Advertisement

Detection of a novel active transposable element in Caldicellulosiruptor hydrothermalis and a new search for elements in this genus

  • Daehwan Chung
  • Joel Farkas
  • Janet Westpheling
Short Communication

Abstract

We show that a previously annotated hypothetical protein is the transposase of a new and active IS element, ISCahy1, widespread in Caldicellulosiruptor species. Transposition generated an 11-bp direct repeat at the insertion site in Caldicellulosiruptor hydrothermalis, suggesting a cut-and-paste mechanism. The discovery of an active insertion sequence in Caldicellulosiruptor species led to a survey of potential IS elements in the genome sequences of eight Caldicellulosiruptor species that identified several new elements, including one novel to this genus.

Keywords

Transposition Thermophilic anaerobes Caldicellulosiruptor IS element ISCahy1 ISCbe4 

Notes

Acknowledgments

We thank Lee Lynd, Dan Olson, and Adam Guss for sharing unpublished results, Jenna Oberstaller for assistance in genome sequence analysis, and Minseok Cha and Jennifer Copeland for helpful discussions during the course of the work. This work was supported by The BioEnergy Science Center supported by a U.S. Department of Energy Bioenergy Research Center supported by the Office of Biological and Environmental Research in the DOE Office of Science. JF was supported in part by a predoctoral Graduate Training In Genetics grant (NIH 5T32GM007103-30) to the Genetics Department of the University of Georgia.

Supplementary material

10295_2013_1244_MOESM1_ESM.docx (21 kb)
Supplementary material 1 (DOCX 20 kb)

References

  1. 1.
    Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25(17):3389–3402PubMedCrossRefGoogle Scholar
  2. 2.
    Blumer-Schuette SE, Kataeva I, Westpheling J, Adams MW, Kelly RM (2008) Extremely thermophilic microorganisms for biomass conversion: status and prospects. Curr Opin Biotechnol 19(3):210–217. doi: 10.1016/j.copbio.2008.04.007 PubMedCrossRefGoogle Scholar
  3. 3.
    Blumer-Schuette SE, Ozdemir I, Mistry D, Lucas S, Lapidus A, Cheng JF, Goodwin LA, Pitluck S, Land ML, Hauser LJ, Woyke T, Mikhailova N, Pati A, Kyrpides NC, Ivanova N, Detter JC, Walston-Davenport K, Han S, Adams MW, Kelly RM (2011) Complete genome sequences for the anaerobic, extremely thermophilic plant biomass-degrading bacteria Caldicellulosiruptor hydrothermalis, Caldicellulosiruptor kristjanssonii, Caldicellulosiruptor kronotskyensis, Caldicellulosiruptor owensensis, and Caldicellulosiruptor lactoaceticus. J Bacteriol 193(6):1483–1484. doi: 10.1128/JB.01515-10 PubMedCrossRefGoogle Scholar
  4. 4.
    Brochet M, Da Cunha V, Couve E, Rusniok C, Trieu-Cuot P, Glaser P (2009) Atypical association of DDE transposition with conjugation specifies a new family of mobile elements. Mol Microbiol 71(4):948–959. doi: 10.1111/j.1365-2958.2008.06579.x PubMedCrossRefGoogle Scholar
  5. 5.
    Chung D, Cha M, Farkas J, Westpheling J (2013) Construction of a stable replicating shuttle vector for Caldicellulosiruptor species: use for extending genetic methodologies to other members of this genus. Plos One (in review)Google Scholar
  6. 6.
    Chung D, Farkas J, Huddleston JR, Olivar E, Westpheling J (2012) Methylation by a unique α-class N4-cytosine methyltransferase is required for DNA transformation of Caldicellulosiruptor bescii DSM6725. PLoS One 7(8):e43844. doi: 10.1371/journal.pone.0043844 PubMedCrossRefGoogle Scholar
  7. 7.
    Elkins JG, Lochner A, Hamilton-Brehm SD, Davenport KW, Podar M, Brown SD, Land ML, Hauser LJ, Klingeman DM, Raman B, Goodwin LA, Tapia R, Meincke LJ, Detter JC, Bruce DC, Han CS, Palumbo AV, Cottingham RW, Keller M, Graham DE (2010) Complete genome sequence of the cellulolytic thermophile Caldicellulosiruptor obsidiansis OB47T. J Bacteriol 192(22):6099–6100. doi: 10.1128/JB.00950-10 PubMedCrossRefGoogle Scholar
  8. 8.
    Farkas J, Chung D, Cha M, Copeland J, Grayeski P, Westpheling J (2013) Improved growth media and culture techniques for genetic analysis and assessment of biomass utilization by Caldicellulosiruptor bescii. J Ind Microbiol Biotechnol 40(1):41–49. doi: 10.1007/s10295-012-1202-1 PubMedCrossRefGoogle Scholar
  9. 9.
    Feinberg L, Foden J, Barrett T, Davenport KW, Bruce D, Detter C, Tapia R, Han C, Lapidus A, Lucas S, Cheng JF, Pitluck S, Woyke T, Ivanova N, Mikhailova N, Land M, Hauser L, Argyros DA, Goodwin L, Hogsett D, Caiazza N (2011) Complete genome sequence of the cellulolytic thermophile Clostridium thermocellum DSM1313. J Bacteriol 193(11):2906–2907. doi: 10.1128/JB.00322-11 PubMedCrossRefGoogle Scholar
  10. 10.
    Kataeva IA, Yang SJ, Dam P, Poole FL 2nd, Yin Y, Zhou F, Chou WC, Xu Y, Goodwin L, Sims DR, Detter JC, Hauser LJ, Westpheling J, Adams MW (2009) Genome sequence of the anaerobic, thermophilic, and cellulolytic bacterium “Anaerocellum thermophilum” DSM 6725. J Bacteriol 191(11):3760–3761. doi: 10.1128/JB.00256-09 PubMedCrossRefGoogle Scholar
  11. 11.
    Larkin MA, Larkin MA, Blackshields G, Brown NP, Chenna R, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG, Higgins DG (2007) ClustalW and ClustalX version 2.0. Bioinformatics 23(21):2947–2948. doi: 10.1093/bioinformatics/btm404 PubMedCrossRefGoogle Scholar
  12. 12.
    Maamar H, de Philip P, Belaich JP, Tardif C (2003) ISCce1 and ISCce2, two novel insertion sequences in Clostridium cellulolyticum. J Bacteriol 185(3):714–725PubMedCrossRefGoogle Scholar
  13. 13.
    Mahillon J, Chandler M (1998) Insertion sequences. Microbiol Mol Biol Rev 62(3):725–774PubMedGoogle Scholar
  14. 14.
    Page RD (1996) TreeView: an application to display phylogenetic trees on personal computers. Comput Appl Biosci 12(4):357–358PubMedGoogle Scholar
  15. 15.
    Price AL, Jones NC, Pevzner PA (2005) De novo identification of repeat families in large genomes. Bioinformatics 21(Suppl 1):i351–i358. doi: 10.1093/bioinformatics/bti1018 PubMedCrossRefGoogle Scholar
  16. 16.
    Siguier P, Perochon J, Lestrade L, Mahillon J, Chandler M (2006) ISfinder: the reference centre for bacterial insertion sequences. Nucleic Acids Res 34(Database issue):D32–D36. doi: 10.1093/nar/gkj014 PubMedCrossRefGoogle Scholar
  17. 17.
    van de Werken HJ, Verhaart MR, VanFossen AL, Willquist K, Lewis DL, Nichols JD, Goorissen HP, Mongodin EF, Nelson KE, van Niel EW, Stams AJ, Ward DE, de Vos WM, van der Oost J, Kelly RM, Kengen SW (2008) Hydrogenomics of the extremely thermophilic bacterium Caldicellulosiruptor saccharolyticus. Appl Environ Microbiol 74(21):6720–6729. doi: 10.1128/AEM.00968-08 PubMedCrossRefGoogle Scholar
  18. 18.
    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. doi: 10.1186/gb-2011-12-3-r30 PubMedCrossRefGoogle Scholar
  19. 19.
    Wagner A, Lewis C, Bichsel M (2007) A survey of bacterial insertion sequences using IScan. Nucleic Acids Res 35(16):5284–5293. doi: 10.1093/nar/gkm597 PubMedCrossRefGoogle Scholar
  20. 20.
    Yang SJ, Kataeva I, Hamilton-Brehm SD, Engle NL, Tschaplinski TJ, Doeppke C, Davis M, Westpheling J, Adams MW (2009) Efficient degradation of lignocellulosic plant biomass, without pretreatment, by the thermophilic anaerobe “Anaerocellum thermophilum” DSM 6725. Appl Environ Microbiol 75(14):4762–4769. doi: 10.1128/AEM.00236-09 PubMedCrossRefGoogle Scholar
  21. 21.
    Zhang Z, Schwartz S, Wagner L, Miller W (2000) A greedy algorithm for aligning DNA sequences. J Comput Biol 7(1–2):203–214. doi: 10.1089/10665270050081478 PubMedCrossRefGoogle Scholar
  22. 22.
    Zverlov VV, Klupp M, Krauss J, Schwarz WH (2008) Mutations in the scaffoldin gene, cipA, of Clostridium thermocellum with impaired cellulosome formation and cellulose hydrolysis: insertions of a new transposable element, IS1447, and implications for cellulase synergism on crystalline cellulose. J Bacteriol 190(12):4321–4327. doi: 10.1128/JB.00097-08 PubMedCrossRefGoogle Scholar

Copyright information

© Society for Industrial Microbiology and Biotechnology 2013

Authors and Affiliations

  • Daehwan Chung
    • 1
    • 2
  • Joel Farkas
    • 1
    • 2
  • Janet Westpheling
    • 1
    • 2
  1. 1.Department of GeneticsUniversity of GeorgiaAthensUSA
  2. 2.The BioEnergy Science Center, Department of EnergyOak Ridge National LaboratoryOak RidgeUSA

Personalised recommendations