rrn DB: Documenting the number of rRNA and tRNA genes in bacteria and archaea

Nucleic Acids Research

Volumn 37, Issue SUPPL. 1, 2009, Pages

  Lee, Zarraz May Ping ^a   Bussema III, Carl ^a   Schmidt, Thomas M ^a  

^a Michigan State University ^*  (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL RNA; INTERNAL TRANSCRIBED SPACER; RIBOSOME RNA; RNA 16S; RNA 23S; RNA 5S; TRANSFER RNA;

ARCHAEBACTERIUM; ARTICLE; BACTERIAL GENE; BACTERIAL STRAIN; GENE DUPLICATION; GENE LOCATION; GENE NUMBER; GENETIC DATABASE; GENOME ANALYSIS; INTERNET; MATHEMATICAL COMPUTING; MICROBIAL GROWTH; MICROBIOLOGY; PHYLOGENY; PREDICTION; PRIORITY JOURNAL; RIBOSOMAL RNA DATABASE; RNA ANALYSIS; TAXONOMY; ARCHAEAL GENE; DATA BASE; GENETICS; GENOMICS; NUCLEIC ACID DATABASE; RNA GENE;

ARCHAEA; BACTERIA (MICROORGANISMS);

DATABASE MANAGEMENT SYSTEMS; DATABASES, NUCLEIC ACID; GENES, ARCHAEAL; GENES, BACTERIAL; GENES, RRNA; GENOMICS; RNA, RIBOSOMAL, 16S;

EID: 58149179980     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkn689     Document Type: Article

References (24)

1. Schuwirth,B.S., Borovinskaya,M.A., Hau,C.W., Zhang,W., Vila-Sanjurjo,A., Holton,J.M. and Cate,J.H. (2005) Structures of the bacterial ribosome at 3.5A resolution. Science, 310, 827-834.
2. Pruesse,E., Quast,C., Knittel,K., Fuchs,B.M., Ludwig,W., Peplies,J. and Glockner,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.
3. Cole,J.R., Chai,B., Farris,R.J., Wang,Q., Kulam-Syed-Mohideen,A.S., McGarrell,D.M., Bandela,A.M., Cardenas,E., Garrity,G.M. and Tiedje,J.M. (2007) The ribosomal database project (RDP-II): Introducing myRDP space and quality controlled public data. Nucleic Acids Res., 35, D169-D172.
4. Desantis,T.Z., Hugenholtz,P., Larsen,N., Rojas,M., Brodie,E.L., Keller,K., Huber,T., Dalevi,D., Hu,P. and Andersen,G.L. (2006) Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl. Environ. Microbiol., 72, 5069-5072.
5. Crosby,L.D. and Criddle,C.S. (2003) Understanding bias in microbial community analysis techniques due to rrn operon copy number heterogeneity. Biotechniques, 34, 790-794, 796, 798 passim.
6. Klappenbach,J.A., Dunbar,J.M. and Schmidt,T.M. (2000) rRNA operon copy number reflects ecological strategies of bacteria. Appl. Environ. Microbiol., 66, 1328-1333.
7. Stevenson,B.S. and Schmidt,T.M. (1998) Growth rate-dependent accumulation of RNA from plasmid-borne rRNA operons in Escherichia coli. J. Bacteriol., 180, 1970-1972.
8. Eichorst,S.A., Breznak,J.A. and Schmidt,T.M. (2007) Isolation and characterization of soil bacteria that define Terriglobus gen. nov., in the phylum Acidobacteria. Appl. Environ. Microbiol., 73, 2708-2717.
9. Cavicchioli,R., Ostrowski,M., Fegatella,F., Goodchild,A. and Guixa-Boixereu,N. (2003) Life under nutrient limitation in oligotrophic marine environments: An eco/physiological perspective of Sphingopyxis alaskensis (formerly Sphingomonas alaskensis). Microb. Ecol. 45, 203-217.
10. Klappenbach,J.A., Saxman,P.R., Cole,J.R. and Schmidt,T.M. (2001) rrndb: the ribosomal RNA operon copy number database. Nucleic Acids Res., 29, 181-184.
11. Einen,J., Thorseth,I.H. and Ovreas,L. (2008) Enumeration of archaea and bacteria in seafloor basalt using real-time quantitative PCR and fluorescence microscopy. FEMS Microbiol. Lett., 282, 182-187.
12. Wang,Y., Zhang,Z. and Ramanan,N. (1997) The actinomycete Thermobispora bispora contains two distinct types of transcriptionally active 16S rRNA genes. J. Bacteriol., 179, 3270-3276.
13. Ojaimi,C., Davidson,B.E., Saint Girons,I. and Old,I.G. (1994) Conservation of gene arrangement and an unusual organization of rRNA genes in the linear chromosomes of the Lyme disease spirochaetes Borrelia burgdorferi, B. garinii and B. afzelii. Microbiology, 140(Pt 11), 2931-2940.
14. Fukunaga,M., Masuzawa,T., Okuzako,N., Mifuchi,I. and Yanagihara,Y. (1990) Linkage of ribosomal RNA genes in Leptospira. Microbiol. Immunol., 34, 565-573.
15. Ree,H.K. and Zimmermann,R.A. (1990) Organization and expression of the 16S, 23S and 5S ribosomal RNA genes from the archaebacterium Thermoplasma acidophilum. Nucleic Acids Res., 18, 4471-4478.
16. Waters,E., Hohn,M.J., Ahel,I., Graham,D.E., Adams,M.D., Barnstead,M., Beeson,K.Y., Bibbs,L., Bolanos,R., Keller,M. et al. (2003) The genome of Nanoarchaeum equitans: Insights into early archaeal evolution and derived parasitism. Proc. Natl Acad. Sci. USA, 100, 12984-12988.
17. Stewart,F.J. and Cavanaugh,C.M. (2007) Intragenomic variation and evolution of the internal transcribed spacer of the rRNA operon in bacteria. J. Mol. Evol., 65, 44-67.
18. Malimas,T., Yukphan,P., Takahashi,M., Potacharoen,W., Tanasupawat,S., Nakagawa,Y., Tanticharoen,M. and Yamada,Y. (2006) Heterogeneity of strains assigned to Gluconobacter frateurii Mason and Claus 1989 based on restriction analysis of 16S-23S rDNA internal transcribed spacer regions. Biosci. Biotechnol. Biochem., 70, 684-690.
19. Dethlefsen,L. and Schmidt,T.M. (2007) Performance of the translational apparatus varies with the ecological strategies of bacteria. J. Bacteriol., 189, 3237-3245.
20. Vezzi,A., Campanaro,S., D'Angelo,M., Simonato,F., Vitulo,N., Lauro,F.M., Cestaro,A., Malacrida,G., Simionati,B., Cannata,N. et al. (2005) Life at depth: Photobacterium profundum genome sequence and expression analysis. Science, 307, 1459-1461.
21. Hashimoto,J.G., Stevenson,B.S. and Schmidt,T.M. (2003) Rates and consequences of recombination between rRNA operons. J. Bacteriol., 185, 966-972.
22. Shaw,A.K., Halpern,A.L., Beeson,K., Tran,B., Venter,J.C. and Martiny,J.B.H. (2008) It's all relative: Ranking the diversity of aquatic bacterial communities. Environ. Microbiol., 10, 2200-2210.
23. Acinas,S.G., Marcelino,L.A., Klepac-Ceraj,V. and Polz,M.F. (2004) Divergence and redundancy of 16S rRNA sequences in genomes with multiple rrn operons. J. Bacteriol., 186, 2629-2635.
24. Acinas,S.G., Klepac-Ceraj,V., Hunt,D.E., Pharino,C., Ceraj,I., Distel,D.L. and Polz,M.F. (2004) Fine-scale phylogenetic architecture of a complex bacterial community. Nature, 430, 551-554.