1887

Abstract

The spread of antibiotic resistance within and between different bacterial populations is a major health problem on a global scale. The identification of genetic transformation in genomic data from Neisseria meningitidis, the meningococcus (Mc), and other bacteria is problematic, since similar or even identical alleles may be involved. A particular challenge in naturally transformable bacteria generally is to distinguish between common ancestry and true recombined sites in sampled genome sequences. Furthermore, the identification of recombination following experimental transformation of homologous alleles requires identifiable differences between donor and recipient, which in itself influences the propensity for homologous recombination (HR). This study identifies the distribution of HR events following intraspecies and interspecies Mc transformations of rpoB alleles encoding rifampicin resistance by whole-genome DNA sequencing and single nucleotide variant analysis. The HR events analysed were confined to the genomic region surrounding the single nucleotide genetic marker used for selection. An exponential length distribution of these recombined events was found, ranging from a few nucleotides to about 72 kb stretches. The lengths of imported sequences were on average found to be longer following experimental transformation of the recipient with genomic DNA from an intraspecies versus an interspecies donor (P<0.001). The recombination events were generally observed to be mosaic, with donor sequences interspersed with recipient sequence. Here, we present four models to explain these observations, by fragmentation of the transformed DNA, by interruptions of the recombination mechanism, by secondary recombination of endogenous self-DNA, or by repair/replication mechanisms.

Loading

Article metrics loading...

/content/journal/mgen/10.1099/mgen.0.000222
2018-09-25
2019-08-24
Loading full text...

Full text loading...

/deliver/fulltext/mgen/4/11/mgen000222.html?itemId=/content/journal/mgen/10.1099/mgen.0.000222&mimeType=html&fmt=ahah

References

  1. Ochman H, Lawrence JG, Groisman EA. Lateral gene transfer and the nature of bacterial innovation. Nature 2000;405:299–304 [CrossRef][PubMed]
    [Google Scholar]
  2. Alexander HE, Redman W. Transformation of type specificity of meningococci; change in heritable type induced by type-specific extracts containing desoxyribonucleic acid. J Exp Med 1953;97:797–806 [CrossRef][PubMed]
    [Google Scholar]
  3. Davidsen T, Tønjum T. Meningococcal genome dynamics. Nat Rev Microbiol 2006;4:11–22 [CrossRef][PubMed]
    [Google Scholar]
  4. Sparling PF. Genetic transformation of Neisseria gonorrhoeae to streptomycin resistance. J Bacteriol 1966;92:1364–1371[PubMed]
    [Google Scholar]
  5. Seitz P, Blokesch M. Cues and regulatory pathways involved in natural competence and transformation in pathogenic and environmental Gram-negative bacteria. FEMS Microbiol Rev 2013;37:336–363 [CrossRef][PubMed]
    [Google Scholar]
  6. Ambur OH. Inter- and intraspecies transformation in the Neisseria: mechanism, evolution and DNA uptake sequence specificity. In Davies JK, Kahler CM. (editors) Pathogenic Neisseria: Genomics, Molecular Biology and Disease Intervention Poole: Caister Academic Press; 2014; pp.59–76
    [Google Scholar]
  7. Catlin BW. Transformation of Neisseria meningitidis by deoxyribonucleates from cells and from culture slime. J Bacteriol 1960;79:579–590[PubMed]
    [Google Scholar]
  8. Jyssum K, Lie S. Genetic factors determining competence in transformation of Neisseria meningitidis. 1. A permanent loss of competence. Acta Pathol Microbiol Scand 1965;63:306–316[PubMed]
    [Google Scholar]
  9. Ambur OH, Engelstädter J, Johnsen PJ, Miller EL, Rozen DE. Steady at the wheel: conservative sex and the benefits of bacterial transformation. Philos Trans R Soc Lond B Biol Sci 2016;371:20150528 [CrossRef][PubMed]
    [Google Scholar]
  10. Johnsborg O, Eldholm V, Håvarstein LS. Natural genetic transformation: prevalence, mechanisms and function. Res Microbiol 2007;158:767–778 [CrossRef][PubMed]
    [Google Scholar]
  11. Lorenz MG, Wackernagel W. Bacterial gene transfer by natural genetic transformation in the environment. Microbiol Rev 1994;58:563–602[PubMed]
    [Google Scholar]
  12. Bennett JS, Bentley SD, Vernikos GS, Quail MA, Cherevach I et al. Independent evolution of the core and accessory gene sets in the genus Neisseria: insights gained from the genome of Neisseria lactamica isolate 020-06. BMC Genomics 2010;11:652 [CrossRef][PubMed]
    [Google Scholar]
  13. Ambur OH, Frye SA, Tønjum T. New functional identity for the DNA uptake sequence in transformation and its presence in transcriptional terminators. J Bacteriol 2007;189:2077–2085 [CrossRef][PubMed]
    [Google Scholar]
  14. Goodman SD, Scocca JJ. Identification and arrangement of the DNA sequence recognized in specific transformation of Neisseria gonorrhoeae. Proc Natl Acad Sci USA 1988;85:6982–6986 [CrossRef][PubMed]
    [Google Scholar]
  15. Frye SA, Nilsen M, Tønjum T, Ambur OH. Dialects of the DNA uptake sequence in Neisseriaceae. PLoS Genet 2013;9:e1003458 [CrossRef][PubMed]
    [Google Scholar]
  16. Budroni S, Siena E, Dunning Hotopp JC, Seib KL, Serruto D et al. Neisseria meningitidis is structured in clades associated with restriction modification systems that modulate homologous recombination. Proc Natl Acad Sci USA 2011;108:4494–4499 [CrossRef][PubMed]
    [Google Scholar]
  17. Thomas CM, Nielsen KM. Mechanisms of, and barriers to, horizontal gene transfer between bacteria. Nat Rev Microbiol 2005;3:711–721 [CrossRef][PubMed]
    [Google Scholar]
  18. Arber W. Genetic variation: molecular mechanisms and impact on microbial evolution. FEMS Microbiol Rev 2000;24:1–7 [CrossRef][PubMed]
    [Google Scholar]
  19. Vasu K, Nagaraja V. Diverse functions of restriction-modification systems in addition to cellular defense. Microbiol Mol Biol Rev 2013;77:53–72 [CrossRef][PubMed]
    [Google Scholar]
  20. Ambur OH, Frye SA, Nilsen M, Hovland E, Tønjum T. Restriction and sequence alterations affect DNA uptake sequence-dependent transformation in Neisseria meningitidis. PLoS One 2012;7:e39742 [CrossRef][PubMed]
    [Google Scholar]
  21. Johnston C, Martin B, Polard P, Claverys JP. Postreplication targeting of transformants by bacterial immune systems?. Trends Microbiol 2013;21:516–521 [CrossRef][PubMed]
    [Google Scholar]
  22. Hovland E, Beyene GT, Frye SA, Homberset H, Balasingham SV et al. DprA from Neisseria meningitidis: properties and role in natural competence for transformation. Microbiology 2017;163:1016–1029 [CrossRef][PubMed]
    [Google Scholar]
  23. Koomey JM, Falkow S. Cloning of the recA gene of Neisseria gonorrhoeae and construction of gonococcal recA mutants. J Bacteriol 1987;169:790–795 [CrossRef][PubMed]
    [Google Scholar]
  24. Mehr IJ, Seifert HS. Differential roles of homologous recombination pathways in Neisseria gonorrhoeae pilin antigenic variation, DNA transformation and DNA repair. Mol Microbiol 1998;30:697–710 [CrossRef][PubMed]
    [Google Scholar]
  25. Rocha EP, Cornet E, Michel B. Comparative and evolutionary analysis of the bacterial homologous recombination systems. PLoS Genet 2005;1:e15 [CrossRef][PubMed]
    [Google Scholar]
  26. Stohl EA, Gruenig MC, Cox MM, Seifert HS. Purification and characterization of the RecA protein from Neisseria gonorrhoeae. PLoS One 2011;6:e17101 [CrossRef][PubMed]
    [Google Scholar]
  27. Didelot X, Lawson D, Darling A, Falush D. Inference of homologous recombination in bacteria using whole-genome sequences. Genetics 2010;186:1435–1449 [CrossRef][PubMed]
    [Google Scholar]
  28. Smith JM, Smith NH, O'Rourke M, Spratt BG. How clonal are bacteria?. Proc Natl Acad Sci USA 1993;90:4384–4388 [CrossRef][PubMed]
    [Google Scholar]
  29. Falush D, Torpdahl M, Didelot X, Conrad DF, Wilson DJ et al. Mismatch induced speciation in Salmonella: model and data. Philos Trans R Soc Lond B Biol Sci 2006;361:2045–2053 [CrossRef][PubMed]
    [Google Scholar]
  30. Fraser C, Hanage WP, Spratt BG. Recombination and the nature of bacterial speciation. Science 2007;315:476–480 [CrossRef][PubMed]
    [Google Scholar]
  31. Hanage WP, Spratt BG, Turner KM, Fraser C. Modelling bacterial speciation. Philos Trans R Soc Lond B Biol Sci 2006;361:2039–2044 [CrossRef][PubMed]
    [Google Scholar]
  32. Roberts MS, Cohan FM. The effect of DNA sequence divergence on sexual isolation in Bacillus. Genetics 1993;134:401–408[PubMed]
    [Google Scholar]
  33. Croucher NJ, Harris SR, Barquist L, Parkhill J, Bentley SD. A high-resolution view of genome-wide pneumococcal transformation. PLoS Pathog 2012;8:e1002745 [CrossRef][PubMed]
    [Google Scholar]
  34. Cowley LA, Petersen FC, Junges R, Jimson D Jimenez M, Morrison DA et al. Evolution via recombination: cell-to-cell contact facilitates larger recombination events in Streptococcus pneumoniae. PLoS Genet 2018;14:e1007410 [CrossRef][PubMed]
    [Google Scholar]
  35. Mell JC, Lee JY, Firme M, Sinha S, Redfield RJ. Extensive cotransformation of natural variation into chromosomes of naturally competent Haemophilus influenzae. G3 2014;4:717–731 [CrossRef][PubMed]
    [Google Scholar]
  36. Dillard JP. Genetic Manipulation of Neisseria gonorrhoeae. Curr Protoc Microbiol 2011;Chapter 4:Unit4A.2 [CrossRef][PubMed]
    [Google Scholar]
  37. Wilson K. Preparation of genomic DNA from bacteria. Curr Protoc Mol Biol 2001;56:2.4.1–2.4.2 [CrossRef][PubMed]
    [Google Scholar]
  38. Carter PE, Abadi FJ, Yakubu DE, Pennington TH. Molecular characterization of rifampin-resistant Neisseria meningitidis. Antimicrob Agents Chemother 1994;38:1256–1261 [CrossRef][PubMed]
    [Google Scholar]
  39. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 2012;19:455–477 [CrossRef][PubMed]
    [Google Scholar]
  40. Galardini M, Biondi EG, Bazzicalupo M, Mengoni A. CONTIGuator: a bacterial genomes finishing tool for structural insights on draft genomes. Source Code Biol Med 2011;6:11 [CrossRef][PubMed]
    [Google Scholar]
  41. Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods 2012;9:357–359 [CrossRef][PubMed]
    [Google Scholar]
  42. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 2009;25:2078–2079 [CrossRef][PubMed]
    [Google Scholar]
  43. Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 2014;30:2114–2120 [CrossRef][PubMed]
    [Google Scholar]
  44. Koboldt DC, Zhang Q, Larson DE, Shen D, McLellan MD et al. VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing. Genome Res 2012;22:568–576 [CrossRef][PubMed]
    [Google Scholar]
  45. Wickham H. ggplot2: Elegant Graphics for Data Analysis Basel: Springer; 2016
    [Google Scholar]
  46. Venables WN, Ripley BD. Modern Applied Statistics with S-PLUS New York: Springer Science & Business Media; 2013
    [Google Scholar]
  47. Darling AC, Mau B, Blattner FR, Perna NT. Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res 2004;14:1394–1403 [CrossRef][PubMed]
    [Google Scholar]
  48. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014;30:2068–2069 [CrossRef][PubMed]
    [Google Scholar]
  49. Zhang Z, Schwartz S, Wagner L, Miller W. A greedy algorithm for aligning DNA sequences. J Comput Biol 2000;7:203–214 [CrossRef][PubMed]
    [Google Scholar]
  50. Guy L, Kultima JR, Andersson SG. genoPlotR: comparative gene and genome visualization in R. Bioinformatics 2010;26:2334–2335 [CrossRef][PubMed]
    [Google Scholar]
  51. Rice P, Longden I, Bleasby A. EMBOSS: the European molecular biology open software suite. Trends Genet 2000;16:276–277 [CrossRef][PubMed]
    [Google Scholar]
  52. Tobiason DM, Seifert HS. The obligate human pathogen, Neisseria gonorrhoeae, is polyploid. PLoS Biol 2006;4:e185 [CrossRef][PubMed]
    [Google Scholar]
  53. Tobiason DM, Seifert HS. Genomic content of Neisseria species. J Bacteriol 2010;192:2160–2168 [CrossRef][PubMed]
    [Google Scholar]
  54. Stuy JH, Walter RB. Addition, deletion, and substitution of long nonhomologous deoxyribonucleic acid segments by genetic transformation of Haemophilus influenzae. J Bacteriol 1981;148:565–571[PubMed]
    [Google Scholar]
  55. Mell JC, Shumilina S, Hall IM, Redfield RJ. Transformation of natural genetic variation into Haemophilus influenzae genomes. PLoS Pathog 2011;7:e1002151 [CrossRef][PubMed]
    [Google Scholar]
  56. Richardson AR, Yu Z, Popovic T, Stojiljkovic I. Mutator clones of Neisseria meningitidis in epidemic serogroup A disease. Proc Natl Acad Sci USA 2002;99:6103–6107 [CrossRef][PubMed]
    [Google Scholar]
  57. Treangen TJ, Ambur OH, Tonjum T, Rocha EP. The impact of the neisserial DNA uptake sequences on genome evolution and stability. Genome Biol 2008;9:R60 [CrossRef][PubMed]
    [Google Scholar]
  58. Roberts RJ, Vincze T, Posfai J, Macelis D. REBASE – a database for DNA restriction and modification: enzymes, genes and genomes. Nucleic Acids Res 2015;43:D298–D299 [CrossRef][PubMed]
    [Google Scholar]
  59. Graves JF, Biswas GD, Sparling PF. Sequence-specific DNA uptake in transformation of Neisseria gonorrhoeae. J Bacteriol 1982;152:1071–1077[PubMed]
    [Google Scholar]
  60. Hoke C, Vedros NA. Taxonomy of the neisseriae: deoxyribonucleic acid base composition, interspecific transformation, and deoxyribonucleic acid hybridization. Int J Syst Bacteriol 1982;32:57–66 [CrossRef]
    [Google Scholar]
  61. Zhang Y, Heidrich N, Ampattu BJ, Gunderson CW, Seifert HS et al. Processing-independent CRISPR RNAs limit natural transformation in Neisseria meningitidis. Mol Cell 2013;50:488–503 [CrossRef][PubMed]
    [Google Scholar]
  62. Harms K, Lunnan A, Hülter N, Mourier T, Vinner L et al. Substitutions of short heterologous DNA segments of intragenomic or extragenomic origins produce clustered genomic polymorphisms. Proc Natl Acad Sci USA 2016;113:15066–15071 [CrossRef][PubMed]
    [Google Scholar]
  63. Linz B, Schenker M, Zhu P, Achtman M. Frequent interspecific genetic exchange between commensal neisseriae and Neisseria meningitidis. Mol Microbiol 2000;36:1049–1058 [CrossRef][PubMed]
    [Google Scholar]
  64. Lin EA, Zhang XS, Levine SM, Gill SR, Falush D et al. Natural transformation of Helicobacter pylori involves the integration of short DNA fragments interrupted by gaps of variable size. PLoS Pathog 2009;5:e1000337 [CrossRef][PubMed]
    [Google Scholar]
  65. Dixit PD, Pang TY, Studier FW, Maslov S. Recombinant transfer in the basic genome of Escherichia coli. Proc Natl Acad Sci USA 2015;112:9070–9075 [CrossRef][PubMed]
    [Google Scholar]
  66. Maddamsetti R, Lenski RE. Analysis of bacterial genomes from an evolution experiment with horizontal gene transfer shows that recombination can sometimes overwhelm selection. PLoS Genet 2018;14:e1007199 [CrossRef][PubMed]
    [Google Scholar]
  67. Arnold BJ, Gutmann MU, Grad YH, Sheppard SK, Corander J et al. Weak epistasis may drive adaptation in recombining bacteria. Genetics 2018;208:1247–1260 [CrossRef][PubMed]
    [Google Scholar]
  68. Ray JL, Harms K, Wikmark OG, Starikova I, Johnsen PJ et al. Sexual isolation in Acinetobacter baylyi is locus-specific and varies 10,000-fold over the genome. Genetics 2009;182:1165–1181 [CrossRef][PubMed]
    [Google Scholar]
  69. Chen I, Dubnau D. DNA transport during transformation. Front Biosci 2003;8:s544–s556[PubMed]
    [Google Scholar]
  70. Facius D, Meyer TF. A novel determinant (comA) essential for natural transformation competence in Neisseria gonorrhoeae and the effect of a comA defect on pilin variation. Mol Microbiol 1993;10:699–712 [CrossRef][PubMed]
    [Google Scholar]
  71. Frye SA, Lång E, Beyene GT, Balasingham SV, Homberset H et al. The inner membrane protein PilG interacts with DNA and the secretin PilQ in transformation. PLoS One 2015;10:e0134954 [CrossRef][PubMed]
    [Google Scholar]
  72. Roberts RJ, Belfort M, Bestor T, Bhagwat AS, Bickle TA et al. A nomenclature for restriction enzymes, DNA methyltransferases, homing endonucleases and their genes. Nucleic Acids Res 2003;31:1805–1812 [CrossRef][PubMed]
    [Google Scholar]
  73. Swanson J, Morrison S, Barrera O, Hill S. Piliation changes in transformation-defective gonococci. J Exp Med 1990;171:2131–2139 [CrossRef][PubMed]
    [Google Scholar]
  74. Zhang QY, Deryckere D, Lauer P, Koomey M. Gene conversion in Neisseria gonorrhoeae: evidence for its role in pilus antigenic variation. Proc Natl Acad Sci USA 1992;89:5366–5370 [CrossRef][PubMed]
    [Google Scholar]
  75. Paulsson J, El Karoui M, Lindell M, Hughes D. The processive kinetics of gene conversion in bacteria. Mol Microbiol 2017;104:752–760 [CrossRef][PubMed]
    [Google Scholar]
  76. Arwidsson O, Hughes D. Evidence against reciprocal recombination as the basis for tuf gene conversion in Salmonella enterica serovar Typhimurium. J Mol Biol 2004;338:463–467 [CrossRef][PubMed]
    [Google Scholar]
  77. Alexander HL, Richardson AR, Stojiljkovic I. Natural transformation and phase variation modulation in Neisseria meningitidis. Mol Microbiol 2004;52:771–783 [CrossRef][PubMed]
    [Google Scholar]
  78. Humbert O, Prudhomme M, Hakenbeck R, Dowson CG, Claverys JP. Homeologous recombination and mismatch repair during transformation in Streptococcus pneumoniae: saturation of the Hex mismatch repair system. Proc Natl Acad Sci USA 1995;92:9052–9056 [CrossRef][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/mgen/10.1099/mgen.0.000222
Loading
/content/journal/mgen/10.1099/mgen.0.000222
Loading

Data & Media loading...

Supplementary File 1

PDF

Most Cited This Month

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error