Advertisement

Mobile Genetic Elements in Pseudomonas stutzeri

  • Leandro Pio de SousaEmail author
Article

Abstract

Mobile genetic elements (MGE) play a large role in the plasticity of genomes, participating in several phenomena which involve genes acquisition. Pseudomonas stutzeri is an environmental widely distributed bacteria. This bacteria has a very large genomic plasticity, which would explain its occurrence in several different environments. NCBI data bank and online programs were used to build an inventory to investigate diversity and structure of MGE in Pseudomonas stutzeri, searching for insertion sequences (IS), integrases/transposases, plasmids and prophages. Five hundred and forty-eight ISs, 62 integrases, 166 transposases, five plasmids and eight complete prophages were found. MGE location and adjacent genes were investigated. Possible implications of the presence of these mobile elements explaining phenotypic diversity of Pseudomonas stutzeri were discussed. The study showed that MGEs might be good clues to understand the dynamics of genomes and their phenotypic plasticity, although they are not the only elements responsible for these characteristics.

Notes

Compliance with Ethical Standards

Conflict of interest

The author declare that he has no conflict of interest.

Supplementary material

284_2019_1812_MOESM1_ESM.pdf (1013 kb)
Supplementary file1 (PDF 1012 kb)
284_2019_1812_MOESM2_ESM.pdf (32 kb)
Supplementary file2 (PDF 32 kb)
284_2019_1812_MOESM3_ESM.pdf (45 kb)
Supplementary file3 (PDF 45 kb)
284_2019_1812_MOESM4_ESM.pdf (47 kb)
Supplementary file4 (PDF 47 kb)
284_2019_1812_MOESM5_ESM.pdf (45 kb)
Supplementary file5 (PDF 44 kb)
284_2019_1812_MOESM6_ESM.pdf (4 kb)
Supplementary file6 (PDF 4 kb)
284_2019_1812_MOESM7_ESM.pdf (9 kb)
Supplementary file7 (PDF 8 kb)
284_2019_1812_MOESM8_ESM.pdf (9 kb)
Supplementary file8 (PDF 9 kb)
284_2019_1812_MOESM9_ESM.pdf (490 kb)
Supplementary file9 (PDF 489 kb)
284_2019_1812_MOESM10_ESM.pdf (291 kb)
Supplementary file10 (PDF 290 kb)
284_2019_1812_MOESM11_ESM.pdf (79 kb)
Supplementary file11 (PDF 74 kb)

References

  1. 1.
    Palleroni NJ (1984) Pseudomonas. In: Krieg NR (ed) Bergey's manual of systematic bacteriology, vol I. Williams and Wilkins, Baltimore, pp 141–199Google Scholar
  2. 2.
    Lalucat J, Bennasar A, Bosch R, García-Valdés E, Palleroni NJ (2006) Biology of Pseudomonas stutzeri. Microbiol Mol Biol Rev 70(2):510–547.  https://doi.org/10.1128/MMBR.00047-05 CrossRefPubMedPubMedCentralGoogle Scholar
  3. 3.
    Ginard M, Lalucat J, Tümmler B, Römling U (1997) Genome organization of Pseudomonas stutzeri and resulting taxonomic and evolutionary considerations. Int J Syst Bacteriol 47(1):132–143.  https://doi.org/10.1099/00207713-47-1-132 CrossRefPubMedGoogle Scholar
  4. 4.
    Singh PK, Bourque G, Craig NL, Dubnau JT, Feschotte C, Flasch DA, Gunderson KL, Malik HS, Moran JV (2014) Mobile genetic elements and genome evolution. Mob DNA.  https://doi.org/10.1186/1759-8753-5-26 CrossRefPubMedPubMedCentralGoogle Scholar
  5. 5.
    Stokes HW, Gillings MR (2011) Gene flow, mobile genetic elements and the recruitment of antibiotic resistance genes into Gram-negative pathogens. FEMS Microbiol Rev 35(5):790–819.  https://doi.org/10.1111/j.1574-6976.2011.00273.x CrossRefPubMedGoogle Scholar
  6. 6.
    Top EM, Springael D (2003) The role of mobile genetic elements in bacterial adaptation to xenobiotic organic compounds. Curr Opin Biotechnol 14(3):262–269.  https://doi.org/10.1016/S0958-1669(03)00066-1 CrossRefPubMedGoogle Scholar
  7. 7.
    Queck SY, Khan BA, Wang R, Bach THL, Kretschmer D, Chen L, Otto M (2009) Mobile genetic element-encoded cytolysin connects virulence to methicillin resistance in MRSA. PLoS Pathog 5(7):e1000533.  https://doi.org/10.1371/journal.ppat.1000533 CrossRefPubMedPubMedCentralGoogle Scholar
  8. 8.
    Fayad N, Awad MK, Mahillon J (2019) Diversity of Bacillus cereus sensu lato mobilome. BMC Genomics 20(1):436.  https://doi.org/10.1186/s12864-019-5764-4 CrossRefPubMedPubMedCentralGoogle Scholar
  9. 9.
    Mathee K, Narasimhan G, Valdes C, Qiu X, Matewish JM, Koehrsen M, Olavarietta R (2008) Dynamics of Pseudomonas aeruginosa genome evolution. Proc Natl Acad Sci USA 105(8):3100–3105.  https://doi.org/10.1073/pnas.0711982105 CrossRefPubMedGoogle Scholar
  10. 10.
    Dziewit L, Baj J, Szuplewska M, Maj A, Tabin M, Czyzkowska A, Tudek A (2012) Insights into the transposable mobilome of Paracoccus spp. (Alphaproteobacteria). PLoS ONE 7(2):e32277.  https://doi.org/10.1371/journal.pone.0032277 CrossRefPubMedPubMedCentralGoogle Scholar
  11. 11.
    Piotrowska M, Popowska M (2015) Insight into the mobilome of Aeromonas strains. Front Microbiol 6:494.  https://doi.org/10.3389/fmicb.2015.00494 CrossRefPubMedPubMedCentralGoogle Scholar
  12. 12.
    Varani AM, Siguier P, Gourbeyre E, Charneau V, Chandler M (2011) ISsaga is an ensemble of web-based methods for high throughput identification and semi-automatic annotation of insertion sequences in prokaryotic genomes. Genome Biol 12(3):R30.  https://doi.org/10.1186/gb-2011-12-3-r30 CrossRefPubMedPubMedCentralGoogle Scholar
  13. 13.
    Conant GC, Wolfe KH (2008) GenomeVx: simple web-based creation of editable circular chromosome maps. Bioinformatics 24(6):861–862.  https://doi.org/10.1093/bioinformatics/btm598 CrossRefPubMedGoogle Scholar
  14. 14.
    Zhou Y, Liang Y, Lynch KH, Dennis JJ, Wishart DS (2011) PHAST: a fast phage search tool. Nucleic Acids Res 39(suppl_2):W347–W352.  https://doi.org/10.1093/nar/gkr485 CrossRefPubMedPubMedCentralGoogle Scholar
  15. 15.
    Ho J, Taiaroa G, Butler MI, Poulter RT (2019) The genome sequence of M228, a Chinese Isolate of Pseudomonas syringae pv. actinidiae, illustrates insertion sequence element mobility. Microbiol Resour Announc 8(1):e01427–e1518CrossRefGoogle Scholar
  16. 16.
    Bardaji L, Pérez-Martínez I, Rodríguez-Moreno L, Rodríguez-Palenzuela P, Sundin GW, Ramos C, Murillo J (2011) Sequence and role in virulence of the three plasmid complement of the model tumor-inducing bacterium Pseudomonas savastanoi pv. savastanoi NCPPB 3335. PLoS ONE 6(10):e25705.  https://doi.org/10.1371/journal.pone.0025705 CrossRefPubMedPubMedCentralGoogle Scholar
  17. 17.
    De Smet J, Hendrix H, Blasdel BG, Danis-Wlodarczyk K, Lavigne R (2017) Pseudomonas predators: understanding and exploiting phage–host interactions. Nat Rev Microbiol 15(9):517.  https://doi.org/10.1038/nrmicro.2017.61 CrossRefPubMedGoogle Scholar
  18. 18.
    Holmes B (1986) Identification and distribution of Pseudomonas stutzeri in clinical material. J Appl Bacteriol 60(5):401–411.  https://doi.org/10.1111/j.1365-2672.1986.tb05085.x CrossRefPubMedGoogle Scholar
  19. 19.
    Kalra D, Sati A, Shankar S, Jha A (2015) Corneal infection by Pseudomonas stutzeri following excision of trigeminal nerve schwannoma. Case Rep 1:11.  https://doi.org/10.1136/bcr-2014-207496 CrossRefGoogle Scholar
  20. 20.
    Halabi Z, Mocadie M, El Zein S, Kanj SS (2019) Pseudomonas stutzeri prosthetic valve endocarditis: a case report and review of the literature. J Infect Pub Health 12(3):434–437.  https://doi.org/10.1016/j.jiph.2018.07.004 CrossRefGoogle Scholar
  21. 21.
    Vandecraen J, Chandler M, Aertsen A, Van Houdt R (2017) The impact of insertion sequences on bacterial genome plasticity and adaptability. Crit Rev Microbiol 43(6):709–730.  https://doi.org/10.1080/1040841X.2017.1303661 CrossRefPubMedGoogle Scholar
  22. 22.
    Canals R, Altarriba M, Vilches S, Horsburgh G, Shaw JG, Tomás JM, Merino S (2006) Analysis of the lateral flagellar gene system of Aeromonas hydrophila AH-3. J Bacteriol 188(3):852–862.  https://doi.org/10.1128/JB.188.3.852-862.2006 CrossRefPubMedPubMedCentralGoogle Scholar
  23. 23.
    Misra N, Habib S, Ranjan A, Hasnain SE, Nath I (1996) Expression and functional characterisation of the clpC gene of Mycobacterium leprae: ClpC protein elicits human antibody response. Gene 172(1):99–104.  https://doi.org/10.1016/0378-1119(96)00053-4 CrossRefPubMedGoogle Scholar
  24. 24.
    Chatterjee I, Becker P, Grundmeier M, Bischoff M, Somerville GA, Peters G, Herrmann M (2005) Staphylococcus aureus ClpC is required for stress resistance, aconitase activity, growth recovery, and death. J Bacteriol 187(13):4488–4496.  https://doi.org/10.1128/JB.187.13.4488-4496.2005 CrossRefPubMedPubMedCentralGoogle Scholar
  25. 25.
    Chan KG, Priya K, Chang CY, Rahman AYA, Tee KK, Yin WF (2016) Transcriptome analysis of Pseudomonas aeruginosa PAO1 grown at both body and elevated temperatures. PeerJ 4:e2223.  https://doi.org/10.7717/peerj.2223 CrossRefPubMedPubMedCentralGoogle Scholar
  26. 26.
    Qiu Y, Zhou S, Mo X, You C, Wang D (1981) Investigation of dinitrogen fixation bacteria isolated from rice rhizosphere. Chin Sci Bull (Kexuetongbao) 26(26):383–384Google Scholar
  27. 27.
    Husnik F, McCutcheon JP (2018) Functional horizontal gene transfer from bacteria to eukaryotes. Nat Rev Microbiol 16(2):67.  https://doi.org/10.1038/nrmicro.2017.137 CrossRefPubMedGoogle Scholar
  28. 28.
    Venieraki A, Dimou M, Vezyri E, Vamvakas A, Katinaki PA, Chatzipavlidis I, Katinakis P (2014) The nitrogen-fixation island insertion site is conserved in diazotrophic Pseudomonas stutzeri and Pseudomonas sp. isolated from distal and close geographical regions. PLoS ONE 9(9):e105837.  https://doi.org/10.1371/journal.pone.0105837 CrossRefPubMedPubMedCentralGoogle Scholar
  29. 29.
    Lau GW, Hassett DJ, Ran H, Kong F (2004) The role of pyocyanin in Pseudomonas aeruginosa infection. Trends Mol Med 10(12):599–606.  https://doi.org/10.1016/j.molmed.2004.10.002 CrossRefPubMedGoogle Scholar
  30. 30.
    Donn S, Kirkegaard JA, Perera G, Richardson AE, Watt M (2015) Evolution of bacterial communities in the wheat crop rhizosphere. Environ Microbiol 17(3):610–621.  https://doi.org/10.1111/1462-2920.12452 CrossRefPubMedGoogle Scholar
  31. 31.
    Rosselló-Mora RA, Lalucat J, García-Valdés E (1994) Comparative biochemical and genetic analysis of naphthalene degradation among Pseudomonas stutzeri strains. Appl Environ Microbiol 60(3):966–972PubMedPubMedCentralGoogle Scholar
  32. 32.
    Feijoo-Siota L, Rosa-Dos-Santos F, de Miguel T, Villa TG (2008) Biodegradation of naphthalene by Pseudomonas stutzeri in marine environments: testing cells entrapment in calcium alginate for use in water detoxification. Bioremediat J 12(4):185–192.  https://doi.org/10.1080/10889860802477168 CrossRefGoogle Scholar
  33. 33.
    Kottara A, Hall JP, Harrison E, Brockhurst MA (2017) Variable plasmid fitness effects and mobile genetic element dynamics across Pseudomonas species. FEMS Microbiol Ecol 94(1):fix172.  https://doi.org/10.1093/femsec/fix172 CrossRefPubMedCentralGoogle Scholar
  34. 34.
    Iustman LJR, Tribelli PM, Ibarra JG, Catone MV, Venero ECS, López NI (2015) Genome sequence analysis of Pseudomonas extremaustralis provides new insights into environmental adaptability and extreme conditions resistance. Extremophiles 19(1):207–220.  https://doi.org/10.1007/s00792-014-0700-7 CrossRefGoogle Scholar
  35. 35.
    Hosseini R, Kuepper J, Koebbing S, Blank LM, Wierckx N, de Winde JH (2017) Regulation of solvent tolerance in Pseudomonas putida S12 mediated by mobile elements. Microb Biotechnol 10(6):1558–1568.  https://doi.org/10.1111/1751-7915.12495 CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Departament of Genetic, Evolution, Microbiology and Imunology, Institute of BiologyState University of CampinasCampinasBrazil

Personalised recommendations