Diversity of 5S rRNA genes within individual prokaryotic genomes

FEMS Microbiology Letters

Volumn 335, Issue 1, 2012, Pages 11-18

  Pei, Anna ^a   Li, Hongru ^b   Oberdorf, William E ^c   Alekseyenko, Alexander V ^c   Parsons, Tamasha ^c   Yang, Liying ^c   Gerz, Erika A ^c   Lee, Peng ^c,d   Xiang, Charlie ^e   Nossa, Carlos W ^f   Pei, Zhiheng ^c,d  

^a NEW YORK UNIVERSITY   (United States)

^b MOUNT SINAI SCHOOL OF MEDICINE   (United States)

^c NEW YORK UNIVERSITY SCHOOL OF MEDICINE   (United States)

^d DEPARTMENT OF VETERANS AFFAIRS   (United States)

^e ZHEJIANG UNIVERSITY SCHOOL OF MEDICINE   (China)

^f RICE UNIVERSITY   (United States)

Author keywords

5S rRNA; Ribosomal constraints; RRNA diversity

Indexed keywords

5S RRNA GENE; ARTICLE; BACTERIAL GENOME; GENETIC VARIABILITY; NONHUMAN; OPERON; PRIORITY JOURNAL; PROKARYOTE; PROTEIN SECONDARY STRUCTURE; RIBOSOME; RNA GENE; SPECIES DIVERSITY; SPECIES RICHNESS;

BACTERIA; DATABASES, NUCLEIC ACID; DNA, RIBOSOMAL; GENETIC VARIATION; GENOME, BACTERIAL; NUCLEIC ACID CONFORMATION; RNA, RIBOSOMAL, 5S;

PROKARYOTA;

EID: 84866180848     PISSN: 03781097     EISSN: 15746968     Source Type: Journal    
DOI: 10.1111/j.1574-6968.2012.02632.x     Document Type: Article

References (24)

1. Abdulkarim F & Hughes D (1996) Homologous recombination between the tuf genes of Salmonella Typhimurium. J Mol Biol 260: 506-522.
2. Acinas SG, Marcelino LA, Klepac-Ceraj V & Polz MF (2004) Divergence and redundancy of 16S rRNA sequences in genomes with multiple rrn operons. J Bacteriol 186: 2629-2635.
3. Babin P, Dolan M, Wollenzien P & Gutell RR (1999) Identity and geometry of a base triple in 16S rRNA determined by comparative sequence analysis and molecular modeling. RNA 5: 1430-1439.
4. Clayton RA, Sutton G, Hinkle PS, Bult C & Fields C (1995) Intraspecific variation in small subunit rRNA sequences in GenBank: why single sequences may not adequately represent prokaryotic taxa. Int J Syst Bacteriol 45: 595-599.
5. Coenye T & Vandamme P (2003) Intragenomic heterogeneity between multiple 16S ribosomal RNA operons in sequenced bacterial genomes. FEMS Microbiol Lett 228: 45-49.
6. De Rijk P & De Wachter R (1997) RnaViz, a program for the visualization of RNA secondary structure. Nucleic Acids Res 25: 4679-4684.
7. Doolittle WF (1999) Phylogenetic classification and the universal tree. Science 284: 2124-2129.
8. Eigen M, Lindemann B, Winkler-Oswatitsch R & Clarke CH (1985) Pattern analysis of 5S rRNA. P Natl Acad Sci USA 82: 2437-2441.
9. Gunderson JH, Sogin ML, Wollet G, Hollingdale M, de la Cruz VF, Waters AP & McCutchan TF (1987) Structurally distinct, stage-specific ribosomes occur in Plasmodium Science 238: 933-937.
10. Gutell RR, Noller HF & Woese CR (1986) Higher order structure in ribosomal RNA. EMBO J 5: 1111-1113.
11. Hashimoto JG, Stevenson BS & Schmidt TM (2003) Rates and consequences of recombination between rRNA operons. J Bacteriol 185: 966-972.
12. Küntzel H, Heidrich M & Piechulla B (1981) Phylogenetic tree derived from bacterial, cytosol and organelle 5S rRNA sequences. Nucleic Acids Res 9: 1451-1461.
13. Lee ZM, Bussema C III & Schmidt TM (2009) rrnDB: documenting the number of rRNA and tRNA genes in bacteria and archaea. Nucleic Acids Res 37: D489-D493.
14. Mashkova TD, Serenkova TL, Mazo AM, Avdonina TA, Timofeyeva Y & Kisselev LL (1981) The primary structure of oocyte and somatic 5S rRNAs from the loach Misgurnus fossilis Nucleic Acids Res 9: 2141-2151.
15. Mathews DH, Disney MD, Childs JL, Schroeder SJ, Zuker M & Turner DH (2004) Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure. P Natl Acad Sci USA 101: 7287-7292.
16. Pei A, Nossa CW, Chokshi P, Blaser MJ, Yang L, Rosmarin DM & Pei Z (2009) Diversity of 23S rRNA genes within individual prokaryotic genomes. PLoS ONE 4: e5437.
17. Pei A, Oberdorf WE, Nossa CW, Agarwal A, Chokshi P, Gerz EA, Jin Z, Lee P, Yang L & Pei Z (2010) Diversity of 16S rRNA genes within individual prokaryotic genomes. Appl Environ Microbiol 76: 3886-3897.
18. Thompson JD, Higgins DG & Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22: 4673-4680.
19. Wegnez MR, Monier R & Denis H (1972) Sequence heterogeneity of 5S rRNA in Xenopus laevis FEBS Lett 25: 13-21.
20. Woese CR (1987) Bacterial evolution. Microbiol Rev 51: 221-271.
21. Woese CR (1998) The universal ancestor. P Natl Acad Sci USA 95: 6854-6859.
22. Woese CR & Gutell RR (1989) Evidence for several higher order structural elements in ribosomal RNA. P Natl Acad Sci USA 86: 3119-3122.
23. Woese CR, Kandler O & Wheelis ML (1990) Towards a natural system of organisms: proposal for the domains Archaea, Bacteria and Eucarya. P Natl Acad Sci USA 87: 4576-4579.
24. Wonacott TH & Wonacott RJ (1990) Introductory Statistics. John Wiley & Son, New York, NY.