Distribution of substitution rates and location of insertion sites in the tertiary structure of ribosomal RNA.

The relative substitution rate of each nucleotide site in bacterial small subunit rRNA, large subunit rRNA and 5S rRNA was calculated from sequence alignments for each molecule. Two-dimensional and three-dimensional variability maps of the rRNAs were obtained by plotting the substitution rates on secondary structure models and on the tertiary structure of the rRNAs available from X-ray diffraction results. This showed that the substitution rates are generally low near the centre of the ribosome, where the nucleotides essential for its function are situated, and that they increase towards the surface. An inventory was made of insertions characteristic of the Archaea, Bacteria and Eucarya domains, and for additional insertions present in specific eukaryotic taxa. All these insertions occur at the ribosome surface. The taxon-specific insertions seem to arise randomly in the eukaryotic evolutionary tree, without any phylogenetic relatedness between the taxa possessing them.

[1]  W. Doolittle,et al.  A kingdom-level phylogeny of eukaryotes based on combined protein data. , 2000, Science.

[2]  Y Van de Peer,et al.  The evolution of stramenopiles and alveolates as derived by "substitution rate calibration" of small ribosomal subunit RNA. , 1996, Journal of molecular evolution.

[3]  Yves Van de Peer,et al.  Evolutionary Relationships Among the Eukaryotic Crown Taxa Taking into Account Site-to-Site Rate Variation in 18S rRNA , 1997, Journal of Molecular Evolution.

[4]  Y. van de Peer,et al.  Construction of a variability map for eukaryotic large subunit ribosomal RNA. , 1999, Nucleic acids research.

[5]  R. Gutell,et al.  Comprehensive comparison of structural characteristics in eukaryotic cytoplasmic large subunit (23 S-like) ribosomal RNA. , 1996, Journal of molecular biology.

[6]  R. Garrett,et al.  The importance of highly conserved nucleotides in the binding region of chloramphenicol at the peptidyl transfer centre of Escherichia coli 23S ribosomal RNA. , 1988, The EMBO journal.

[7]  W. Ford Doolittle,et al.  An Updated and Comprehensive rRNA Phylogeny of (Crown) Eukaryotes Based on Rate-Calibrated Evolutionary Distances , 2000, Journal of Molecular Evolution.

[8]  F. Zemlin,et al.  Correlation of the expansion segments in mammalian rRNA with the fine structure of the 80 S ribosome; a cryoelectron microscopic reconstruction of the rabbit reticulocyte ribosome at 21 A resolution. , 1998, Journal of molecular biology.

[9]  John M. Hancock,et al.  Analysis of the Primary Sequence and Secondary Structure of the Unusually Long SSU rRNA of the Soil Bug, Armadillidium vulgare , 1999, Journal of Molecular Evolution.

[10]  J. Neefs,et al.  Compilation of small ribosomal subunit RNA sequences. , 1990, Nucleic acids research.

[11]  H. Philippe,et al.  Evidence for loss of mitochondria in Microsporidia from a mitochondrial-type HSP70 in Nosema locustae. , 1997, Molecular and biochemical parasitology.

[12]  T. Cavalier-smith.  Archaebacteria and Archezoa , 1989, Nature.

[13]  Yves Van de Peer,et al.  The European Large Subunit Ribosomal RNA database , 2000, Nucleic Acids Res..

[14]  N. B. Petrov,et al.  The unusually long small subunit ribosomal RNA gene found in amitochondriate amoeboflagellate Pelomyxa palustris: its rRNA predicted secondary structure and phylogenetic implication. , 2001, Gene.

[15]  Y Van de Peer,et al.  Comparative analysis of more than 3000 sequences reveals the existence of two pseudoknots in area V4 of eukaryotic small subunit ribosomal RNA. , 2000, Nucleic acids research.

[16]  Robin Ray Gutell,et al.  Collection of small subunit (16S- and 16S-like) ribosomal RNA structures , 1993, Nucleic Acids Res..

[17]  Yves Van de Peer,et al.  The European Small Subunit Ribosomal RNA database , 2000, Nucleic Acids Res..

[18]  R. Gutell,et al.  Collection of small subunit (16S- and 16S-like) ribosomal RNA structures: 1994. , 1993, Nucleic acids research.

[19]  Molecular phylogeny. Archaebacteria and Archezoa. , 1989, Nature.

[20]  Miroslawa Z. Barciszewska,et al.  5S ribosomal RNA database Y2K , 2000, Nucleic Acids Res..

[21]  Y Van de Peer,et al.  A quantitative map of nucleotide substitution rates in bacterial rRNA. , 1996, Nucleic acids research.

[22]  J. W. Taylor,et al.  Positions of multiple insertions in SSU rDNA of lichen-forming fungi. , 1995, Molecular biology and evolution.

[23]  M. Sogin,et al.  A mitochondrial-like chaperonin 60 gene in Giardia lamblia: evidence that diplomonads once harbored an endosymbiont related to the progenitor of mitochondria. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[24]  Yves Van de Peer,et al.  Database on the structure of small subunit ribosomal RNA , 1999, Nucleic Acids Res..

[25]  T. Earnest,et al.  Crystal Structure of the Ribosome at 5.5 Å Resolution , 2001, Science.

[26]  R. Gutell,et al.  A compilation of large subunit (23S and 23S-like) ribosomal RNA structures: 1993. , 1992, Nucleic acids research.

[27]  T. Steitz,et al.  The complete atomic structure of the large ribosomal subunit at 2.4 A resolution. , 2000, Science.

[28]  John M. Hancock,et al.  How slippage-derived sequences are incorporated into rRNA variable-region secondary structure: implications for phylogeny reconstruction. , 2000, Molecular phylogenetics and evolution.

[29]  Yves Van de Peer,et al.  Database on the structure of large subunit ribosomal RNA , 1999, Nucleic Acids Res..

[30]  M. Hasegawa,et al.  Secondary absence of mitochondria in Giardia lamblia and Trichomonas vaginalis revealed by valyl-tRNA synthetase phylogeny. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[31]  H. Ishikawa.  Evolution of ribosomal RNA. , 1977, Comparative biochemistry and physiology. B, Comparative biochemistry.

[32]  Yves Van de Peer,et al.  TREECON for Windows: a software package for the construction and drawing of evolutionary trees for the Microsoft Windows environment , 1994, Comput. Appl. Biosci..

[33]  C. Vonrhein,et al.  Structure of the 30S ribosomal subunit , 2000, Nature.

[34]  Rodrigo Lopez,et al.  The EMBL Nucleotide Sequence Database , 1999, Nucleic Acids Res..