Phylogenetic screening of a bacterial, metagenomic library using homing endonuclease restriction and marker insertion

Nucleic Acids Research

Volumn 37, Issue 21, 2009, Pages

  Yung, Pui Yi ^a   Burke, Catherine ^a   Lewis, Matt ^b   Egan, Suhelen ^a   Kjelleberg, Staffan ^a   Thomas, Torsten ^a  

^a UNIVERSITY OF NEW SOUTH WALES   (Australia)

^b J CRAIG VENTER INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DEOXYRIBONUCLEASE I; DNA FRAGMENT; RIBOSOME RNA; RNA 16S; RNA 23S; DEOXYRIBONUCLEASE; ENDODEOXYRIBONUCLEASE I CEUI; ENDODEOXYRIBONUCLEASE I-CEUI; RESTRICTION ENDONUCLEASE;

ARTICLE; CONTROLLED STUDY; CYMBASTELA CONCENTRICA; DNA FRAGMENTATION; DNA SEQUENCE; ESCHERICHIA COLI; GENE INSERTION; GENE LIBRARY; MARINE SPECIES; MARKER GENE; METAGENOMICS; MOLECULAR CLONING; MOLECULAR PHYLOGENY; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; RNA CLEAVAGE; SPONGE (PORIFERA); TAXONOMIC IDENTIFICATION; ANIMAL; BACTERIAL GENOME; BACTERIUM; CLASSIFICATION; GENETIC MARKER; GENETICS; METHODOLOGY; MICROBIOLOGY; MOLECULAR GENETICS; PHYLOGENY; RNA GENE;

BACTERIA (MICROORGANISMS); CYMBASTELA CONCENTRICA;

ANIMALS; BACTERIA; BASE SEQUENCE; DNA RESTRICTION ENZYMES; ENDODEOXYRIBONUCLEASES; GENES, RRNA; GENETIC MARKERS; GENOME, BACTERIAL; GENOMIC LIBRARY; METAGENOMICS; MOLECULAR SEQUENCE DATA; PHYLOGENY; PORIFERA; RNA, RIBOSOMAL, 23S;

EID: 75749089679     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkp746     Document Type: Article

References (50)

1. Ferrer, M., Beloqui, A., Timmis, K.N. and Golyshin, P.N. (2009) Metagenomics for mining new genetic resources of microbial communities. J. Mol. Microbiol. Biotechnol., 16, 109-123.
2. Handelsman, J. (2004) Metagenomics: application of genomics to uncultured microorganisms. Microbiol. Mol. Biol. Rev., 68, 669-685.
3. Li, X. and Qin, L. (2005) Metagenomics-based drug discovery and marine microbial diversity. Trends Biotechnol., 23, 539-543.
4. Streit, W.R. and Schmitz, R.A. (2004) Metagenomics - the key to the uncultured microbes. Curr. Opin. Microbiol., 7, 492-498.
5. Rusch, D.B., Halpern, A.L., Sutton, G., Heidelberg, K.B., Williamson, S., Yooseph, S., Wu, D., Eisen, J.A., Hoffman, J.M., Remington, K. et al. (2007) The Sorcerer II Global Ocean Sampling expedition: northwest Atlantic through eastern tropical Pacific. PLoS Biol., 5, e77:0398-0431.
6. Venter, J.C., Remington, K., Heidelberg, J.F., Halpern, A.L., Rusch, D., Eisen, J.A., Wu, D., Paulsen, I., Nelson, K.E., Nelson, W. et al. (2004) Environmental genome shotgun sequencing of the Sargasso Sea. Nature, 304, 66-74.
7. Martin-Cuadrado, A.B., Rodriguez-Valera, F., Moreira, D., Alba, J.C., Ivars-Martínez, E., Henn, M.R., Talla, E. and López-García, P. (2008) Hindsight in the relative abundance, metabolic potential and genome dynamics of uncultivated marine archaea from comparative metagenomic analyses of bathypelagic plankton of different oceanic regions. ISME J., 2, 865-886.
8. Allen, H.K., Moe, L.A., Rodbumrer, J., Gaarder, A. and Handelsman, J. (2009) Functional metagenomics reveals diverse beta-lactamases in a remote Alaskan soil. ISME J., 3, 243-251.
9. Daniel, R. (2005) The metagenomics of soil. Nat. Rev. Microbiol., 3, 470-478.
10. Schlüter, A., Bekel, T., Diaz, N.N., Dondrup, M., Eichenlaub, R., Gartemann, K.H., Krahn, I., Krause, L., Krömeke, H., Kruse, O. et al. (2008) The metagenome of a biogas-producing microbial community of a production-scale biogas plant fermenter analysed by the 454-pyrosequencing technology. J. Biotechnol., 136, 77-90.
11. Tringe, S.G., Zhang, T., Liu, X., Yu, Y., Lee, W.H., Yap, J., Yao, F., Suan, S.T., Ing, S.K., Haynes, M. et al. (2008) The airborne metagenome in an indoor urban environment. PLoS ONE, 3, e1862.
12. Fieseler, L., Quaiser, A., Schleper, C. and Hentschel, U. (2006) Analysis of the first genome fragment from the marine spongeassociated, novel cadidate phylum Poribacteria by environmental genomics. Environ. Microbiol., 8, 612-624.
13. Jones, B.V., Begley, M., Hill, C., Gahan, C.G. and Marchesi, J.R. (2008) Functional and comparative metagenomic analysis of bile salt hydrolase activity in the human gut microbiome. Proc. Natl Sci. USA, 105, 13580-13585.
14. Warnecke, F., Luginbühl, P., Ivanova, N., Ghassemian, M., Richardson, T., Stege, J., Cayouette, M., McHardy, A., Djordjevic, G., Aboushadi, N. et al. (2007) Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite. Nature, 450, 560-565.
15. Dinsdale, E., Edwards, R., Hall, D., Angly, F., Breitbart, M., Brulc, J., Furlan, M., Desnues, C., Haynes, M., Li, L. et al. (2008) Functional metagenomic profiling of nine biomes. Nature, 452, 629-632.
16. Mardis, E. (2008) Next-generation DNA sequencing methods. Annu. Rev. Genomics Hum Genet., 9, 387-402.
17. Tringe, S., von Mering, C., Kobayashi, A., Salamov, A., Chen, K., Chang, H., Podar, M., Short, J., Mathur, E., Detter, J. et al. (2005) Comparative metagenomics of microbial communities. Science, 308, 554-557.
18. Kunin, V., Copeland, A., Lapidus, A., Mavromatis, K. and Hugenholtz, P. (2008) A bioinformatician's guide to metagenomics. Microbiol. Mol. Biol. Rev., 72, 557-578.
19. McHardy, A.C., Martin, H.G., Tsirigos, A., Hugenholtz, P. and Rigoutsos, I. (2007) Accurate phylogenetic classification of variablelength DNA fragments Nat. Methods, 4, 63-72.
20. Teeling, H., Waldman, J., Lombardot, T., Bauer, M. and Glöckner, F. (2004) TETRA: a web-service and a stand-alone program for the analysis and comparison of tetranucleotide usage patterns in DNA sequences. BMC Bioinformatics, 5, 163.
21. Diaz, N., Krause, L., Goesmann, A., Niehaus, K. and Nattkemper, T. (2009) TACOA: taxonomic classification of environmental genomic fragments using a kernelized nearest neighbor approach. BMC Bioinformatics, 10, 56.
22. Beja, O., Suzuki, M.T., Koonin, E.V., Aravind, L., Hadd, A., Nguyen, L.P., Villacorta, R., Amjadi, M., Garrigues, C., Jovanovich, S.B. et al. (2000) Construction and analysis of bacterial artificial chromosome libraries from a marine microbial assemblage. Environ. Microbiol., 2, 516-529.
23. Moreira, D., Rodríguez-Valera, F. and López-García, P. (2006) Metagenomic analysis of mesopelagic Antarctic plankton reveals a novel deltaproteobacterial group. Microbiology, 152, 505-517.
24. Stein, J.L., Marsh, T.L., Yu, K.Y., Shizuya, H. and DeLong, E.F. (1996) Characterization of uncultivated prokaryotes: isolation and analysis of a 40-kilobase-pair genome fragment from a planktonic marine archaeon. J. Bacteriol., 178, 591-599.
25. Liles, M.R., Manske, B.F., Bintrim, S.B., Handelsman, J. and Goodman, R.M. (2003) A census of rRNA genes and linked genomic sequences within a soil metagenomic library. Appl. Environ. Microbiol., 69, 2684-2691.
26. Gilbert, J.A., Mühling, M. and Joint, I. (2008) A rare SAR11 fosmid clone confirming genetic variability in the 'Candidatus Pelagibacter ubique' genome. ISME J., 2, 106-116.
27. Meng, J., Wang, F., Zheng, Y., Peng, X., Zhou, H. and Xiao, X. (2009) An uncultivated crenarchaeota contains functional bacteriochlorophyll a synthase. ISME J., 3, 106-116.
28. Martín-Cuadrado, A., López-García, P., Alba, J., Moreira, D., Monticelli, L., Strittmatter, A., Gottschalk, G. and Rodríguez-Valera, F. (2007) Metagenomics of the deep Mediterranean, a warm bathypelagic habitat. PLoS ONE, 2, e914.
29. Quaiser, A., López-García, P., Zivanovic, Y., Henn, M., Rodriguez-Valera, F. and Moreira, D. (2008) Comparative analysis of genome fragments of Acidobacteria from deep Mediterranean plankton. Environ. Micro., 10, 2704-2717.
30. Massana, R., Karniol, B., Pommier, T., Bodaker, I. and Béjà, O. (2008) Metagenomic retrieval of a ribosomal DNA repeat array from an uncultured marine alveolate. Environ. Micro., 10, 1335-1343.
31. Marshall, P. and Lemieux, C. (1992) The I-CeuI endonuclease recognizes a sequnce of 19 base pairs and preferentially cleaves the coding strand of the Chlamydomonas moewusii chloroplast large subunit rRNA gene. Nucleic Acids Res., 20, 6401-6407.
32. Marshall, P. and Lemieux, C. (1991) Cleavage pattern of the homing endomuclease encoded by the fifth intron in the chloroplast large subunit rRNA-encoding gene of Chlamydomonas eugametos. Gene, 104, 241-245.
33. Muyzer, G., Brinkhoff, T., Nübel, U., Santegoeds, C., Schäfer, H. and Wawer, C. (1997) In Akkermans, A.D.L., van Elsas, J.D. and de Bruijn, F.J. (eds), Molecular Microbial Ecology Manual, Vol. 3.4.4. Kluwer, Dordrecht, The Netherlands, pp. 1-27.
34. Hunt, D.E., Klepac-Ceraj, V., Acinas, S.G., Gautier, C., Bertilsson, S. and Polz, M.F. (2006) Evaluation of 23S rRNA PCR primers for use in phylogenetic studies of bacterial diversity. Appl. Environ. Microbiol., 72, 2221-2225.
35. Lane, D.J. (1991) 16S/23S rRNA sequencing. In Stachebrandt, E. and Goodfellow, M. (eds), Nucleic Acid Techniques in Bacterial Systematics. Wiley, Chichester, New York, pp. 115-175.
36. Altschul, S., Gish, W., Miller, W., Myers, E. and Lipman, D. (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403-410.
37. Pruesse, E., Quast, C., Knittel, K., Fuchs, B., Ludwig, W., Peplies, J. and Glöckner, F.O. (2007) SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res., 35, 7188-7196.
38. Ludwig, W., Strunk, O., Westram, R., Richter, L., Meier, H., Yadhukumar., Buchner, A., Lai, T., Steppi, S., Jobb, G. et al. (2004) ARB: a software environment for sequence data. Nucleic Acids Res., 32, 1363-1371.
39. Gordon, D., Abajian, C. and Green, P. (1998) Consed: a graphical tool for sequence finishing. Genome Res., 8, 195-202.
40. Woyke, T., Teeling, H., Ivanova, N., Huntemann, M., Richter, M., Gloeckner, F., Boffelli, D., Anderson, I., Barry, K., Shapiro, H. et al. (2006) Symbiosis insights through metagenomic analysis of a microbial consortium. Nature, 443, 950-955.
41. Eisen, M., Spellman, P., Brown, P. and Botstein, D. (1998) Cluster analysis and display of genome-wide expression patterns. Proc. Natl Acad. Sci. USA, 95, 14863-14868.
42. Nesbø, C.L., Boucher, Y., Dlutek, M. and Doolittle, W.F. (2005) Lateral gene transfer and phylogenetic assignment of environmental fosmid clones. Environ. Microbiol., 7, 2011-2026.
43. Liu, S.-H., Hessel, A. and Sanderson, K.E. (1993) Genomic mapping with I-Ceu I, an intron-encoded endonuclease specific for genes for ribosomal RNA, in Salmonella spp., Escherichia coli, and other bacteria Proc. Natl Acad. Sci. USA, 90, 6874-6878.
44. Aagaard, C., Awayez, M.J. and Garrett, R.A. (1997) Profile of the DNA recognition site of the archaeal homing endonuclease I-DmoI. Nucleic Acids Res., 25, 1523-1530.
45. Jurica, M.S., Monnat, R.J. Jr and Stoddard, B.L. (1998) DNA recognition and cleavage by the LAGLIDADG homing endonuclease i-crei. Mol. Cell, 2, 469-476.
46. Lim, H.K., Chung, E.J., Kim, J.C., Choi, G.J., Jang, K.S., Chung, Y.R., Cho, K.Y. and Lee, S.W. (2005) Characterization of a forest soil metagenome clone that confers indirubin and indigo production on Escherichia coli. Appl. Environ. Microbiol., 71, 7768-7777.
47. Rondon, M.R., August, P.R., Bettermann, A.D., Brady, S.F., Grossman, T.H., Liles, M.R., Loiacono, K.A., Lynch, B.A., MacNeil, I.A., Minor, C. et al. (2000) Cloning the soil metagenome: a strategy for accessing the genetic and functional diversity of uncultured microorganisms. Appl. Environ. Microbiol., 66, 2541-2517.
48. MacNeil, I.A., Tiong, C.L., Minor, C., August, P.R., Grossman, T.H., Loiacono, K.A., Lynch, B.A., Phillips, T., Narula, S., Sundaramoorthi, R. et al. (2001) Expression and isolation of antimicrobial small molecules from soil DNA libraries. J. Mol. Microbiol. Biotechnol., 3, 301-308.
49. Tringe, S. and Hugenholtz, P. (2008) A renaissance for the pioneering 16S rRNA gene. Curr. Opin. Microbiol., 11, 442-446.
50. Arnould, S., Chames, P., Perez, C., Lacroix, E., Duclert, A., Epinat, J., Stricher, F., Petit, A., Patin, A., Guillier, S. et al. (2006) Engineering of large numbers of highly specific homing endonucleases that induce recombination on novel DNA targets. J. Mol. Biol., 355, 443-458.