Skip Navigation

This Article
Right arrow Full Text Freely available
Right arrow Print PDF (955K) Freely available
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in ISI Web of Science
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Search for citing articles in:
ISI Web of Science (75)
Right arrowRequest Permissions
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Wuyts, J.
Right arrow Articles by De Wachter, R.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Wuyts, J.
Right arrow Articles by De Wachter, R.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Nucleic Acids Research, 2000, Vol. 28, No. 23 4698-4708
© 2000 Oxford University Press

Comparative analysis of more than 3000 sequences reveals the existence of two pseudoknots in area V4 of eukaryotic small subunit ribosomal RNA

Jan Wuyts1, Peter De Rijk1, Yves Van de Peer1,2, Greet Pison3, Peter Rousseeuw3 and Rupert De Wachter1,*

1Departement Biochemie, Universiteit Antwerpen (UIA), Universiteitsplein 1, B 2610 Antwerpen, Belgium, 2Fakultät Biologie, Universität Konstanz, Postfach 5560 M618, D-78457 Konstanz, Germany and 3Departement Wiskunde en Informatica, Universiteit Antwerpen (UIA), Universiteitsplein 1, B 2610 Antwerpen, Belgium

The secondary structure of V4, the largest variable area of eukaryotic small subunit ribosomal RNA, was re-examined by comparative analysis of 3253 nucleotide sequences distributed over the animal, plant and fungal kingdoms and a diverse set of protist taxa. An extensive search for compensating base pair substitutions and for base covariation revealed that in most eukaryotes the secondary structure of the area consists of 11 helices and includes two pseudoknots. In one of the pseudoknots, exchange of base pairs between the two stems seems to occur, and covariation analysis points to the presence of a base triple. The area also contains three potential insertion points where additional hairpins or branched structures are present in a number of taxa scattered throughout the eukaryotic domain.

* To whom correspondence should be addressed. Tel: +32 3 8202319; Fax: +32 3 8202248; Email: dwachter{at}uia.ua.ac.be


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Proc R Soc BHome page
M. J Raupach, C. Mayer, M. Malyutina, and J.-W. Wagele
Multiple origins of deep-sea Asellota (Crustacea: Isopoda) from shallow waters revealed by molecular data
Proc R Soc B, March 7, 2009; 276(1658): 799 - 808.
[Abstract] [Full Text] [PDF]

Home page
 Appl. Environ. Microbiol.Home page
C. Baschien, W. Manz, T. R. Neu, L. Marvanova, and U. Szewzyk
In Situ Detection of Freshwater Fungi in an Alpine Stream by New Taxon-Specific Fluorescence In Situ Hybridization Probes
Appl. Envir. Microbiol., October 15, 2008; 74(20): 6427 - 6436.
[Abstract] [Full Text] [PDF]

Home page
 Am. J. Bot.Home page
A. A. Gontcharov and M. Melkonian
In search of monophyletic taxa in the family Desmidiaceae (Zygnematophyceae, Viridiplantae): the genus Cosmarium
Am. J. Botany, September 1, 2008; 95(9): 1079 - 1095.
[Abstract] [Full Text] [PDF]

Home page
 Proc R Soc BHome page
D. Bass, A. Howe, N. Brown, H. Barton, M. Demidova, H. Michelle, L. Li, H. Sanders, S. C Watkinson, S. Willcock, et al.
Yeast forms dominate fungal diversity in the deep oceans
Proc R Soc B, December 22, 2007; 274(1629): 3069 - 3077.
[Abstract] [Full Text] [PDF]

Home page
 MicrobiologyHome page
R. Ueno, V. A. R. Huss, N. Urano, and S. Watabe
Direct evidence for redundant segmental replacement between multiple 18S rRNA genes in a single Prototheca strain
Microbiology, November 1, 2007; 153(11): 3879 - 3893.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
S. Smit, J. Widmann, and R. Knight
Evolutionary rates vary among rRNA structural elements
Nucleic Acids Res., May 11, 2007; 35(10): 3339 - 3354.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
M. Holterman, A. van der Wurff, S. van den Elsen, H. van Megen, T. Bongers, O. Holovachov, J. Bakker, and J. Helder
Phylum-Wide Analysis of SSU rDNA Reveals Deep Phylogenetic Relationships among Nematodes and Accelerated Evolution toward Crown Clades
Mol. Biol. Evol., September 1, 2006; 23(9): 1792 - 1800.
[Abstract] [Full Text] [PDF]

Home page
 Proc R Soc BHome page
C. Berney and J. Pawlowski
A molecular time-scale for eukaryote evolution recalibrated with the continuous microfossil record
Proc R Soc B, August 7, 2006; 273(1596): 1867 - 1872.
[Abstract] [Full Text] [PDF]

Home page
 Appl. Environ. Microbiol.Home page
C. Lovejoy, R. Massana, and C. Pedros-Alio
Diversity and distribution of marine microbial eukaryotes in the arctic ocean and adjacent seas.
Appl. Envir. Microbiol., May 1, 2006; 72(5): 3085 - 3095.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
H. Gao, M. J. Ayub, M. J. Levin, and J. Frank
The structure of the 80S ribosome from Trypanosoma cruzi reveals unique rRNA components
PNAS, July 19, 2005; 102(29): 10206 - 10211.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
S. Pasquali, H. H. Gan, and T. Schlick
Modular RNA architecture revealed by computational analysis of existing pseudoknots and ribosomal RNAs
Nucleic Acids Res., March 3, 2005; 33(4): 1384 - 1398.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
S. I. Nikolaev, C. Berney, J. F. Fahrni, I. Bolivar, S. Polet, A. P. Mylnikov, V. V. Aleshin, N. B. Petrov, and J. Pawlowski
From the Cover: The twilight of Heliozoa and rise of Rhizaria, an emerging supergroup of amoeboid eukaryotes
PNAS, May 25, 2004; 101(21): 8066 - 8071.
[Abstract] [Full Text] [PDF]

Home page
 RNAHome page
G. ALKEMAR and O. NYGARD
Secondary structure of two regions in expansion segments ES3 and ES6 with the potential of forming a tertiary interaction in eukaryotic 40S ribosomal subunits
RNA, March 1, 2004; 10(3): 403 - 411.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
A. A. Gontcharov, B. Marin, and M. Melkonian
Are Combined Analyses Better Than Single Gene Phylogenies? A Case Study Using SSU rDNA and rbcL Sequence Comparisons in the Zygnematophyceae (Streptophyta)
Mol. Biol. Evol., March 1, 2004; 21(3): 612 - 624.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
J. F. Fahrni, I. Bolivar, C. Berney, E. Nassonova, A. Smirnov, and J. Pawlowski
Phylogeny of Lobose Amoebae Based on Actin and Small-Subunit Ribosomal RNA Genes
Mol. Biol. Evol., November 1, 2003; 20(11): 1881 - 1886.
[Abstract] [Full Text] [PDF]

Home page
 RNAHome page
G. ALKEMAR and O. NYGARD
A possible tertiary rRNA interaction between expansion segments ES3 and ES6 in eukaryotic 40S ribosomal subunits
RNA, January 1, 2003; 9(1): 20 - 24.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
G. Caetano-Anolles
Tracing the evolution of RNA structure in ribosomes
Nucleic Acids Res., June 1, 2002; 30(11): 2575 - 2587.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
J. Wuyts, Y. Van de Peer, T. Winkelmans, and R. De Wachter
The European database on small subunit ribosomal RNA
Nucleic Acids Res., January 1, 2002; 30(1): 183 - 185.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
J. Wuyts, Y. Van de Peer, and R. De Wachter
Distribution of substitution rates and location of insertion sites in the tertiary structure of ribosomal RNA
Nucleic Acids Res., December 15, 2001; 29(24): 5017 - 5028.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.