Advertisement

Prediction of Type II Toxin-Antitoxin Loci in Klebsiella pneumoniae Genome Sequences

  • Yi-Qing Wei
  • De-Xi Bi
  • Dong-Qing WeiEmail author
  • Hong-Yu OuEmail author
Original Research Article

Abstract

Klebsiella pneumoniae is an increasingly important bacterial pathogen to human. This Gram-negative bacterium species has become a serious concern due to its dramatic increase in the levels of multiple antibiotic resistances, particularly to carbapenems. The toxin-antitoxin (TA) system has recently been reported to be involved in the formation of drug-tolerant persister cells. The type II TA system is composed of a stable toxin protein and a relatively unstable antitoxin protein that is able to inhibit the toxin. Here, we examine the type II TA locus distribution and compare the TA diversity throughout ten completely sequenced K. pneumoniae genomes by using bioinformatics approaches. Two hundred and twelve putative type II TA loci were identified in 30 replicons of these K. pneumoniae strains. The amino acid sequence similarity-based grouping shows that these loci distribute differently not only among different K. pneumoniae strains isolated from diverse sources, but also between their chromosomes and plasmids.

Keywords

Type II toxin-antitoxin loci Klebsiella pneumoniae In silico detection 

Notes

Acknowledgments

This study was supported by partial funding from the 973 program, Ministry of Science and Technology, China (2015CB554202, 2012CB721000); the National Natural Science Foundation of China (31170082); the Specialized Research Fund for the Doctoral Program of Higher Education, China (20130073110062).

Supplementary material

12539_2015_135_MOESM1_ESM.pdf (219 kb)
Supplementary material 1 (PDF 220 kb)
12539_2015_135_MOESM2_ESM.xlsx (15 kb)
Supplementary material 2 (XLSX 15 kb)
12539_2015_135_MOESM3_ESM.xlsx (46 kb)
Supplementary material 3 (XLSX 46 kb)
12539_2015_135_MOESM4_ESM.xlsx (16 kb)
Supplementary material 4 (XLSX 16 kb)
12539_2015_135_MOESM5_ESM.xlsx (14 kb)
Supplementary material 5 (XLSX 15 kb)

References

  1. 1.
    Nordmann P, Cuzon G, Naas T (2009) The real threat of Klebsiella pneumoniae carbapenemase-producing bacteria. Lancet Infect Dis 9(4):228–236CrossRefGoogle Scholar
  2. 2.
    Liu P, Li P, Jiang X, Bi D, Xie Y, Tai C, Deng Z, Rajakumar K, Ou HY (2012) Complete genome sequence of Klebsiella pneumoniae subsp. pneumoniae HS11286, a multidrug-resistant strain isolated from human sputum. J Bacteriol 194(7):1841–1842CrossRefGoogle Scholar
  3. 3.
    Zhang J, van Aartsen JJ, Jiang X, Shao Y, Tai C, He X, Tan Z, Deng Z, Jia S, Rajakumar K, Ou HY (2011) Expansion of the known Klebsiella pneumoniae species gene pool by characterization of novel alien DNA islands integrated into tmRNA gene sites. J Microbiol Methods 84(2):283–289CrossRefGoogle Scholar
  4. 4.
    Yamaguchi Y, Park JH, Inouye M (2011) Toxin-antitoxin systems in bacteria and archaea. Annu Rev Genet 45:61–79CrossRefGoogle Scholar
  5. 5.
    Ghafourian S, Raftari M, Nourkhoda S, Sekawi Z. (2013) Toxin-antitoxin systems: classification, biological function and application in biotechnology. Horizon Scientific Press, New York, vol 16, no Biol, pp 9–14Google Scholar
  6. 6.
    Wang X, Wood TK (2011) Toxin-antitoxin systems influence biofilm and persister cell formation and the general stress response. Appl Environ Microbiol 77(16):5577–5583CrossRefGoogle Scholar
  7. 7.
    Maisonneuve E, Gerdes K (2014) Molecular mechanisms underlying bacterial persisters. Cell 157(3):539–548CrossRefGoogle Scholar
  8. 8.
    Masuda H, Tan Q, Awano N, Wu KP, Inouye M (2012) YeeU enhances the bundling of cytoskeletal polymers of MreB and FtsZ, antagonizing the CbtA (YeeV) toxicity in Escherichia coli. Mol Microbiol 84(5):979–989CrossRefGoogle Scholar
  9. 9.
    Wang X, Lord DM, Cheng HY, Osbourne DO, Hong SH, Sanchez-Torres V, Quiroga C, Zheng K, Herrmann T, Peti W, Benedik MJ, Page R, Wood TK (2012) A new type V toxin-antitoxin system where mRNA for toxin GhoT is cleaved by antitoxin GhoS. Nat Chem Biol 8(10):855–861CrossRefGoogle Scholar
  10. 10.
    Pandey DP, Gerdes K (2005) Toxin-antitoxin loci are highly abundant in free-living but lost from host-associated prokaryotes. Nucleic Acids Res 33(3):966–976CrossRefGoogle Scholar
  11. 11.
    Ou HY, Wei Y, Bi D (2013) Type II toxin-antitoxin loci: phylogeny. In: Prokaryotic toxin-antitoxins. Springer, Heidelberg, pp 239–247Google Scholar
  12. 12.
    Sala A, Bordes P, Genevaux P (2014) Multiple toxin-antitoxin systems in Mycobacterium tuberculosis. Toxins (Basel) 6(3):1002–1020CrossRefGoogle Scholar
  13. 13.
    Sevin EW, Barloy-Hubler F (2007) RASTA-Bacteria: a web-based tool for identifying toxin-antitoxin loci in prokaryotes. Genome Biol 8(8):R155CrossRefGoogle Scholar
  14. 14.
    Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, Hauser LJ (2010) Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinform 11:119CrossRefGoogle Scholar
  15. 15.
    Shao Y, Harrison EM, Bi D, Tai C, He X, Ou HY, Rajakumar K, Deng Z (2011) TADB: a web-based resource for type 2 toxin-antitoxin loci in bacteria and archaea, Nucleic Acids Res 39(Database issue):D606–D611CrossRefGoogle Scholar
  16. 16.
    Finn RD, Clements J, Eddy SR (2011) HMMER web server: interactive sequence similarity searching. Nucleic Acids Res 39(Web Server issue):W29–W37CrossRefGoogle Scholar
  17. 17.
    Wozniak RA, Waldor MK (2009) A toxin-antitoxin system promotes the maintenance of an integrative conjugative element. PLoS Genet 5(3):e1000439CrossRefGoogle Scholar
  18. 18.
    Black DS, Kelly AJ, Mardis MJ, Moyed HS (1991) Structure and organization of hip, an operon that affects lethality due to inhibition of peptidoglycan or DNA synthesis. J Bacteriol 173(18):5732–5739CrossRefGoogle Scholar
  19. 19.
    Van Melderen L, Saavedra De Bast M (2009) Bacterial toxin-antitoxin systems: more than selfish entities? PLoS Genet 5(3):e1000437CrossRefGoogle Scholar
  20. 20.
    Boggild A, Sofos N, Andersen KR, Feddersen A, Easter AD, Passmore LA, Brodersen DE (2012) The crystal structure of the intact E. coli RelBE toxin-antitoxin complex provides the structural basis for conditional cooperativity. Structure 20(10):1641–1648CrossRefGoogle Scholar
  21. 21.
    Tashiro Y, Kawata K, Taniuchi A, Kakinuma K, May T, Okabe S (2012) RelE-mediated dormancy is enhanced at high cell density in Escherichia coli. J Bacteriol 194(5):1169–1176CrossRefGoogle Scholar
  22. 22.
    Makarova KS, Wolf YI, Koonin EV (2009) Comprehensive comparative-genomic analysis of type 2 toxin-antitoxin systems and related mobile stress response systems in prokaryotes. Biol Direct 4:19CrossRefGoogle Scholar
  23. 23.
    Jurenaite M, Markuckas A, Suziedeliene E (2013) Identification and characterization of type II toxin-antitoxin systems in the opportunistic pathogen Acinetobacter baumannii. J Bacteriol 195(14):3165–3172CrossRefGoogle Scholar
  24. 24.
    Castro-Roa D, Garcia-Pino A, De Gieter S, van Nuland NA, Loris R, Zenkin N (2013) The Fic protein Doc uses an inverted substrate to phosphorylate and inactivate EF-Tu. Nat Chem Biol 9(12):811–817CrossRefGoogle Scholar

Copyright information

© International Association of Scientists in the Interdisciplinary Areas and Springer-Verlag Berlin Heidelberg 2015

Authors and Affiliations

  1. 1.State Key Laboratory for Microbial Metabolism and School of Life Sciences and BiotechnologyShanghai Jiaotong UniversityShanghaiChina

Personalised recommendations