1887

Abstract

Integrative and conjugative elements (ICEs) are mobile genetic elements encoding their own excision from a replicon of their bacterial host, transfer by conjugation to a recipient bacterium and reintegration for maintenance. The conjugation, recombination and regulation modules of ICEs of the ICE family are grouped together in a region called the ICE ‘core region’. In addition to this core region, elements belonging to this family carry a highly variable region including cargo genes that could be involved in bacterial adaptation or in the maintenance of the element. Although ICEs are a major class of mobile elements through bacterial genomes, the functionality of an element encoding only its excision, transfer, integration and regulation has never been demonstrated experimentally. We engineered MiniICE, an artificial ICE derived from ICE, devoid of its cargo genes and thus only harbouring the core region. The functionality of this minimal element was assessed. MiniICE was found to be able to excise at a rate of 3.1 %, transfer with a frequency of 1.0 × 10 transconjugants per donor cell and stably maintain by site-specific integration into the 3′ end of the gene, the same as ICE. Furthermore, MiniICE was found in ∼10 copies per chromosome, this multicopy state likely contributing to its stability for >100 generations even in the absence of selection. Therefore, although ICEs were primarily assumed to only replicate along with the chromosome, our results uncovered extrachromosomal rolling-circle replicating plasmid-like forms of MiniICE.

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2016-04-01
2021-07-28
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References

  1. Bahl M. I., Hansen L. H., Licht T. R., Sørensen S. J. 2007a; Conjugative transfer facilitates stable maintenance of IncP-1 plasmid pKJK5 in in vitro cells colonizing the gastrointestinal tract of the germfree rat. Appl Environ Microbiol 73:341–343 [View Article][PubMed]
    [Google Scholar]
  2. Bahl M. I., Hansen L. H., Sørensen S. J. 2007b; Impact of conjugal transfer on the stability of IncP-1 plasmid pKJK5 in bacterial populations. FEMS Microbiol Lett 266:250–256 [View Article][PubMed]
    [Google Scholar]
  3. Beaber J. W., Hochhut B., Waldor M. K. 2004; SOS response promotes horizontal dissemination of antibiotic resistance genes. Nature 427:72–74 [View Article][PubMed]
    [Google Scholar]
  4. Bellanger X., Roberts A. P., Morel C., Choulet F., Pavlovic G., Mullany P., Decaris B., Guédon G. 2009; Conjugative transfer of the integrative conjugative elements ICESt1 and ICESt3 from Streptococcus thermophilus . J Bacteriol 191:2764–2775 [View Article][PubMed]
    [Google Scholar]
  5. Bellanger X., Morel C., Gonot F., Puymege A., Decaris B., Guédon G. 2011; Site-specific accretion of an integrative conjugative element together with a related genomic island leads to cis mobilization and gene capture. Mol Microbiol 81:912–925 [View Article][PubMed]
    [Google Scholar]
  6. Bellanger X., Payot S., Leblond-Bourget N., Guédon G. 2014; Conjugative and mobilizable genomic islands in bacteria: evolution and diversity. FEMS Microbiol Rev 38:720–760 [View Article][PubMed]
    [Google Scholar]
  7. Bose B., Grossman A. D. 2011; Regulation of horizontal gene transfer in Bacillus subtilis by activation of a conserved site-specific protease. J Bacteriol 193:22–29 [View Article][PubMed]
    [Google Scholar]
  8. Brenciani A., Tiberi E., Tili E., Mingoia M., Palmieri C., Varaldo P. E., Giovanetti E. 2014; Genetic determinants and elements associated with antibiotic resistance in viridans group streptococci. J Antimicrob Chemother 69:1197–1204 [View Article][PubMed]
    [Google Scholar]
  9. Brochet M., Rusniok C., Couvé E., Dramsi S., Poyart C., Trieu-Cuot P., Kunst F., Glaser P. 2008; Shaping a bacterial genome by large chromosomal replacements, the evolutionary history of Streptococcus agalactiae . Proc Natl Acad Sci U S A 105:15961–15966 [View Article][PubMed]
    [Google Scholar]
  10. Brown-Jaque M., Calero-Cáceres W., Muniesa M. 2015; Transfer of antibiotic-resistance genes via phage-related mobile elements. Plasmid 79:1–7 [View Article][PubMed]
    [Google Scholar]
  11. Burrus V., Waldor M. K. 2004; Shaping bacterial genomes with integrative and conjugative elements. Res Microbiol 155:376–386 [View Article][PubMed]
    [Google Scholar]
  12. Burrus V., Bontemps C., Decaris B., Guédon G. 2001; Characterization of a novel type II restriction-modification system, Sth368I, encoded by the integrative element ICESt1 of Streptococcus thermophilus CNRZ368. Appl Environ Microbiol 67:1522–1528 [View Article][PubMed]
    [Google Scholar]
  13. Burrus V., Pavlovic G., Decaris B., Guédon G. 2002a; Conjugative transposons: the tip of the iceberg. Mol Microbiol 46:601–610 [View Article][PubMed]
    [Google Scholar]
  14. Burrus V., Pavlovic G., Decaris B., Guédon G. 2002b; The ICESt1 element of Streptococcus thermophilus belongs to a large family of integrative and conjugative elements that exchange modules and change their specificity of integration. Plasmid 48:77–97 [View Article][PubMed]
    [Google Scholar]
  15. Cabezón E., Ripoll-Rozada J., Peña A., de la Cruz F., Arechaga I. 2015; Towards an integrated model of bacterial conjugation. FEMS Microbiol Rev 39:81–95
    [Google Scholar]
  16. Carraro N., Burrus V. 2014; Biology of three ICE families: SXT/R391, ICEBs1, and ICESt1/ICESt3. Microbiol Spectr 2:MDNA3–0008-2014
    [Google Scholar]
  17. Carraro N., Burrus V. 2015; The dualistic nature of integrative and conjugative elements. Mob Genet Elements 5:98–102 [View Article]
    [Google Scholar]
  18. Carraro N., Libante V., Morel C., Decaris B., Charron-Bourgoin F., Leblond P., Guédon G. 2011; Differential regulation of two closely related integrative and conjugative elements from Streptococcus thermophilus . BMC Microbiol 11:238 [View Article][PubMed]
    [Google Scholar]
  19. Carraro N., Matteau D., Luo P., Rodrigue S., Burrus V. 2014a; The master activator of IncA/C conjugative plasmids stimulates genomic islands and multidrug resistance dissemination. PLoS Genet 10:e1004714 [View Article][PubMed]
    [Google Scholar]
  20. Carraro N., Sauvé M., Matteau D., Lauzon G., Rodrigue S., Burrus V. 2014b; Development of pVCR94ΔX from Vibrio cholerae, a prototype for studying multidrug resistant IncA/C conjugative plasmids. Front Microbiol 5:44 [View Article][PubMed]
    [Google Scholar]
  21. Carraro N., Poulin D., Burrus V. 2015; Replication and active partition of integrative and conjugative elements (ICEs) of the SXT/R391 family: the line between ICEs and conjugative plasmids is getting thinner. PLoS Genet 11:e1005298 [View Article][PubMed]
    [Google Scholar]
  22. Chaffanel F., Charron-Bourgoin F., Libante V., Leblond-Bourget N., Payot S. 2015; Resistance genes and genetic elements associated with antibiotic resistance in clinical and commensal isolates of Streptococcus salivarius . Appl Environ Microbiol 81:4155–4163 [View Article][PubMed]
    [Google Scholar]
  23. Chuzeville S., Puymège A., Madec J.-Y., Haenni M., Payot S. 2012; Characterization of a new CAMP factor carried by an integrative and conjugative element in Streptococcus agalactiae and spreading in Streptococci. PLoS One 7:e48918 [View Article][PubMed]
    [Google Scholar]
  24. Chuzeville S., Dramsi S., Madec J.-Y., Haenni M., Payot S. 2015; Antigen I/II encoded by integrative and conjugative elements of Streptococcus agalactiae and role in biofilm formation. Microb Pathog 88:1–9 [View Article][PubMed]
    [Google Scholar]
  25. Clewell D. B., Weaver K. E., Dunny G. M., Coque T. M., Francia M. V., Hayes F. 2014; Extrachromosomal and mobile elements in enterococci: transmission, maintenance, and epidemiology. In Enterococci: From Commensals to Leading Causes of Drug Resistant Infection Boston, MA: Massachusetts Eye and Ear Infirmary; http://www.ncbi.nlm.nih.gov/books/NBK190430 /
    [Google Scholar]
  26. Colmin C., Pebay M., Simonet J. M., Decaris B. 1991; A species-specific DNA probe obtained from Streptococcus salivarius subsp. thermophilus detects strain restriction polymorphism. FEMS Microbiol Lett 81:123–128 [View Article][PubMed]
    [Google Scholar]
  27. Daccord A., Ceccarelli D., Rodrigue S., Burrus V. 2013; Comparative analysis of mobilizable genomic islands. J Bacteriol 195:606–614 [View Article][PubMed]
    [Google Scholar]
  28. de la Cruz F., Frost L. S., Meyer R. J., Zechner E. L. 2010; Conjugative DNA metabolism in Gram-negative bacteria. FEMS Microbiol Rev 34:18–40 [View Article][PubMed]
    [Google Scholar]
  29. Doublet B., Boyd D., Mulvey M. R., Cloeckaert A. 2005; The Salmonella genomic island 1 is an integrative mobilizable element. Mol Microbiol 55:1911–1924 [View Article][PubMed]
    [Google Scholar]
  30. Faelen M., Resibois A., Toussaint A. 1979; Mini-mu: an insertion element derived from temperate phage mu-1. Cold Spring Harb Symp Quant Biol 43:1169–1177 [View Article][PubMed]
    [Google Scholar]
  31. Gaillard M., Pradervand N., Minoia M., Sentchilo V., Johnson D. R., van der Meer J. R. 2010; Transcriptome analysis of the mobile genome ICEclc in Pseudomonas knackmussii B13. BMC Microbiol 10:153 [View Article][PubMed]
    [Google Scholar]
  32. Gardan R., Besset C., Guillot A., Gitton C., Monnet V. 2009; The oligopeptide transport system is essential for the development of natural competence in Streptococcus thermophilus strain LMD-9. J Bacteriol 191:4647–4655 [View Article][PubMed]
    [Google Scholar]
  33. Goessweiner-Mohr N., Arends K., Keller W., Grohmann E. 2013; Conjugative type IV secretion systems in Gram-positive bacteria. Plasmid 70:289–302 [View Article][PubMed]
    [Google Scholar]
  34. Gregorova D., Matiasovicova J., Sebkova A., Faldynova M., Rychlik I. 2004; Salmonella enterica subsp. enterica serovar Enteritidis harbours ColE1, ColE2, and rolling-circle-like replicating plasmids. Can J Microbiol 50:107–112 [View Article][PubMed]
    [Google Scholar]
  35. Guglielmini J., Quintais L., Garcillán-Barcia M. P., de la Cruz F., Rocha E.P.C. 2011; The repertoire of ICE in prokaryotes underscores the unity, diversity, and ubiquity of conjugation. PLoS Genet 7:e1002222 [View Article][PubMed]
    [Google Scholar]
  36. Guglielmini J., Néron B., Abby S. S., Garcillán-Barcia M. P., de la Cruz F., Rocha E.P.C. 2014; Key components of the eight classes of type IV secretion systems involved in bacterial conjugation or protein secretion. Nucleic Acids Res 42:5715–5727 [View Article][PubMed]
    [Google Scholar]
  37. Hayakawa Y., Matsubara K. 1979; Construction and some properties of packageable plasmid F. Mol Gen Genet 169:107–112 [View Article][PubMed]
    [Google Scholar]
  38. Kobayashi I. 2001; Behavior of restriction-modification systems as selfish mobile elements and their impact on genome evolution. Nucleic Acids Res 29:3742–3756 [View Article][PubMed]
    [Google Scholar]
  39. Lee C. A., Babic A., Grossman A. D. 2010; Autonomous plasmid-like replication of a conjugative transposon. Mol Microbiol 75:268–279 [View Article][PubMed]
    [Google Scholar]
  40. Lorenzo-Díaz F., Fernández-López C., Garcillán-Barcia M. P., Espinosa M. 2014; Bringing them together: plasmid pMV158 rolling circle replication and conjugation under an evolutionary perspective. Plasmid 74:15–31 [View Article][PubMed]
    [Google Scholar]
  41. Menard K. L., Grossman A. D. 2013; Selective pressures to maintain attachment site specificity of integrative and conjugative elements. PLoS Genet 9:e1003623 [View Article][PubMed]
    [Google Scholar]
  42. Novick R. P., Christie G. E., Penadés J. R. 2010; The phage-related chromosomal islands of Gram-positive bacteria. Nat Rev Microbiol 8:541–551 [View Article][PubMed]
    [Google Scholar]
  43. Ochman H., Lawrence J. G., Groisman E. A. 2000; Lateral gene transfer and the nature of bacterial innovation. Nature 405:299–304 [View Article][PubMed]
    [Google Scholar]
  44. Pavlovic G., Burrus V., Gintz B., Decaris B., Guédon G. 2004; Evolution of genomic islands by deletion and tandem accretion by site-specific recombination: ICESt1-related elements from Streptococcus thermophilus . Microbiology 150:759–774 [View Article][PubMed]
    [Google Scholar]
  45. Pour-El I., Adams C., Minion F. C. 2002; Construction of mini-Tn4001tet and its use in Mycoplasma gallisepticum . Plasmid 47:129–137 [View Article][PubMed]
    [Google Scholar]
  46. Pradervand N., Sulser S., Delavat F., Miyazaki R., Lamas I., van der Meer J. R. 2014; An operon of three transcriptional regulators controls horizontal gene transfer of the integrative and conjugative element ICEclc in Pseudomonas knackmussii B13. PLoS Genet 10:e1004441 [View Article][PubMed]
    [Google Scholar]
  47. Puymège A., Bertin S., Chuzeville S., Guédon G., Payot S. 2013; Conjugative transfer and cis-mobilization of a genomic island by an integrative and conjugative element of Streptococcus agalactiae . J Bacteriol 195:1142–1151 [View Article][PubMed]
    [Google Scholar]
  48. Raha A. R., Hooi W. Y., Mariana N. S., Radu S., Varma N.R.S., Yusoff K. 2006; DNA sequence analysis of a small cryptic plasmid from Lactococcus lactis subsp. lactis M14. Plasmid 56:53–61 [View Article][PubMed]
    [Google Scholar]
  49. Ramsay J. P., Sullivan J. T., Stuart G. S., Lamont I. L., Ronson C. W. 2006; Excision and transfer of the Mesorhizobium loti R7A symbiosis island requires an integrase IntS, a novel recombination directionality factor RdfS, and a putative relaxase RlxS. Mol Microbiol 62:723–734 [View Article][PubMed]
    [Google Scholar]
  50. Roberts A. P., Allan E., Mullany P. 2014; The impact of horizontal gene transfer on the biology of Clostridium difficile . Adv Microb Physiol 65:63–82 [View Article][PubMed]
    [Google Scholar]
  51. Ruiz-Masó J. A., Anand S. P., Espinosa M., Khan S. A., del Solar G. 2006; Genetic and biochemical characterization of the Streptococcus pneumoniae PcrA helicase and its role in plasmid rolling circle replication. J Bacteriol 188:7416–7425 [View Article][PubMed]
    [Google Scholar]
  52. Sambrook J., Russell D. W. 2006 Molecular Cloning: A Laboratory Manual Cold Spring Harbor, NY: Cold Spring Harbor Laboratory;
    [Google Scholar]
  53. Sitkiewicz I., Green N. M., Guo N., Mereghetti L., Musser J. M. 2011; Lateral gene transfer of streptococcal ICE element RD2 (region of difference 2) encoding secreted proteins. BMC Microbiol 11:65 [View Article][PubMed]
    [Google Scholar]
  54. Smillie C., Garcillán-Barcia M. P., Francia M. V., Rocha E.P.C., de la Cruz F. 2010; Mobility of plasmids. Microbiol Mol Biol Rev 74:434–452 [View Article][PubMed]
    [Google Scholar]
  55. Stingele F., Neeser J. R., Mollet B. 1996; Identification and characterization of the eps (exopolysaccharide) gene cluster from Streptococcus thermophilus Sfi6. J Bacteriol 178:1680–1690[PubMed]
    [Google Scholar]
  56. Takamatsu D., Osaki M., Sekizaki T. 2001; Thermosensitive suicide vectors for gene replacement in Streptococcus suis . Plasmid 46:140–148 [View Article][PubMed]
    [Google Scholar]
  57. Taylor R. G., Walker D. C., McInnes R. R. 1993; E. coli host strains significantly affect the quality of small scale plasmid DNA preparations used for sequencing. Nucleic Acids Res 21:1677–1678 [View Article][PubMed]
    [Google Scholar]
  58. Toussaint A., Merlin C. 2002; Mobile elements as a combination of functional modules. Plasmid 47:26–35 [View Article][PubMed]
    [Google Scholar]
  59. van de Guchte M., van der Vossen J. M., Kok J., Venema G. 1989; Construction of a lactococcal expression vector: expression of hen egg white lysozyme in Lactococcus lactissubsp. lactis . Appl Environ Microbiol 55:224–228[PubMed]
    [Google Scholar]
  60. Wickner S. H., Chattoraj D. K. 1987; Replication of mini-P1 plasmid DNA in vitro requires two initiation proteins, encoded by the repA gene of phage P1 and the dnaA gene of in vitro . Proc Natl Acad Sci U S A 84:3668–3672 [View Article][PubMed]
    [Google Scholar]
  61. Wozniak R.A.F., Waldor M. K. 2009; A toxin-antitoxin system promotes the maintenance of an integrative conjugative element. PLoS Genet 5:e1000439 [View Article][PubMed]
    [Google Scholar]
  62. Wozniak R.A.F., Waldor M. K. 2010; Integrative and conjugative elements: mosaic mobile genetic elements enabling dynamic lateral gene flow. Nat Rev Microbiol 8:552–563 [View Article][PubMed]
    [Google Scholar]
  63. Wright L. D., Johnson C. M., Grossman A. D. 2015; Identification of a single strand origin of replication in the integrative and conjugative element ICEBs1 of Bacillus subtilis . PLoS Genet 11:e1005556 [CrossRef]
    [Google Scholar]
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