosomal transfer in traditional conjugation systems. F episome plasmid transfer. The is nicked and a single strand is guided into the engaged recipient by a plasmid-encoded relaxase. Upon transfer, relaxase catalyzes recircularization at , and host polymerases synthesize a complementary strand. The recipient chromosome is unaltered, but the cell now exhibits a donor phenotype (blue). Hfr strains have a plasmid integrated into the chromosome, shown as a single strand for simplicity. The integrated functions as it would in the plasmid scenario above, except that transfer of the chromosome is usually incomplete. The linear chromosomal fragment must be incorporated into the recipient chromosome by homologous recombination for stable inheritance. Homologous recombination excludes the , and, while the transconjugant chromosome now has some donor sequences, it retains a recipient phenotype (yellow). For an Hfr transconjugant to become a donor, the entire donor chromosome must be transferred to regenerate .
microbiolspec/2/1/MGM2-0022-2013-fig1_thmb.gif
microbiolspec/2/1/MGM2-0022-2013-fig1.gif
Image of FIGURE 1

Click to view

FIGURE 1

directs both plasmid and chromosomal transfer in traditional conjugation systems. F episome plasmid transfer. The is nicked and a single strand is guided into the engaged recipient by a plasmid-encoded relaxase. Upon transfer, relaxase catalyzes recircularization at , and host polymerases synthesize a complementary strand. The recipient chromosome is unaltered, but the cell now exhibits a donor phenotype (blue). Hfr strains have a plasmid integrated into the chromosome, shown as a single strand for simplicity. The integrated functions as it would in the plasmid scenario above, except that transfer of the chromosome is usually incomplete. The linear chromosomal fragment must be incorporated into the recipient chromosome by homologous recombination for stable inheritance. Homologous recombination excludes the , and, while the transconjugant chromosome now has some donor sequences, it retains a recipient phenotype (yellow). For an Hfr transconjugant to become a donor, the entire donor chromosome must be transferred to regenerate .

Source: microbiolspec January 2014 vol. 2 no. 1 doi:10.1128/microbiolspec.MGM2-0022-2013
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/content/microbiolspec/10.1128/microbiolspec.MGM2-0022-2013.fig2
FIGURE 2
An outline of the mycobacterial mating procedure. Selectable markers for donor and recipient are chromosomally encoded. Efficient transfer requires prolonged incubation (overnight) on solid medium. Transfer does not take place in liquid cultures, probably reflecting the need to force cell-cell contact on the solid medium. The transfer frequency is 1 event per 10 donors. However, this only reflects successful transfer of and therefore is an underestimate of the total number of events.
microbiolspec/2/1/MGM2-0022-2013-fig2_thmb.gif
microbiolspec/2/1/MGM2-0022-2013-fig2.gif
Image of FIGURE 2

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FIGURE 2

An outline of the mycobacterial mating procedure. Selectable markers for donor and recipient are chromosomally encoded. Efficient transfer requires prolonged incubation (overnight) on solid medium. Transfer does not take place in liquid cultures, probably reflecting the need to force cell-cell contact on the solid medium. The transfer frequency is 1 event per 10 donors. However, this only reflects successful transfer of and therefore is an underestimate of the total number of events.

Source: microbiolspec January 2014 vol. 2 no. 1 doi:10.1128/microbiolspec.MGM2-0022-2013
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FIGURE 3
Donor chromosomal sites mobilize plasmids and mediate recircularization by gap repair in the recipient. Episomal plasmids are not subject to conjugal transfer unless they carry chromosomal DNA segments functionally defined as (basis of mobility) sites. Recovery of the transferred plasmids, and sequencing of the sites, revealed the presence of embedded recipient SNPs, suggesting a gap-repair mechanism. In this model, transfer would be initiated in the donor via a break in . Following transfer of the linear plasmid, the homologous region of the recipient chromosome would act as the template for gap repair to seal the break and recircularize the plasmid. As a consequence, recipient SNPs would be incorporated into the plasmid DNA. This model was confirmed by the use of two adjacent sites, separated by a nonhomologous sequence. The region of nonidentity was replaced by the intervening recipient chromosomal sequence upon transfer. In this two- model a break could occur at both s to create a gap spanning hypothetical gene . Alternatively, a break could occur at just one site (as shown) and then the nonhomologous region resected by exonucleases to generate ends suitable for gap repair, capture of gene and plasmid circularization.
microbiolspec/2/1/MGM2-0022-2013-fig3_thmb.gif
microbiolspec/2/1/MGM2-0022-2013-fig3.gif
Image of FIGURE 3

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FIGURE 3

Donor chromosomal sites mobilize plasmids and mediate recircularization by gap repair in the recipient. Episomal plasmids are not subject to conjugal transfer unless they carry chromosomal DNA segments functionally defined as (basis of mobility) sites. Recovery of the transferred plasmids, and sequencing of the sites, revealed the presence of embedded recipient SNPs, suggesting a gap-repair mechanism. In this model, transfer would be initiated in the donor via a break in . Following transfer of the linear plasmid, the homologous region of the recipient chromosome would act as the template for gap repair to seal the break and recircularize the plasmid. As a consequence, recipient SNPs would be incorporated into the plasmid DNA. This model was confirmed by the use of two adjacent sites, separated by a nonhomologous sequence. The region of nonidentity was replaced by the intervening recipient chromosomal sequence upon transfer. In this two- model a break could occur at both s to create a gap spanning hypothetical gene . Alternatively, a break could occur at just one site (as shown) and then the nonhomologous region resected by exonucleases to generate ends suitable for gap repair, capture of gene and plasmid circularization.

Source: microbiolspec January 2014 vol. 2 no. 1 doi:10.1128/microbiolspec.MGM2-0022-2013
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FIGURE 4
Transconjugant chromosomes are mosaic blends of the parental strains. Whole-genome sequencing of transconjugants and alignment with the parental sequences used the presence or absence of parental SNPs to define tracts of transferred donor DNA. A Circos projection of the 7-Mb chromosome is shown as concentric circles, with the recipient genome on the outside (yellow), the donor on the inside (blue), and four transconjugants in between. The segment containing the gene used for postmating selection is indicated (green); the recipient antibiotic marker is episomally encoded. The outer three transconjugants have a donor mating identity, and all have inherited the locus from the donor strain (indicated at 0.1 Mb on the chromosome). The innermost transconjugant lacks the locus and is a recipient strain. These data and additional Circos plots can be seen in reference 15 .
microbiolspec/2/1/MGM2-0022-2013-fig4_thmb.gif
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FIGURE 4

Transconjugant chromosomes are mosaic blends of the parental strains. Whole-genome sequencing of transconjugants and alignment with the parental sequences used the presence or absence of parental SNPs to define tracts of transferred donor DNA. A Circos projection of the 7-Mb chromosome is shown as concentric circles, with the recipient genome on the outside (yellow), the donor on the inside (blue), and four transconjugants in between. The segment containing the gene used for postmating selection is indicated (green); the recipient antibiotic marker is episomally encoded. The outer three transconjugants have a donor mating identity, and all have inherited the locus from the donor strain (indicated at 0.1 Mb on the chromosome). The innermost transconjugant lacks the locus and is a recipient strain. These data and additional Circos plots can be seen in reference 15 .

Source: microbiolspec January 2014 vol. 2 no. 1 doi:10.1128/microbiolspec.MGM2-0022-2013
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FIGURE 5
Models for chromosome fragmentation in DCT. DCT could follow one of two pathways, depending on whether fragmentation of the transferred chromosome occurs in the donor cell before transfer (left) or following transfer in the recipient (right and indicated by arrows). The left-hand model posits that multiple chromosome segments are cotransferred into the recipient, where they are recombined into the recipient chromosome to generate a mosaic pattern. Large chunk transfer (right) would be predicted to result in fewer large integrated segments rather than many widely distributed donor segments. Current results, as seen in Fig. 4 , are more consistent with the fragmentation-before-transfer model.
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FIGURE 5

Models for chromosome fragmentation in DCT. DCT could follow one of two pathways, depending on whether fragmentation of the transferred chromosome occurs in the donor cell before transfer (left) or following transfer in the recipient (right and indicated by arrows). The left-hand model posits that multiple chromosome segments are cotransferred into the recipient, where they are recombined into the recipient chromosome to generate a mosaic pattern. Large chunk transfer (right) would be predicted to result in fewer large integrated segments rather than many widely distributed donor segments. Current results, as seen in Fig. 4 , are more consistent with the fragmentation-before-transfer model.

Source: microbiolspec January 2014 vol. 2 no. 1 doi:10.1128/microbiolspec.MGM2-0022-2013
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FIGURE 6
DCT brings large and small changes to transconjugant genomes. Transferred donor segments can be contiguous blocks hundreds of kilobases in length, spanning hundreds of genes. These large blocks can exchange recipient for donor orthologs (left). The large segments may also contain additional genes not present in the original recipient sequence (insertion) or may lack some genes that had been present (deletion). At the opposite end of the size spectrum, donor segments of <100 bp are often found in clusters to generate microcomplexity, with the potential to fine-tune genes or functional elements (right). Comparison of M. canettii genomes has identified similar mosaicism, in which sequences of entire genes are identical between some isolates, while other regions contain short regions of exchanged SNPs consistent with the recombinant patterns observed with DCT ( 14 ).
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FIGURE 6

DCT brings large and small changes to transconjugant genomes. Transferred donor segments can be contiguous blocks hundreds of kilobases in length, spanning hundreds of genes. These large blocks can exchange recipient for donor orthologs (left). The large segments may also contain additional genes not present in the original recipient sequence (insertion) or may lack some genes that had been present (deletion). At the opposite end of the size spectrum, donor segments of <100 bp are often found in clusters to generate microcomplexity, with the potential to fine-tune genes or functional elements (right). Comparison of M. canettii genomes has identified similar mosaicism, in which sequences of entire genes are identical between some isolates, while other regions contain short regions of exchanged SNPs consistent with the recombinant patterns observed with DCT ( 14 ).

Source: microbiolspec January 2014 vol. 2 no. 1 doi:10.1128/microbiolspec.MGM2-0022-2013
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FIGURE 7
DCT generates instant diversity on a genome-wide scale. Progeny from a bacterial cross are shown for -mediated chromosomal transfer (left) and for DCT (right). In a single Hfr cross, transconjugants can acquire segments of DNA proximal to Depending on the length of transfer, all progeny will have overlapping regions of the donor chromosome extending from . By contrast, all DCT progeny are different because transfer initiates from sites all around the chromosome. In addition, DCT recombination results in both large segment exchanges and smaller regions of micro-heterogeneity, creating further diversity. The extreme diversity in the transconjugant population allows for rapid expansion under changing selective pressures.
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FIGURE 7

DCT generates instant diversity on a genome-wide scale. Progeny from a bacterial cross are shown for -mediated chromosomal transfer (left) and for DCT (right). In a single Hfr cross, transconjugants can acquire segments of DNA proximal to Depending on the length of transfer, all progeny will have overlapping regions of the donor chromosome extending from . By contrast, all DCT progeny are different because transfer initiates from sites all around the chromosome. In addition, DCT recombination results in both large segment exchanges and smaller regions of micro-heterogeneity, creating further diversity. The extreme diversity in the transconjugant population allows for rapid expansion under changing selective pressures.

Source: microbiolspec January 2014 vol. 2 no. 1 doi:10.1128/microbiolspec.MGM2-0022-2013
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FIGURE 8
Mating identity is determined by genes within The . locus spans 26 homologous genes in the donor (blue) and recipient (orange) parental strains (top). Genes and define the ends of the locus. and encode the primary secreted substrates EsxA and EsxB. Whole-genome sequencing and genome-wide association mapping of F1 transconjugants that exhibited a donor phenotype revealed that all donor-proficient transconjugants had an locus of donor origin ( Fig. 4 ). Mapping of the ating entity () locus—the donor genes associated with the donor conjugal phenotype—to was confirmed by successively backcrossing donor-proficient transconjugants with the recipient, while maintaining the donor phenotype (transconjugant donor). Backcrossed transconjugants that showed a recipient conjugal phenotype (transconjugant recipient) all shared a region of their locus that was composed of recipient-derived genes, further refining the locus to six genes ( and ) near the 3′ end of . White-filled gene symbols represent repetitive elements.
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FIGURE 8

Mating identity is determined by genes within The . locus spans 26 homologous genes in the donor (blue) and recipient (orange) parental strains (top). Genes and define the ends of the locus. and encode the primary secreted substrates EsxA and EsxB. Whole-genome sequencing and genome-wide association mapping of F1 transconjugants that exhibited a donor phenotype revealed that all donor-proficient transconjugants had an locus of donor origin ( Fig. 4 ). Mapping of the ating entity () locus—the donor genes associated with the donor conjugal phenotype—to was confirmed by successively backcrossing donor-proficient transconjugants with the recipient, while maintaining the donor phenotype (transconjugant donor). Backcrossed transconjugants that showed a recipient conjugal phenotype (transconjugant recipient) all shared a region of their locus that was composed of recipient-derived genes, further refining the locus to six genes ( and ) near the 3′ end of . White-filled gene symbols represent repetitive elements.

Source: microbiolspec January 2014 vol. 2 no. 1 doi:10.1128/microbiolspec.MGM2-0022-2013
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