Transformation of Natural Genetic Variation into Genomes
Many bacteria are able to efficiently bind and take up double-stranded DNA fragments, and the resulting natural transformation shapes bacterial genomes, transmits antibiotic resistance, and allows escape from immune surveillance. The genomes of many competent pathogens show evidence of extensive historical recombination between lineages, but the actual recombination events have not been well characterized. We used DNA from a clinical isolate of Haemophilus influenzae to transform competent cells of a laboratory strain. To identify which of the ∼40,000 polymorphic differences had recombined into the genomes of four transformed clones, their genomes and their donor and recipient parents were deep sequenced to high coverage. Each clone was found to contain ∼1000 donor polymorphisms in 3–6 contiguous runs (8.1±4.5 kb in length) that collectively comprised ∼1–3% of each transformed chromosome. Seven donor-specific insertions and deletions were also acquired as parts of larger donor segments, but the presence of other structural variation flanking 12 of 32 recombination breakpoints suggested that these often disrupt the progress of recombination events. This is the first genome-wide analysis of chromosomes directly transformed with DNA from a divergent genotype, connecting experimental studies of transformation with the high levels of natural genetic variation found in isolates of the same species.
Vyšlo v časopise:
Transformation of Natural Genetic Variation into Genomes. PLoS Pathog 7(7): e32767. doi:10.1371/journal.ppat.1002151
Kategorie:
Research Article
prolekare.web.journal.doi_sk:
https://doi.org/10.1371/journal.ppat.1002151
Souhrn
Many bacteria are able to efficiently bind and take up double-stranded DNA fragments, and the resulting natural transformation shapes bacterial genomes, transmits antibiotic resistance, and allows escape from immune surveillance. The genomes of many competent pathogens show evidence of extensive historical recombination between lineages, but the actual recombination events have not been well characterized. We used DNA from a clinical isolate of Haemophilus influenzae to transform competent cells of a laboratory strain. To identify which of the ∼40,000 polymorphic differences had recombined into the genomes of four transformed clones, their genomes and their donor and recipient parents were deep sequenced to high coverage. Each clone was found to contain ∼1000 donor polymorphisms in 3–6 contiguous runs (8.1±4.5 kb in length) that collectively comprised ∼1–3% of each transformed chromosome. Seven donor-specific insertions and deletions were also acquired as parts of larger donor segments, but the presence of other structural variation flanking 12 of 32 recombination breakpoints suggested that these often disrupt the progress of recombination events. This is the first genome-wide analysis of chromosomes directly transformed with DNA from a divergent genotype, connecting experimental studies of transformation with the high levels of natural genetic variation found in isolates of the same species.
Zdroje
1. MaughanHSinhaSWilsonLRedfieldRJ 2008 Competence, DNA uptake and transformation in the Pasteurellaceae. KuhnertPChristensenH Pasteurellaceae: Biology, Genomics and Molecular Aspects Norfolk, UK Caister Academic Press
2. ChenIChristiePJDubnauD 2005 The ins and outs of DNA transfer in bacteria. Science 310 1456 1460
3. ClaverysJPMartinB 2003 Bacterial “competence” genes: signatures of active transformation, or only remnants? Trends Microbiol 11 161 165
4. CroucherNJHarrisSRFraserCQuailMABurtonJ 2011 Rapid pneumococcal evolution in response to clinical interventions. Science 331 430 434
5. HanageWPFraserCTangJConnorTRCoranderJ 2009 Hyper-recombination, diversity, and antibiotic resistance in pneumococcus. Science 324 1454 1457
6. Garcia-CobosSCamposJLazaroERomanFCercenadoE 2007 Ampicillin-resistant non-beta-lactamase-producing Haemophilus influenzae in Spain: recent emergence of clonal isolates with increased resistance to cefotaxime and cefixime. Antimicrob Agents Chemother 51 2564 2573
7. CodyAJFieldDFeilEJStringerSDeadmanME 2003 High rates of recombination in otitis media isolates of non-typeable Haemophilus influenzae. Infect Genet Evol 3 57 66
8. MaidenMC 1998 Horizontal genetic exchange, evolution, and spread of antibiotic resistance in bacteria. Clin Infect Dis 27 Suppl 1 S12 20
9. SeifertHSAjiokaRSMarchalCSparlingPFSoM 1988 DNA transformation leads to pilin antigenic variation in Neisseria gonorrhoeae. Nature 336 392 395
10. KrollJSHopkinsIMoxonER 1988 Capsule loss in H. influenzae type b occurs by recombination-mediated disruption of a gene essential for polysaccharide export. Cell 53 347 356
11. Perez-LosadaMBrowneEBMadsenAWirthTViscidiRP 2006 Population genetics of microbial pathogens estimated from multilocus sequence typing (MLST) data. Infect Genet Evol 6 97 112
12. FeilEJHolmesECBessenDEChanMSDayNP 2001 Recombination within natural populations of pathogenic bacteria: short-term empirical estimates and long-term phylogenetic consequences. Proc Natl Acad Sci U S A 98 182 187
13. FeilEJSprattBG 2001 Recombination and the population structures of bacterial pathogens. Annu Rev Microbiol 55 561 590
14. DidelotXLawsonDDarlingAFalushD 2010 Inference of homologous recombination in bacteria using whole-genome sequences. Genetics 186 1435 1449
15. DidelotXMaidenMC 2010 Impact of recombination on bacterial evolution. Trends Microbiol 18 315 322
16. CoxMM 1993 Relating biochemistry to biology: how the recombinational repair function of RecA protein is manifested in its molecular properties. Bioessays 15 617 623
17. BergeMMortier-BarriereIMartinBClaverysJP 2003 Transformation of Streptococcus pneumoniae relies on DprA- and RecA-dependent protection of incoming DNA single strands. Mol Microbiol 50 527 536
18. GoodgalSHHerriottRM 1961 Studies on transformations of Hemophilus influenzae. I. Competence. J Gen Physiol 44 1201 1227
19. VulicMDionisioFTaddeiFRadmanM 1997 Molecular keys to speciation: DNA polymorphism and the control of genetic exchange in enterobacteria. Proc Natl Acad Sci U S A 94 9763 9767
20. ZawadzkiPRobertsMSCohanFM 1995 The log-linear relationship between sexual isolation and sequence divergence in Bacillus transformation is robust. Genetics 140 917 932
21. BianchiMERaddingCM 1983 Insertions, deletions and mismatches in heteroduplex DNA made by recA protein. Cell 35 511 520
22. StuyJHWalterRB 1981 Addition, deletion, and substitution of long nonhomologous deoxyribonucleic acid segments by genetic transformation of Haemophilus influenzae. J Bacteriol 148 565 571
23. BuckaAStasiakA 2001 RecA-mediated strand exchange traverses substitutional heterologies more easily than deletions or insertions. Nucleic Acids Res 29 2464 2470
24. StambukSRadmanM 1998 Mechanism and control of interspecies recombination in Escherichia coli. I. Mismatch repair, methylation, recombination and replication functions. Genetics 150 533 542
25. HumbertOPrudhommeMHakenbeckRDowsonCGClaverysJP 1995 Homeologous recombination and mismatch repair during transformation in Streptococcus pneumoniae: saturation of the Hex mismatch repair system. Proc Natl Acad Sci U S A 92 9052 9056
26. MajewskiJZawadzkiPPickerillPCohanFMDowsonCG 2000 Barriers to genetic exchange between bacterial species: Streptococcus pneumoniae transformation. J Bacteriol 182 1016 1023
27. KislyukAOHaegemanBBergmanNHWeitzJS 2011 Genomic fluidity: an integrative view of gene diversity within microbial populations. BMC Genomics 12 32
28. TreangenTJAmburOHTonjumTRochaEP 2008 The impact of the neisserial DNA uptake sequences on genome evolution and stability. Genome Biol 9 R60
29. HillerNLJantoBHoggJSBoissyRYuS 2007 Comparative genomic analyses of seventeen Streptococcus pneumoniae strains: insights into the pneumococcal supragenome. J Bacteriol 189 8186 8195
30. HoggJSHuFZJantoBBoissyRHayesJ 2007 Characterization and modeling of the Haemophilus influenzae core and supragenomes based on the complete genomic sequences of Rd and 12 clinical nontypeable strains. Genome Biol 8 R103
31. MediniDDonatiCTettelinHMasignaniVRappuoliR 2005 The microbial pan-genome. Curr Opin Genet Dev 15 589 594
32. RayJLHarmsKWikmarkOGStarikovaIJohnsenPJ 2009 Sexual isolation in Acinetobacter baylyi is locus-specific and varies 10,000-fold over the genome. Genetics 182 1165 1181
33. LinEAZhangXSLevineSMGillSRFalushD 2009 Natural transformation of Helicobacter pylori involves the integration of short DNA fragments interrupted by gaps of variable size. PLoS Pathog 5 e1000337
34. KulickSMocciaCDidelotXFalushDKraftC 2008 Mosaic DNA imports with interspersions of recipient sequence after natural transformation of Helicobacter pylori. PLoS ONE 3 e3797
35. PojeGRedfieldRJ 2003 Transformation of Haemophilus influenzae. Methods Mol Med 71 57 70
36. MaughanHRedfieldRJ 2009 Tracing the evolution of competence in Haemophilus influenzae. PLoS One 4 e5854
37. BentleyDRBalasubramanianSSwerdlowHPSmithGPMiltonJ 2008 Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456 53 59
38. FleischmannRDAdamsMDWhiteOClaytonRAKirknessEF 1995 Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269 496 512
39. HarrisonADyerDWGillaspyARayWCMungurR 2005 Genomic sequence of an otitis media isolate of nontypeable Haemophilus influenzae: comparative study with H. influenzae serotype d, strain KW20. J Bacteriol 187 4627 4636
40. LiHDurbinR 2010 Fast and accurate long read alignment with Burrows-Wheeler transform. Bioinformatics 26 589 95
41. LiHHandsakerBWysokerAFennellTRuanJ 2009 The Sequence Alignment/Map format and SAMtools. Bioinformatics 25 2078 2079
42. DarlingACMauBBlattnerFRPernaNT 2004 Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res 14 1394 1403
43. ShakSCaponDJHellmissRMarstersSABakerCL 1990 Recombinant human DNase I reduces the viscosity of cystic fibrosis sputum. Proc Natl Acad Sci U S A 87 9188 9192
44. LacrossNCMarrsCFPatelMSandstedtSAGilsdorfJR 2008 High genetic diversity of nontypeable Haemophilus influenzae isolates from two children attending a day care center. J Clin Microbiol 46 3817 3821
45. FarjoRSFoxmanBPatelMJZhangLPettigrewMM 2004 Diversity and sharing of Haemophilus influenzae strains colonizing healthy children attending day-care centers. Pediatr Infect Dis J 23 41 46
46. RedfieldRJFindlayWABosseJKrollJSCameronAD 2006 Evolution of competence and DNA uptake specificity in the Pasteurellaceae. BMC Evol Biol 6 82
47. BaroukiRSmithHO 1986 Initial steps in Haemophilus influenzae transformation. Donor DNA binding in the com10 mutant. J Biol Chem 261 8617 8623
48. LinzBSchenkerMZhuPAchtmanM 2000 Frequent interspecific genetic exchange between commensal Neisseriae and Neisseria meningitidis. Mol Microbiol 36 1049 1058
49. HumbertODorerMSSalamaNR 2011 Characterization of Helicobacter pylori factors that control transformation frequency and integration length during inter-strain DNA recombination. Mol Microbiol 79 387 401
50. PiferMLSmithHO 1985 Processing of donor DNA during Haemophilus influenzae transformation: analysis using a model plasmid system. Proc Natl Acad Sci U S A 82 3731 3735
51. StinglKMullerSScheidgen-KleyboldtGClausenMMaierB 2010 Composite system mediates two-step DNA uptake into Helicobacter pylori. Proc Natl Acad Sci U S A 107 1184 1189
52. McKaneMMilkmanR 1995 Transduction, restriction and recombination patterns in Escherichia coli. Genetics 139 35 43
53. SiscoKLSmithHO 1979 Sequence-specific DNA uptake in Haemophilus transformation. Proc Natl Acad Sci U S A 76 972 976
54. SmithHOTombJFDoughertyBAFleischmannRDVenterJC 1995 Frequency and distribution of DNA uptake signal sequences in the Haemophilus influenzae Rd genome. Science 269 538 540
55. CahoonLASeifertHS 2009 An alternative DNA structure is necessary for pilin antigenic variation in Neisseria gonorrhoeae. Science 325 764 767
56. MaughanHRedfieldRJ 2009 Extensive Variation in Natural Competence in Haemophilus Influenzae. Evolution 63 1852 66
57. NakamuraSShchepetovMDaliaABClarkSEMurphyTF 2011 Molecular basis of increased serum resistance among pulmonary isolates of non-typeable Haemophilus influenzae. PLoS Pathog 7 e1001247
58. WilliamsBJMorlinGValentineNSmithAL 2001 Serum resistance in an invasive, nontypeable Haemophilus influenzae strain. Infect Immun 69 695 705
59. PojeGRedfieldRJ 2003 General methods for culturing Haemophilus influenzae. Methods Mol Med 71 51 56
60. TaylorJSchenckIBlankenbergDNekrutenkoA 2007 Using galaxy to perform large-scale interactive data analyses. Curr Protoc Bioinformatics Chapter 10: Unit 10 15
61. R_Development_Core_Team 2009 R: A language and environment for statistical computing. Vienna, Austria R Foundation for Statistical Computing
62. GuyLKultimaJRAnderssonSG 2010 genoPlotR: comparative gene and genome visualization in R. Bioinformatics 26 2334 2335
63. The IGV Team at the Broad Institute 2010 Interactive Genomics Viewer. Broad Institute. Available: http://www.broadinstitute.org/igv
64. KurtzSPhillippyADelcherALSmootMShumwayM 2004 Versatile and open software for comparing large genomes. Genome Biol 5 R12
65. OhtsuboYIkeda-OhtsuboWNagataYTsudaM 2008 GenomeMatcher: a graphical user interface for DNA sequence comparison. BMC Bioinformatics 9 376
Štítky
Hygiena a epidemiológia Infekčné lekárstvo LaboratóriumČlánok vyšiel v časopise
PLOS Pathogens
2011 Číslo 7
- Parazitičtí červi v terapii Crohnovy choroby a dalších zánětlivých autoimunitních onemocnění
- Očkování proti virové hemoragické horečce Ebola experimentální vakcínou rVSVDG-ZEBOV-GP
- Koronavirus hýbe světem: Víte jak se chránit a jak postupovat v případě podezření?
Najčítanejšie v tomto čísle
- Requires Glycerol for Maximum Fitness During The Tick Phase of the Enzootic Cycle
- Comparative Genomics Yields Insights into Niche Adaptation of Plant Vascular Wilt Pathogens
- “Persisters”: Survival at the Cellular Level
- The Role of IL-15 Deficiency in the Pathogenesis of Virus-Induced Asthma Exacerbations