In situ accessibility of small-subunit rRNA of members of the domains Bacteria, Archaea, and Eucarya to Cy3-labeled oligonucleotide probes

Applied and Environmental Microbiology

Volumn 69, Issue 3, 2003, Pages 1748-1758

  Behrens, Sebastian ^a   Rühland, Caroline ^a   Inácio, João ^c   Huber, Harald ^b   Fonseca, A ^c   Spencer Martins, I ^c   Fuchs, Bernhard M ^a   Amann, Rudolf ^a  

^a MAX PLANCK INSTITUTE FOR MARINE MICROBIOLOGY   (Germany)

^b UNIVERSITY OF REGENSBURG   (Germany)

^c UNIVERSIDADE NOVA DE LISBOA   (Portugal)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL MEMBRANES; DATA REDUCTION; RNA;

FLOW CYTOMETRY;

BACTERIA;

OLIGONUCLEOTIDE; RIBOSOME RNA;

MICROORGANISM;

ARCHAEBACTERIUM; ARTICLE; BACTERIAL STRAIN; CONTROLLED STUDY; CRENARCHAEOTA; ESCHERICHIA COLI; FLOW CYTOMETRY; FLUORESCENCE; GRAM NEGATIVE BACTERIUM; IN SITU HYBRIDIZATION; METALLOSPHAERA SEDULA; NONHUMAN; PHYLOGENY; PROKARYOTE; RIBOSOME; SACCHAROMYCES CEREVISIAE; STANDARDIZATION;

BACTERIA; CARBOCYANINES; CRENARCHAEOTA; ESCHERICHIA COLI; FLOW CYTOMETRY; FLUORESCENT DYES; IN SITU HYBRIDIZATION, FLUORESCENCE; OLIGONUCLEOTIDE PROBES; RNA, RIBOSOMAL, 16S; RNA, RIBOSOMAL, 18S; SACCHAROMYCES CEREVISIAE;

ARCHAEA; BACTERIA (MICROORGANISMS); CRENARCHAEOTA; ESCHERICHIA COLI; GAMMAPROTEOBACTERIA; METALLOSPHAERA; METALLOSPHAERA SEDULA; NEGIBACTERIA; PIRELLULA; PIRELLULA SP.; PLANCTOMYCETES; PROKARYOTA; PROTEOBACTERIA; SACCHAROMYCES; SACCHAROMYCES CEREVISIAE;

EID: 0344406194     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/AEM.69.3.1748-1758.2003     Document Type: Article

References (24)

1. Amann, R. I., L. Krumholz, and D. A. Stahl. 1990. Fluorescent-oligonucleotide probing of whole cells for determinative, phylogenetic, and environmental studies in microbiology. J. Bacteriol. 172:762-770.
2. Ban, N., P. Nissen, J. Hansen, M. Capel, P. B. Moore, and T. A. Steitz. 1999. Placement of protein and RNA structures into a 5 Å-resolution map of the 50S ribosomal subunit. Nature 400:841-847.
3. Brosius, J., T. J. Dull, D. D. Sleeter, and H. F. Noller. 1981. Gene organization and primary structure of a ribosomal RNA operon from Escherichia coli. J. Mol. Biol. 148:107-127.
4. Cai, J., I. N. Roberts, and M. D. Collins. 1996. Phylogenetic relationships among members of the Ascomycetous yeast genera Brettanomyces, Debaryomyces, Dekkera, and Kluyveromyces deduced by small-subunit rRNA gene sequences. Int. J. Syst. Bacteriol. 46:525-549.
5. Cannone, J. J., S. Subramanian, M. N. Schnare, J. R. Collett, L. M. D'Souza, Y. Du, B. Feng, N. Lin, L. V. Madabusi, K. M. Muller, N. Pande, Z. Shang, N. Yu, and R. R. Gutell. 2002. The Comparative RNA Web (CRW) site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs. BMC Bioinformatics 3:15.
6. Clemons, W. M., J. L. C. May, B. T. Wimberly, J. P. McCutcheon, M. S. Capel, and V. Ramakrishnan. 1999. Structure of a bacterial 30S ribosomal subunit at 5.5 Å resolution. Nature 400:833-840.
7. Crockett, A. O., and C. T. Wittwer. 2001. Fluorescein-labeled oligonucleotides for real-time PCR: using the inherent quenching of deoxyguanosine nucleotides. Anal. Biochem. 290:89-97.
8. DeLong, E. F., G. S. Wickham, and N. R. Pace. 1989. Phylogenetic stains: ribosomal RNA-based probes for the identification of single microbial cells. Science 243:1360-1363.
9. Fuchs, B. M., F. O. Glöckner, J. Wulf, and R. Amann. 2000. Unlabeled helper oligonucleotides increase the in situ accessibility of 16S rRNA for fluorescently labeled oligonucleotide probes. Appl. Environ. Microbiol. 66: 3603-3607.
10. Fuchs, B. M., K. Syutsubo, W. Ludwig, and R. Amann. 2001. In situ accessibility of the Escherichia coli 23S rRNA for fluorescently labeled oligonucleotide probes. Appl. Environ. Microbiol. 67:961-968.
11. Fuchs, B. M., G. Wallner, W. Beisker, I. Schwippl, W. Ludwig, and R. Amann. 1998. Flow cytometric analysis of the in situ accessibility of Escherichia coli 16S rRNA for fluorescently labeled oligonucleotide probes. Appl. Environ. Microbiol. 64:4973-4982.
12. Huber, G., C. Spinnler, A. Gambacorta, and K. O. Stetter. 1989. Metallosphaera sedula gen. and sp. nov. Represents a new genus of aerobic, metal-mobilizing, thermoacidophilic Archaebacteria. Syst. Appl. Microbiol. 12:38-47.
13. Norman, D. G., R. J. Grainger, D. Uhrin, and D. M. J. Lilley, 2000. Location of cyanine-3 on double-stranded DNA: importance for fluorescence resonance energy transfer studies. Biochemistry 39:6317-6324.
14. Olsen, G. J., D. J. Lane, S. J. Giovannoni, N. R. Pace, and D. A. Stahl. 1986. Microbial ecology and evolution: a ribosomal rRNA approach. Annu. Rev. Microbiol. 40:337-365.
15. Sampaio, J. P., M. Gadanho, and R. Bauer. 2001. Taxonomic studies on the genus Cystofilobasidium: description of Cystofilobasidium ferigula sp. nov. and clarification of the status of Cystofilobasidium lari-marini. Int. J. Syst. Bacteriol. 51:221-229.
16. Schlesner, H. 1994. The development of media suitable for the microorganisms morphologically resembling Planctomyces spp., Pirellula spp., and other Planctomycetales from various aquatic habitats using dilute media. Syst. Appl. Microbiol. 17:135-145.
17. Schluenzen, F., A. Tocilj, R. Zarivach, J. Harms, M. Gluehmann, D. Janell, A. Bashan, H. Bartels, I. Agmon, F. Franceschi, and A. Yonath. 2000. Structure of functionally activated small ribosomal subunit at 3.3 Å resolution. Cell 102:15-623.
18. Suggs, S. V., T. Hirose, T. Miyake, E. H. Kawashima, M. J. Johnson, K. Itakura, and R. B. Wallace. 1981. Use of synthetic oligodeoxyribonucleotides for the isolation of specific cloned DNA sequences, p. 683-693. In D. Brown and C. F. Fox (ed.), Developmental biology using purified genes. Academic Press, Inc., New York, N.Y.
19. Torimura, M., S. Kurata, K. Yamada, T. Yokomaku, Y. Kamagata, T. Kanagawa, and R. Kurane. 2001. Fluorescence-quenching phenomenon by photoinduced electron transfer between a fluorescent dye and a nucleotide base. Anal. Sci. 17:155-160.
20. Tung, C. S., S. Joseph, and K. Y. Sanbonmatsu. 2002. All-atom homology model of the Escherichia coli 30S ribosomal subunit. Nat. Struct. Biol. 9:750-755.
21. Wallner, G., R. Amann, and W. Beisker. 1993. Optimizing fluorescent in situ-hybridization with rRNA-targeted oligonucleotide probes for flow cytometric identification of microorganisms. Cytometry 14:136-143.
22. Wallner, G., B. Fuchs, W. Beisker, S. Spring, and R. Amann. 1997. Flow cytometric sorting of microorganisms for molecular analysis. Appl. Environ. Microbiol. 63:4223-4331.
23. Wimberly, B. T., D. E. Brodersen, W. M. Clemons, R. J. Morgan-Warren, A. P. Carter, C. Vonrhein, T. Hartsch, and V. Ramakrishnan. 2000. Structure of the 30S ribosomal subunit. Nature 407:327-339.
24. Zahavy, E., and M. A. Fox. 1999. Photophysical quenching mediated by guanine groups in pyrenyl-N-alkylbutanoamide end-labeled oligonucleotides. J. Phys. Chem. 103:9321-9327.