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Application of DNA Microarray for Screening Metagenome Library Clones

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Metagenomics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 668))

Abstract

Sequence-based screening tools of a metagenome library can expedite metagenome researches considering tremendous metagenome diversities. Several critical disadvantages of activity-based screening of metagenome libraries could be overcome by sequence-based screening approaches. DNA microarray technology widely used for monitoring environmental genes can be employed for screening environmental fosmid and BAC clones harboring target genes due to its high throughput nature. DNAs of fosmid clones are extracted and spotted on a glass slide and fluorescence-labeled probes are hybridized to the microarray. Specific hybridization signals can be obtained only for the fosmid clones that contain the target gene with high sensitivity (10 ng/μL of fosmid clone DNA) and quantitativeness.

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References

  1. Kowalchuk, G.A., Speksnijder, A.G., Zhang, K., Goodman, R.M., and van Veen, J.A. (2007) Finding the needles in the metagenome haystack. Microb Ecol 53, 475–485.

    Article  PubMed  Google Scholar 

  2. Schmeisser, C., Steele, H., and Streit, W.R. (2007) Metagenomics, biotechnology with non-culturable microbes. Appl Microbiol Biotechnol 75, 955–962.

    Article  PubMed  CAS  Google Scholar 

  3. Williamson, L.L., Borlee, B.R., Schloss, P.D., Guan, C., Allen, H. K., and Handelsman, J. (2005) Intracellular screen to identify metagenomic clones that induce or inhibit a quorum-sensing biosensor. Appl Environ Microbiol 71, 6335–6344.

    Article  PubMed  CAS  Google Scholar 

  4. van Hellemond, E.W., Janssen, D.B., and Fraaije, M.W. (2007) Discovery of a novel styrene monooxygenase originating from the metagenome. Appl Environ Microbiol 73, 5832–5839.

    Article  PubMed  Google Scholar 

  5. Kim, B.S., Kim, S.Y., Park, J., Park, W., Hwang, K.Y., Yoon, Y. J., et al. (2007) Sequence-based screening for self-sufficient P450 monooxygenase from a metagenome library. J Appl Microbiol 102, 1392–1400.

    Article  PubMed  CAS  Google Scholar 

  6. Hallam, S.J., Mincer, T.J., Schleper, C., Preston, C.M., Roberts, K., Richardson, P.M., et al. (2006) Pathways of carbon assimilation and ammonia oxidation suggested by environmental genomic analyses of marine Crenarchaeota. PLoS Biol 4, e95.

    Article  PubMed  Google Scholar 

  7. Hallam, S.J., Konstantinidis, K.T., Putnam, N., Schleper, C., Watanabe, Y., Sugahara, J., et al. (2006) Genomic analysis of the uncultivated marine crenarchaeote Cenarchaeum symbiosum. Proc Natl Acad Sci USA 103, 18296–18301.

    Article  PubMed  CAS  Google Scholar 

  8. Majernik, A., Gottschalk, G., and Daniel, R. (2001) Screening of environmental DNA libraries for the presence of genes conferring Na(+)(Li(+))/H(+) antiporter activity on Escherichia coli: characterization of the recovered genes and the corresponding gene products. J Bacteriol 183, 6645–6653.

    Article  PubMed  CAS  Google Scholar 

  9. Henne, A., Schmitz, R.A., Bomeke, M., Gottschalk, G., and Daniel, R. (2000) Screening of environmental DNA libraries for the presence of genes conferring lipolytic activity on Escherichia coli. Appl Environ Microbiol 66, 3113–3116.

    Article  PubMed  CAS  Google Scholar 

  10. Bae, J.W., Rhee, S.K., Park, J.R., Chung, W.H., Nam, Y.D., Lee, I., et al. (2005) Development and evaluation of genome-probing microarrays for monitoring lactic acid bacteria. Appl Environ Microbiol 71, 8825–8835.

    Article  PubMed  CAS  Google Scholar 

  11. Bodrossy, L., Stralis-Pavese, N., Murrell, J.C., Radajewski, S., Weilharter, A., and Sessitsch, A. (2003) Development and validation of a diagnostic microbial microarray for methanotrophs. Environ Microbiol 5, 566–582.

    Article  PubMed  CAS  Google Scholar 

  12. Rhee, S.K., Liu, X., Wu, L., Chong, S.C., Wan, X., and Zhou, J. (2004) Detection of genes involved in biodegradation and biotransformation in microbial communities by using 50-mer oligonucleotide microarrays. Appl Environ Microbiol 70, 4303–4317.

    Article  PubMed  CAS  Google Scholar 

  13. Ward, B.B., Eveillard, D., Kirshtein, J.D., Nelson, J.D., Voytek, M.A., and Jackson, G.A. (2007) Ammonia-oxidizing bacterial community composition in estuarine and oceanic environments assessed using a functional gene microarray. Environ Microbiol 9, 2522–2538.

    Article  PubMed  CAS  Google Scholar 

  14. Wu, L., Thompson, D.K., Liu, X., Fields, M.W., Bagwell, C.E., Tiedje, J.M., et al. (2004) Development and evaluation of microarray-based whole-genome hybridization for detection of microorganisms within the context of environmental applications. Environ Sci Technol 38, 6775–6782.

    Article  PubMed  CAS  Google Scholar 

  15. Hallam, S.J., Putnam, N., Preston, C.M., Detter, J.C., Rokhsar, D., Richardson, P.M., et al. (2004) Reverse methanogenesis: testing the hypothesis with environmental genomics. Science 305, 1457–1462.

    Article  PubMed  CAS  Google Scholar 

  16. Park, S.J., Kang, C.H., Chae, J.C., and Rhee, S.K. (2008) Metagenome microarray for screening of fosmid clones containing specific genes. FEMS Microbiol Lett 284, 28–34.

    Article  PubMed  CAS  Google Scholar 

  17. Quaiser, A., Ochsenreiter, T., Klenk, H.P., Kletzin, A., Treusch, A.H., Meurer, G., et al. (2002) First insight into the genome of an uncultivated crenarchaeote from soil. Environ Microbiol 4, 603–611.

    Article  PubMed  CAS  Google Scholar 

  18. Zhou, J., Bruns, M.A., and Tiedje, J.M. (1996) DNA recovery from soils of diverse composition. Appl Environ Microbiol 62, 316–322.

    PubMed  CAS  Google Scholar 

  19. Muyzer, G., de Waal, E.C., and Uitterlinden, A.G. (1993) Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl Environ Microbiol 59, 695–700.

    PubMed  CAS  Google Scholar 

  20. Park, S.J., Kang, C.H., and Rhee, S.K. (2006) Characterization of the microbial diversity in a Korean solar saltern by 16S rRNA gene analysis. J Microbiol Biotechnol 16, 1640–1645.

    CAS  Google Scholar 

  21. Weisburg, W.G., Barns, S.M., Pelletier, D.A., and Lane, D.J. (1991) 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 173, 697–703.

    PubMed  CAS  Google Scholar 

  22. Verdnick, D., Handran, S., and Pickett, S. (2002) Key considerations for accurate microarray scanning and image analysis. In: Kamberova, G. Ed. DNA Image Analysis: Nuts and Bolts. DNA Press, Salem, MA, pp. 83–98.

    Google Scholar 

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Acknowledgments

This work was supported by the Korea Science and Engineering Foundation (KOSEF) grant R01-2007-000-20806-0 and program 2007-04269 (System development for application of genomic sequence information) funded by the Korean Government (MEST).

Author information

Authors and Affiliations

  1. Department of Microbiology, College of Natural Science, Chungbuk National University, Cheongju, Korea

    Soo-Je Park & Sung-Keun Rhee

  2. Division of Biotechnology, College of Environmental and Bioresource Sciences, Chonbuk National University, Iksan, Korea

    Jong-Chan Chae

Authors
  1. Soo-Je Park
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  2. Jong-Chan Chae
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  3. Sung-Keun Rhee
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Corresponding author

Correspondence to Sung-Keun Rhee .

Editor information

Editors and Affiliations

  1. Biocenter Klein Flottbek, Microbiology & Biotechnology, University of Hamburg, Ohnhorststr. 18, Hamburg, 22609, Germany

    Wolfgang R. Streit

  2. Institute of Microbiology and Genetics, Dept. of Genomic & Applied Microbiology, Georg August University, Grisebachstraße 8, Göttingen, 37077, Germany

    Rolf Daniel

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© 2010 Humana Press

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Park, SJ., Chae, JC., Rhee, SK. (2010). Application of DNA Microarray for Screening Metagenome Library Clones. In: Streit, W., Daniel, R. (eds) Metagenomics. Methods in Molecular Biology, vol 668. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-60761-823-2_22

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  • DOI: https://doi.org/10.1007/978-1-60761-823-2_22

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  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-60761-822-5

  • Online ISBN: 978-1-60761-823-2

  • eBook Packages: Springer Protocols

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