This document discusses the identification of U-turn motifs in ribosomal RNA (rRNA) through comparative sequence analysis. U-turns are structural motifs characterized by a sharp reversal in the RNA backbone that facilitate tertiary interactions. The authors define a consensus sequence and structural signature for U-turn motifs based on experimentally determined structures. They identify 58 potential U-turn candidates in 16S and 23S rRNA sequences based on this signature. These candidates are classified into families based on sequence pattern, loop type, and flanking bases. Thirteen candidates are strong possibilities as they involve tertiary interactions near the U-turn.
Gardner D.P., Ren P., Ozer S., and Gutell R.R. (2011).
Statistical Potentials for Hairpin and Internal Loops Improve the Accuracy of the Predicted RNA Structure.
Journal of Molecular Biology, 413(2):473-483.2011. pp 15-22.
Lee J.C. and Gutell R.R. (2012).
A Comparison of the Crystal Structures of the Eukaryotic and Bacterial SSU Ribosomal RNAs Reveals Common Structural Features in the Hypervariable Regions.
PLoS ONE, 7(5):e38203.
Ozer S., Doshi K.J., Xu W., and Gutell R.R. (2011).
rCAD: A Novel Database Schema for the Comparative Analysis of RNA.
7th IEEE International Conference on e-Science, Stockholm, Sweden. December 5-8, 2011. pp 15-22.
Gutell R.R. (2013).
Comparative Analysis of the Higher-Order Structure of RNA.
in: Biophysics of RNA Folding. Volume editor: Rick Russell. Series title: Biophysics for the Life Sciences. Series editors: Norma Allewell, Ivan Rayment, Bertrand Garcia-Moreno, Jonathan Dinman, and Michael McCarthy. pp. 11-22. Publisher: Springer, New York, NY.
This document summarizes Carl Woese's contributions to science, particularly his discovery of the third domain of life (Archaea) through analysis of rRNA sequences. It describes how his work established the use of comparative analysis to determine rRNA secondary structure and identify structural motifs. It highlights that he envisioned comparative analysis providing details about RNA structure and energetics. The summary discusses Woese's seminal concepts regarding the need for a universal phylogenetic framework and how analysis of rRNA satisfied criteria to reconstruct evolutionary relationships across all life.
Gutell 123.app environ micro_2013_79_1803Robin Gutell
This document summarizes a study examining the host specificity of Lactobacillus bacteria associated with different hymenopteran (bee and ant) hosts. The researchers compiled nearly full-length 16S rRNA gene sequences of Lactobacillus from public databases and used these to construct phylogenetic trees. They also included shorter 16S sequences from surveys of bacteria associated with sweat bees, fungus-growing ants, and fire ants. The results showed that lactobacilli associated with honey bees and bumble bees are highly host specific, while sweat bees and ants associate with lactobacilli more closely related to those found in diverse environments or vertebrate hosts. The high host specificity seen in corbiculate bees (honey bees
Gardner D.P., Ren P., Ozer S., and Gutell R.R. (2011).
Statistical Potentials for Hairpin and Internal Loops Improve the Accuracy of the Predicted RNA Structure.
Journal of Molecular Biology, 413(2):473-483.2011. pp 15-22.
Lee J.C. and Gutell R.R. (2012).
A Comparison of the Crystal Structures of the Eukaryotic and Bacterial SSU Ribosomal RNAs Reveals Common Structural Features in the Hypervariable Regions.
PLoS ONE, 7(5):e38203.
Ozer S., Doshi K.J., Xu W., and Gutell R.R. (2011).
rCAD: A Novel Database Schema for the Comparative Analysis of RNA.
7th IEEE International Conference on e-Science, Stockholm, Sweden. December 5-8, 2011. pp 15-22.
Gutell R.R. (2013).
Comparative Analysis of the Higher-Order Structure of RNA.
in: Biophysics of RNA Folding. Volume editor: Rick Russell. Series title: Biophysics for the Life Sciences. Series editors: Norma Allewell, Ivan Rayment, Bertrand Garcia-Moreno, Jonathan Dinman, and Michael McCarthy. pp. 11-22. Publisher: Springer, New York, NY.
This document summarizes Carl Woese's contributions to science, particularly his discovery of the third domain of life (Archaea) through analysis of rRNA sequences. It describes how his work established the use of comparative analysis to determine rRNA secondary structure and identify structural motifs. It highlights that he envisioned comparative analysis providing details about RNA structure and energetics. The summary discusses Woese's seminal concepts regarding the need for a universal phylogenetic framework and how analysis of rRNA satisfied criteria to reconstruct evolutionary relationships across all life.
Gutell 123.app environ micro_2013_79_1803Robin Gutell
This document summarizes a study examining the host specificity of Lactobacillus bacteria associated with different hymenopteran (bee and ant) hosts. The researchers compiled nearly full-length 16S rRNA gene sequences of Lactobacillus from public databases and used these to construct phylogenetic trees. They also included shorter 16S sequences from surveys of bacteria associated with sweat bees, fungus-growing ants, and fire ants. The results showed that lactobacilli associated with honey bees and bumble bees are highly host specific, while sweat bees and ants associate with lactobacilli more closely related to those found in diverse environments or vertebrate hosts. The high host specificity seen in corbiculate bees (honey bees
This document summarizes a study that found evidence of a base triple interaction in the 58 nucleotide domain of 23S ribosomal RNA through comparative sequence analysis and experiments. The analysis identified covariations between positions 1092/1099 and the unpaired position 1072, suggesting they form a base triple. Mutation experiments showed disruption of the tertiary structure and reduced protein binding when position 1072 was altered, but not when the base pair 1092/1099 was altered, supporting a base triple. Fully compensating the mutations restored wild-type tertiary structure and binding.
Magnon crystallization in kagomé antiferromagnetsRyutaro Okuma
This document summarizes research on magnon crystallization in kagomé antiferromagnets. Key points include:
1) Observation of a series of magnetization plateaus up to 160 T in CdK and a 1/3 magnetization plateau over 150 T in herbertsmithite.
2) Theoretical calculation showing hexagonal magnon localization and crystallization phases with different magnetization values as the field is increased.
3) Experimental studies of the S=1/2 kagomé magnets volborthite, herbertsmithite, and Cd-kapellasite using ultra-high magnetic fields up to 200 T to observe magnon crystallization phenomena.
This document discusses evidence of lateral transfer of a group IE intron between fungal and red algal small subunit rRNA genes. It finds that a group IE intron inserted at position 989 in the nuclear SSU rRNA gene of the red alga Hildenbrandia rubra is closely related to similar fungal IE introns, providing evidence the intron was laterally transferred rather than vertically inherited. Phylogenetic analysis of intron sequences and comparisons of intron secondary structures support a relationship between the red algal intron and fungal introns, making lateral transfer the most likely explanation for the intron's presence in H. rubra.
This study analyzed the conserved A:A and A:G base pairs found at the ends of helices in 16S and 23S rRNA. It found that 30% of helix ends in 16S rRNA and 28% in 23S rRNA have an A:A or A:G pair in at least 90% of bacterial sequences, far more than expected by chance. Most A:G pairs have the guanine on the 3' side of the helix. These non-canonical base pairs are found in a variety of structural contexts and may be important for structural rearrangements associated with RNA function.
This document describes a study that used nucleotide analog interference mapping (NAIM) to investigate the importance of individual adenosine functional groups for the activity of the Tetrahymena group I intron. Eight adenosine analogs were synthesized and incorporated into intron transcripts. The analogs allowed probing of the N6 amino, N2 amino, N7 imino, and 29-OH groups of adenosine. Sites where an analog interfered with the intron's ability to ligate exons indicated positions where that particular functional group is important. The interference patterns provided biochemical constraints supporting aspects of the intron's proposed structure, including an essential A-platform and tertiary interactions involving conserved adenosine motifs.
This document summarizes studies on the structure and function of 16S ribosomal RNA using chemical probes. Specifically:
1) 16S rRNA from both active and inactive 30S ribosomal subunits was probed with chemical reagents to identify changes in accessibility of nucleotides between the active and inactive states. A conformational change was observed in the decoding region of 16S rRNA.
2) Additional studies probed the naked 16S rRNA under different ionic conditions and identified nucleotides involved in tertiary interactions, a potentially important core structure, and supported the proposed secondary structure model.
3) The studies provide new insights into the structure and function of 16S rRNA in protein synthesis.
This document describes the lonepair triloop (LPTL), a new RNA structural motif identified through comparative sequence analysis. The LPTL contains a single base pair ("lonepair") capped by a hairpin loop of three nucleotides. Analysis of ribosomal crystal structures validated seven previously predicted LPTLs and identified 16 additional examples. In total, 24 LPTLs were found in ribosomal RNAs and tRNAs. These LPTLs fall into different classes and groups based on their structure and tertiary interactions. At least one nucleotide in the triloop forms tertiary interactions in most examples, demonstrating the three-dimensional functional role of this motif.
This study investigated the role of a putative ionic interaction between residue D2.63176 in the second transmembrane helix and residue K373 in the third extracellular loop of the cannabinoid receptor CB1. Mutational analysis showed that disrupting this interaction impaired receptor signaling without affecting ligand binding. Conversely, a charge reversal mutation that restored the interaction also regained normal receptor function. Computational modeling suggested this ionic interaction influences the conformation of the third extracellular loop, which may be important for CB1 signal transduction. These findings provide novel insights into the CB1 receptor signaling mechanism.
DNA is a molecule composed of two chains that coil around each other to form a double helix carrying genetic instructions for the development, functioning, growth and reproduction of all known organism. DNA are nucleic acids;. The two DNA strands are also known as polynucleotides as they are composed of simpler monomeric units called nucleotides. Each nucleotide is composed of one of four nitrogen-containing nucleo bases (cytosine[C], guanine[G], adenine[A] or thymine[T]), a sugar called deoxyribose, and a phosphate group.
Nucleotide :- nitrogenous base,sugar,phosphate
Nucleoside :- :- nitrogenous base,sugar
This document summarizes the results of a comprehensive comparison of secondary structure models for the cytoplasmic large subunit (23S-like) rRNA of eukaryotes. It finds that while eukaryotic 23S-like rRNAs range greatly in length, they share a common conserved core secondary structure with a few distinct differences from prokaryotes. Variable regions outside the core accommodate size variation between species. Newly proposed or refined secondary structures were defined for many variable regions based on comparative evidence, improving structural models across eukaryotes.
This document summarizes DNA triplex structures. It discusses:
1) The different types of triplex structures that can form, including intramolecular and intermolecular triplexes with various strand compositions.
2) How triplex-forming oligonucleotides can bind specifically to DNA duplexes through Hoogsteen base-pairing and may have applications as gene-targeting drugs.
3) Evidence that unusual DNA structures called H-DNA and R-DNA, which contain triplex elements, may form in vivo and play a role in processes like DNA replication and homologous recombination.
This document summarizes a study examining the function of the Neurospora crassa mitochondrial tyrosyl-tRNA synthetase (CYT-18 protein) in splicing group I introns. The researchers used an E. coli genetic assay to test CYT-18's ability to suppress mutations that disrupt the structure of its binding site in the P4-P6 domain of group I introns. They analyzed all possible nucleotide combinations at positions P4 bp-1 and P6 bp-1, which form the junction of the stacked P4-P6 helices. Most single mutations inhibited splicing but could be suppressed by CYT-18, though it had difficulty with combinations disrupting both base pairing and
This document summarizes evidence from comparative analysis of ribosomal RNA sequences that suggests two new higher order structural interactions in 16S ribosomal RNA:
1) A double helical structure involving positions 505-507 and 524-526, supported by examples of co-variation between these positions in various organisms. This represents a pseudoknot structure.
2) An interaction between the region around position 130 and the helix located between positions 180-195. In many bacteria, an insertion of a nucleotide near position 130 correlates with the helix in the 180-195 region being lengthened from 3 base pairs to around 10 base pairs.
The document provides detailed evidence for these proposed higher order structures from comparative analysis of rRNA
The effect of core destabilisation on the mechanical resistance of i27John Clarkson
D.J. Brockwell, G.S. Beddard, J. Clarkson, R.C. Zinober, A.W. Blake, J. Trinick, P.D. Olmsted, D.A. Smith & S.E. Radford, “The Effect of Core Destabilisation on the Mechanical Resistance of I27”, Biophys. J., 83(1), 472-483, 2002.
This document analyzes the distribution of paired and unpaired nucleotides in comparative structure models of bacterial 16S and 23S ribosomal RNAs. It finds that adenosine nucleotides have a strong bias toward being unpaired, while guanine, cytosine, and uracil nucleotides predominantly form base pairs. Approximately 66% of adenosine nucleotides are unpaired, compared to 30-41% of other nucleotides. Certain sequence motifs involving unpaired adenosines, like GNRA tetraloops and E-loops, are overrepresented. This document aims to associate specific unpaired nucleotide distribution patterns with three-dimensional structural motifs.
This document provides scientific background on the 2009 Nobel Prize in Chemistry, which was awarded for studies of the structure and function of the ribosome. It summarizes the key contributions of Venkatraman Ramakrishnan, Thomas Steitz, and Ada Yonath, including obtaining the first high resolution crystal structures of the ribosomal subunits, solving the long-standing mysteries of the ribosome's catalytic mechanisms and role in protein synthesis, and advancing understanding of its accuracy and interactions with antibiotic drugs. Their work over decades was instrumental in revealing the ribosome's structure and function at the atomic level.
Edmund Kunjii Medical Research Council. Mitochondrial Biology Unit. Cambridge. Fundación Ramón Areces
El lunes y martes 20 y 21 de noviembre coordinamos un simposio internacional en la Fundación Ramón Areces, sobre los defectos del transporte de aminoácidos.
Edmund Kunjii - Medical Research Council. Mitochondrial Biology Unit. Cambrid...Fundación Ramón Areces
El lunes y martes 20 y 21 de noviembre coordinamos un simposio internacional en la Fundación Ramón Areces, sobre los defectos del transporte de aminoácidos.
This document summarizes research on the mitochondrial large subunit rRNA gene sequence and microevolution in the ciliate Paramecium. Key findings include:
- The large subunit rRNA gene complex in Paramecium consists of a 283-base "5.8S-like" segment followed by the previously described 20S segment.
- The gene sequences from Paramecium primaurelia and Paramecium tetraurelia were 4% divergent.
- The genes lie adjacent to each other near the end of the linear mitochondrial genome and are transcribed from a common 23S precursor.
- Precise gene boundaries were determined using nuclease protection assays. The complex spans approximately 2654 base pairs.
Gardner D.P., Xu W., Miranker D.P., Ozer S., Cannone J.J., and Gutell R.R. (2012).
An Accurate Scalable Template-based Alignment Algorithm.
Proceedings of 2012 IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2012), Philadelphia, PA. October 4-7, 2012. IEEE Computer Society, Washington, DC, USA. pp. 237-243.
Jiang Y., Xu W., Thompson L.P., Gutell R., and Miranker D. (2011).
R-PASS: A Fast Structure-based RNA Sequence Alignment Algorithm.
Proceedings of 2011 IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2011), Atlanta, GA. November 12-15, 2011. IEEE Computer Society, Washington, DC, USA. pp. 618-622.
This document summarizes a study that found evidence of a base triple interaction in the 58 nucleotide domain of 23S ribosomal RNA through comparative sequence analysis and experiments. The analysis identified covariations between positions 1092/1099 and the unpaired position 1072, suggesting they form a base triple. Mutation experiments showed disruption of the tertiary structure and reduced protein binding when position 1072 was altered, but not when the base pair 1092/1099 was altered, supporting a base triple. Fully compensating the mutations restored wild-type tertiary structure and binding.
Magnon crystallization in kagomé antiferromagnetsRyutaro Okuma
This document summarizes research on magnon crystallization in kagomé antiferromagnets. Key points include:
1) Observation of a series of magnetization plateaus up to 160 T in CdK and a 1/3 magnetization plateau over 150 T in herbertsmithite.
2) Theoretical calculation showing hexagonal magnon localization and crystallization phases with different magnetization values as the field is increased.
3) Experimental studies of the S=1/2 kagomé magnets volborthite, herbertsmithite, and Cd-kapellasite using ultra-high magnetic fields up to 200 T to observe magnon crystallization phenomena.
This document discusses evidence of lateral transfer of a group IE intron between fungal and red algal small subunit rRNA genes. It finds that a group IE intron inserted at position 989 in the nuclear SSU rRNA gene of the red alga Hildenbrandia rubra is closely related to similar fungal IE introns, providing evidence the intron was laterally transferred rather than vertically inherited. Phylogenetic analysis of intron sequences and comparisons of intron secondary structures support a relationship between the red algal intron and fungal introns, making lateral transfer the most likely explanation for the intron's presence in H. rubra.
This study analyzed the conserved A:A and A:G base pairs found at the ends of helices in 16S and 23S rRNA. It found that 30% of helix ends in 16S rRNA and 28% in 23S rRNA have an A:A or A:G pair in at least 90% of bacterial sequences, far more than expected by chance. Most A:G pairs have the guanine on the 3' side of the helix. These non-canonical base pairs are found in a variety of structural contexts and may be important for structural rearrangements associated with RNA function.
This document describes a study that used nucleotide analog interference mapping (NAIM) to investigate the importance of individual adenosine functional groups for the activity of the Tetrahymena group I intron. Eight adenosine analogs were synthesized and incorporated into intron transcripts. The analogs allowed probing of the N6 amino, N2 amino, N7 imino, and 29-OH groups of adenosine. Sites where an analog interfered with the intron's ability to ligate exons indicated positions where that particular functional group is important. The interference patterns provided biochemical constraints supporting aspects of the intron's proposed structure, including an essential A-platform and tertiary interactions involving conserved adenosine motifs.
This document summarizes studies on the structure and function of 16S ribosomal RNA using chemical probes. Specifically:
1) 16S rRNA from both active and inactive 30S ribosomal subunits was probed with chemical reagents to identify changes in accessibility of nucleotides between the active and inactive states. A conformational change was observed in the decoding region of 16S rRNA.
2) Additional studies probed the naked 16S rRNA under different ionic conditions and identified nucleotides involved in tertiary interactions, a potentially important core structure, and supported the proposed secondary structure model.
3) The studies provide new insights into the structure and function of 16S rRNA in protein synthesis.
This document describes the lonepair triloop (LPTL), a new RNA structural motif identified through comparative sequence analysis. The LPTL contains a single base pair ("lonepair") capped by a hairpin loop of three nucleotides. Analysis of ribosomal crystal structures validated seven previously predicted LPTLs and identified 16 additional examples. In total, 24 LPTLs were found in ribosomal RNAs and tRNAs. These LPTLs fall into different classes and groups based on their structure and tertiary interactions. At least one nucleotide in the triloop forms tertiary interactions in most examples, demonstrating the three-dimensional functional role of this motif.
This study investigated the role of a putative ionic interaction between residue D2.63176 in the second transmembrane helix and residue K373 in the third extracellular loop of the cannabinoid receptor CB1. Mutational analysis showed that disrupting this interaction impaired receptor signaling without affecting ligand binding. Conversely, a charge reversal mutation that restored the interaction also regained normal receptor function. Computational modeling suggested this ionic interaction influences the conformation of the third extracellular loop, which may be important for CB1 signal transduction. These findings provide novel insights into the CB1 receptor signaling mechanism.
DNA is a molecule composed of two chains that coil around each other to form a double helix carrying genetic instructions for the development, functioning, growth and reproduction of all known organism. DNA are nucleic acids;. The two DNA strands are also known as polynucleotides as they are composed of simpler monomeric units called nucleotides. Each nucleotide is composed of one of four nitrogen-containing nucleo bases (cytosine[C], guanine[G], adenine[A] or thymine[T]), a sugar called deoxyribose, and a phosphate group.
Nucleotide :- nitrogenous base,sugar,phosphate
Nucleoside :- :- nitrogenous base,sugar
This document summarizes the results of a comprehensive comparison of secondary structure models for the cytoplasmic large subunit (23S-like) rRNA of eukaryotes. It finds that while eukaryotic 23S-like rRNAs range greatly in length, they share a common conserved core secondary structure with a few distinct differences from prokaryotes. Variable regions outside the core accommodate size variation between species. Newly proposed or refined secondary structures were defined for many variable regions based on comparative evidence, improving structural models across eukaryotes.
This document summarizes DNA triplex structures. It discusses:
1) The different types of triplex structures that can form, including intramolecular and intermolecular triplexes with various strand compositions.
2) How triplex-forming oligonucleotides can bind specifically to DNA duplexes through Hoogsteen base-pairing and may have applications as gene-targeting drugs.
3) Evidence that unusual DNA structures called H-DNA and R-DNA, which contain triplex elements, may form in vivo and play a role in processes like DNA replication and homologous recombination.
This document summarizes a study examining the function of the Neurospora crassa mitochondrial tyrosyl-tRNA synthetase (CYT-18 protein) in splicing group I introns. The researchers used an E. coli genetic assay to test CYT-18's ability to suppress mutations that disrupt the structure of its binding site in the P4-P6 domain of group I introns. They analyzed all possible nucleotide combinations at positions P4 bp-1 and P6 bp-1, which form the junction of the stacked P4-P6 helices. Most single mutations inhibited splicing but could be suppressed by CYT-18, though it had difficulty with combinations disrupting both base pairing and
This document summarizes evidence from comparative analysis of ribosomal RNA sequences that suggests two new higher order structural interactions in 16S ribosomal RNA:
1) A double helical structure involving positions 505-507 and 524-526, supported by examples of co-variation between these positions in various organisms. This represents a pseudoknot structure.
2) An interaction between the region around position 130 and the helix located between positions 180-195. In many bacteria, an insertion of a nucleotide near position 130 correlates with the helix in the 180-195 region being lengthened from 3 base pairs to around 10 base pairs.
The document provides detailed evidence for these proposed higher order structures from comparative analysis of rRNA
The effect of core destabilisation on the mechanical resistance of i27John Clarkson
D.J. Brockwell, G.S. Beddard, J. Clarkson, R.C. Zinober, A.W. Blake, J. Trinick, P.D. Olmsted, D.A. Smith & S.E. Radford, “The Effect of Core Destabilisation on the Mechanical Resistance of I27”, Biophys. J., 83(1), 472-483, 2002.
This document analyzes the distribution of paired and unpaired nucleotides in comparative structure models of bacterial 16S and 23S ribosomal RNAs. It finds that adenosine nucleotides have a strong bias toward being unpaired, while guanine, cytosine, and uracil nucleotides predominantly form base pairs. Approximately 66% of adenosine nucleotides are unpaired, compared to 30-41% of other nucleotides. Certain sequence motifs involving unpaired adenosines, like GNRA tetraloops and E-loops, are overrepresented. This document aims to associate specific unpaired nucleotide distribution patterns with three-dimensional structural motifs.
This document provides scientific background on the 2009 Nobel Prize in Chemistry, which was awarded for studies of the structure and function of the ribosome. It summarizes the key contributions of Venkatraman Ramakrishnan, Thomas Steitz, and Ada Yonath, including obtaining the first high resolution crystal structures of the ribosomal subunits, solving the long-standing mysteries of the ribosome's catalytic mechanisms and role in protein synthesis, and advancing understanding of its accuracy and interactions with antibiotic drugs. Their work over decades was instrumental in revealing the ribosome's structure and function at the atomic level.
Edmund Kunjii Medical Research Council. Mitochondrial Biology Unit. Cambridge. Fundación Ramón Areces
El lunes y martes 20 y 21 de noviembre coordinamos un simposio internacional en la Fundación Ramón Areces, sobre los defectos del transporte de aminoácidos.
Edmund Kunjii - Medical Research Council. Mitochondrial Biology Unit. Cambrid...Fundación Ramón Areces
El lunes y martes 20 y 21 de noviembre coordinamos un simposio internacional en la Fundación Ramón Areces, sobre los defectos del transporte de aminoácidos.
This document summarizes research on the mitochondrial large subunit rRNA gene sequence and microevolution in the ciliate Paramecium. Key findings include:
- The large subunit rRNA gene complex in Paramecium consists of a 283-base "5.8S-like" segment followed by the previously described 20S segment.
- The gene sequences from Paramecium primaurelia and Paramecium tetraurelia were 4% divergent.
- The genes lie adjacent to each other near the end of the linear mitochondrial genome and are transcribed from a common 23S precursor.
- Precise gene boundaries were determined using nuclease protection assays. The complex spans approximately 2654 base pairs.
Gardner D.P., Xu W., Miranker D.P., Ozer S., Cannone J.J., and Gutell R.R. (2012).
An Accurate Scalable Template-based Alignment Algorithm.
Proceedings of 2012 IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2012), Philadelphia, PA. October 4-7, 2012. IEEE Computer Society, Washington, DC, USA. pp. 237-243.
Jiang Y., Xu W., Thompson L.P., Gutell R., and Miranker D. (2011).
R-PASS: A Fast Structure-based RNA Sequence Alignment Algorithm.
Proceedings of 2011 IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2011), Atlanta, GA. November 12-15, 2011. IEEE Computer Society, Washington, DC, USA. pp. 618-622.
Xu W., Wongsa A., Lee J., Shang L., Cannone J.J., and Gutell R.R. (2011).
RNA2DMap: A Visual Exploration Tool of the Information in RNA's Higher-Order Structure.
Proceedings of 2011 IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2011), Atlanta, GA. November 12-15, 2011. IEEE Computer Society, Washington, DC, USA. pp. 613-617.
Muralidhara C., Gross A.M., Gutell R.R., and Alter O. (2011).
Tensor Decomposition Reveals Concurrent Evolutionary Convergences and Divergences and Correlations with Structural Motifs in Ribosomal RNA.
PLoS ONE, 6(4):e18768.
Xia Z., Gardner D.P., Gutell R.R., and Ren P. (2010).
Coarse-Grained Model for Simulation of RNA Three-Dimensional Structures.
The Journal of Physical Chemistry B, 114(42):13497-13506.
The document describes research on fragmentation of the large subunit ribosomal RNA (LSU rRNA) gene in oyster mitochondrial genomes. Key findings include:
1) The LSU rRNA gene is split into two fragments separated by thousands of nucleotides in three species of oysters.
2) RT-PCR and EST analysis showed the two fragments are transcribed separately in Crassostrea virginica and are not spliced together.
3) Secondary structure models of the fragmented LSU rRNA genes were predicted for C. virginica, C. gigas, and C. hongkongensis based on comparative sequence analysis. This fragmentation represents a novel phenomenon in bilateral metazoan mitochondrial genomes.
Mueller U.G., Ishak H., Lee J.C., Sen R., and Gutell R.R. (2010).
Placement of attine ant-associated Pseudonocardia in a global phylogeny (Pseudonocardiaceae, Actinomycetales): a test of two symbiont-association models.
Antonie van Leeuwenhoek International Journal of General and Molecular Microbiology, 98(2):195-212.
Theriot E.C., Cannone J.J., Gutell R.R., and Alverson A.J. (2009).
The limits of nuclear encoded SSU rDNA for resolving the diatom phylogeny.
European Journal of Phycology, 44(3):277-290.
Wu J.C., Gardner D.P., Ozer S., Gutell R.R. and Ren P. (2009).
Correlation of RNA Secondary Structure Statistics with Thermodynamic Stability and Applications to Folding.
Journal of Molecular Biology, 391(4):769-783.
Xu W., Ozer S., and Gutell R.R. (2009).
Covariant Evolutionary Event Analysis for Base Interaction Prediction Using a Relational Database Management System for RNA.
21st International Conference on Scientific and Statistical Database Management. June 2-4, 2009. Springer-Verlag. pp. 200-216.
Chen Y.P., Evans J.D., Murphy C., Gutell R., Zuker M., Gundersen-Rindal D., and Pettis J.S. (2009).
Morphological, Molecular, and Phylogenetic Characterization of Nosema cerenae, a Microsporidian Parasite Isolated from the European Honey Bee, Apis mellifera.
The Journal of Eukaryotic Microbiology, 56(2):142-147.
Maddison D.R., Moore W., Baker M.D., Ellis T.M., Ober K.A., Cannone J.J., and Gutell R.R. (2009).
Monophyly of terrestrial adephagan beetles as indicated by three nuclear genes (Coleoptera: Carabidae and Trachypachidae).
Zoologica Scripta, 38(1):43-62.
The document discusses the origin and evolution of the ribosome. It finds:
1) There is no single self-folding RNA segment that defines the small subunit's decoding site, while the large subunit's peptidyl transfer center is defined by one self-folding RNA segment.
2) The proteins contacting the small subunit's decoding site use universally alignable sequence blocks, while the large subunit's contact proteins use bacterial- or archaeal-specific blocks.
3) These differences support an earlier origin for the large subunit's peptidyl transfer center, with the small subunit's decoding site evolving later as an addition to the ribosome. The implications are that a single self-folding
Chandramouli P., Topf M., Ménétret J.-F., Eswar N., Cannone J.J., Gutell R.R., Sali A., and Akey C.W. (2008).
Structure of the Mammalian 80S Ribosome at 8.7 Å Resolution.
Structure, 16(4):535-548.
This document describes a new method called BlockMSA for performing local multiple sequence alignment (MSA) of non-coding RNA sequences. BlockMSA uses a biclustering approach that simultaneously clusters sequences and identifies conserved subsequences within the clusters. The authors test BlockMSA on benchmark RNA datasets and two large biological datasets, finding it outperforms other MSA tools for larger problems with highly variable sequences. BlockMSA is able to scale to larger datasets while identifying functionally conserved regions missed by other methods.
Lee C.-Y., Lee J.C., and Gutell R.R. (2007).
Networks of interactions in the secondary and tertiary structure of ribosomal RNA.
Physica A, 386(1):564-572.
Gillespie J.J., Johnston J.S., Cannone J.J., and Gutell R.R. (2006).
Characteristics of the nuclear (18S, 5.8S, 28S and 5S) and mitochondrial (12S and 16S) rRNA genes of Apis mellifera (Insecta:Hymenoptera): structure, organization, and retrotransposable elements.
Insect Molecular Biology, 15(5):657-686.
Weinstock et al. (81 authors), Gillespie J.J., Cannone J.J., Gutell R.R., et al. (100 authors) (2006).
Insights into social insects from the genome of the honeybee Apis mellifera.
Nature, 443(7114):931-949.
Lee J.C., Gutell R.R., and Russell R. (2006).
The UAA/GAN internal loop motif: a new RNA structural element that forms a cross-strand AAA stack and long-range tertiary interactions.
Journal of Molecular Biology, 360(5):978-988.
TrustArc Webinar - 2024 Global Privacy SurveyTrustArc
How does your privacy program stack up against your peers? What challenges are privacy teams tackling and prioritizing in 2024?
In the fifth annual Global Privacy Benchmarks Survey, we asked over 1,800 global privacy professionals and business executives to share their perspectives on the current state of privacy inside and outside of their organizations. This year’s report focused on emerging areas of importance for privacy and compliance professionals, including considerations and implications of Artificial Intelligence (AI) technologies, building brand trust, and different approaches for achieving higher privacy competence scores.
See how organizational priorities and strategic approaches to data security and privacy are evolving around the globe.
This webinar will review:
- The top 10 privacy insights from the fifth annual Global Privacy Benchmarks Survey
- The top challenges for privacy leaders, practitioners, and organizations in 2024
- Key themes to consider in developing and maintaining your privacy program
HCL Notes and Domino License Cost Reduction in the World of DLAUpanagenda
Webinar Recording: https://www.panagenda.com/webinars/hcl-notes-and-domino-license-cost-reduction-in-the-world-of-dlau/
The introduction of DLAU and the CCB & CCX licensing model caused quite a stir in the HCL community. As a Notes and Domino customer, you may have faced challenges with unexpected user counts and license costs. You probably have questions on how this new licensing approach works and how to benefit from it. Most importantly, you likely have budget constraints and want to save money where possible. Don’t worry, we can help with all of this!
We’ll show you how to fix common misconfigurations that cause higher-than-expected user counts, and how to identify accounts which you can deactivate to save money. There are also frequent patterns that can cause unnecessary cost, like using a person document instead of a mail-in for shared mailboxes. We’ll provide examples and solutions for those as well. And naturally we’ll explain the new licensing model.
Join HCL Ambassador Marc Thomas in this webinar with a special guest appearance from Franz Walder. It will give you the tools and know-how to stay on top of what is going on with Domino licensing. You will be able lower your cost through an optimized configuration and keep it low going forward.
These topics will be covered
- Reducing license cost by finding and fixing misconfigurations and superfluous accounts
- How do CCB and CCX licenses really work?
- Understanding the DLAU tool and how to best utilize it
- Tips for common problem areas, like team mailboxes, functional/test users, etc
- Practical examples and best practices to implement right away
Trusted Execution Environment for Decentralized Process MiningLucaBarbaro3
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DLAU und die Lizenzen nach dem CCB- und CCX-Modell sind für viele in der HCL-Community seit letztem Jahr ein heißes Thema. Als Notes- oder Domino-Kunde haben Sie vielleicht mit unerwartet hohen Benutzerzahlen und Lizenzgebühren zu kämpfen. Sie fragen sich vielleicht, wie diese neue Art der Lizenzierung funktioniert und welchen Nutzen sie Ihnen bringt. Vor allem wollen Sie sicherlich Ihr Budget einhalten und Kosten sparen, wo immer möglich. Das verstehen wir und wir möchten Ihnen dabei helfen!
Wir erklären Ihnen, wie Sie häufige Konfigurationsprobleme lösen können, die dazu führen können, dass mehr Benutzer gezählt werden als nötig, und wie Sie überflüssige oder ungenutzte Konten identifizieren und entfernen können, um Geld zu sparen. Es gibt auch einige Ansätze, die zu unnötigen Ausgaben führen können, z. B. wenn ein Personendokument anstelle eines Mail-Ins für geteilte Mailboxen verwendet wird. Wir zeigen Ihnen solche Fälle und deren Lösungen. Und natürlich erklären wir Ihnen das neue Lizenzmodell.
Nehmen Sie an diesem Webinar teil, bei dem HCL-Ambassador Marc Thomas und Gastredner Franz Walder Ihnen diese neue Welt näherbringen. Es vermittelt Ihnen die Tools und das Know-how, um den Überblick zu bewahren. Sie werden in der Lage sein, Ihre Kosten durch eine optimierte Domino-Konfiguration zu reduzieren und auch in Zukunft gering zu halten.
Diese Themen werden behandelt
- Reduzierung der Lizenzkosten durch Auffinden und Beheben von Fehlkonfigurationen und überflüssigen Konten
- Wie funktionieren CCB- und CCX-Lizenzen wirklich?
- Verstehen des DLAU-Tools und wie man es am besten nutzt
- Tipps für häufige Problembereiche, wie z. B. Team-Postfächer, Funktions-/Testbenutzer usw.
- Praxisbeispiele und Best Practices zum sofortigen Umsetzen
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FREE A4 Cyber Security Awareness Posters-Social Engineering part 3
Gutell 071.jmb.2000.300.0791
1. Predicting U-turns in Ribosomal RNA with
Comparative Sequence Analysis
Robin R. Gutell1
*, Jamie J. Cannone1
, Danielle Konings2
and Daniel Gautheret3
1
Institute for Cellular and
Molecular Biology, University
of Texas at Austin, 2500
Speedway, Austin, TX 78712-
1095, USA
2
Department of Molecular
Cellular and Developmental
Biology, University of Colorado
Campus Box 347, Boulder
CO 80309-0347, USA
3
Structural and Genetic
Information, CNRS UMR
1889, 31 chemin Joseph
Aiguier, 13 402, Marseille
Cedex 20, France
The U-turn is a well-known RNA motif characterized by a sharp reversal
of the RNA backbone following a single-stranded uridine base. In exper-
imentally determined U-turn motifs, the nucleotides 3H
to the turn are fre-
quently involved in tertiary interactions, rendering this motif particularly
attractive in RNA modeling and functional studies. The U-turn signature
is composed of an UNR sequence pattern ¯anked by a Y:Y, Y:A
(Y ˆ pyrimidine) or G:A base juxtaposition. We have identi®ed 33 poten-
tial UNR-type U-turns and 25 related GNRA-type U-turns in a large set
of aligned 16 S and 23 S rRNA sequences. U-turn candidates occur in
hairpin loops (34 times) as well as in internal and multi-stem loops (24
times). These are classi®ed into ten families based on loop type, sequence
pattern (UNR or GNRA) and the nature of the closing base juxtaposition.
In 13 cases, the bases on the 3H
side of the turn, or on the immediate 5H
side, are involved in tertiary covariations, making these sites strong can-
didates for tertiary interactions.
# 2000 Academic Press
Keywords: ribosomal RNA; comparative sequence analysis; U-turns;
tertiary interactions*Corresponding author
Introduction
U-turns are small RNA structural motifs that
were ®rst discovered in the anticodon and TcC-
loop of tRNA (Quigley & Rich, 1976) and later
identi®ed in the hammerhead ribozyme (Pley et al.,
1994a), the GNRA tetraloop (Jucker & Pardi, 1995),
23 S rRNA (Huang et al., 1996; Conn et al., 1999;
Culver et al., 1999), U2 snRNA (Stallings & Moore,
1997) and the HIV RNA (Puglisi & Puglisi, 1998).
U-turns are stable structures that, as their name
implies, induce a sharp change in the direction of
their backbone. U-turns are one way to close hair-
pin loops, but one of their most signi®cant proper-
ties is their ability to create anchors for long-range
tertiary interactions due to the strong level of
exposure to solvent of the bases located 3H
to the
turn. Probably the best example of this principle is
utilized in protein synthesis to facilitate codon-
anticodon base-pairing. The three nucleotides
of the anticodon are located immediately 3H
of a U-
turn, rendering them accessible to long-range
contacts with the codon and with the P site in 16 S
rRNA (Prince et al., 1982; Cate et al., 1999). The
majority of the experimentally determined U-turns
have been associated with tertiary contacts. In the
tRNA TcC-loop, the base located 3H
to the turn
makes a Watson-Crick pair with a guanosine base
in the D-loop (G19:C56 in Yeast tRNAPhe
), and the
base located immediately 5H
to the turn is involved
in the U54:A58 reverse Hoogsteen base-pair. In
several ribozymes, the bases following the G of
GNRA tetraloops are involved in a variety of long-
range interactions (Jaeger et al., 1994; Pley et al.,
1994b; Costa & Michel, 1995; Brown et al., 1996;
Cate et al., 1996). Recently, U-turns have been
inferred in the formation of RNA/RNA inter-
actions in natural antisense RNAs (Franch et al.,
1999).
The most salient structural feature of all U-turn
motifs is a sharp reversal of the RNA phosphodie-
ster backbone, following a uridine base in the two
tRNA U-turns (Quigley & Rich, 1976; Sussman &
Kim, 1976), or a guanosine base in the GNRA U-
turn (Jucker & Pardi, 1995). The turn is stabilized
by one or two hydrogen bonds forming between
the uridine or guanosine base that precedes the
turn and the second base and phosphate following
the turn. These stabilizing interactions are associ-
ated with a set of sequence constraints that help
E-mail address of the corresponding author:
robin.gutell@mail.utexas.edu
doi:10.1006/jmbi.2000.3900 available online at http://www.idealibrary.com on J. Mol. Biol. (2000) 300, 791±803
0022-2836/00/040791±13 $35.00/0 # 2000 Academic Press
2. to identify them using comparative sequence
analysis.
Since U-turns are essential anchors for long-
range interactions, their detection in large RNA
molecules such as rRNA could highlight signi®cant
structural elements in the folding and assembly of
these complex entities. The goal here was to detect
potential U-turns in 16 S and 23 S rRNA. From the
structural characteristics of experimentally deter-
mined U-turns, we de®ned a sequence/structure
signature for U-turns and sought instances thereof
in our collection of comparative rRNA structure
models. Potential U-turns in individual rRNA
sequences were evaluated from a comparative
structural perspective. Those present in the
majority of the rRNA sequences at homologous
positions were considered likely. The resulting
U-turn candidates were classi®ed into ten
distinct families, according to the predominant
sequence (GNRA or UNR), loop type (hairpin,
internal or multi-stem loop) and ¯anking base
juxtapositions (G:A, Y:N, etc.); candidates with
tertiary interactions in proximity are considered
more likely. Our previous (Gutell et al., 1994;
Gutell, 1996) and current (see the CRW Web
site, http://www.rna.icmb.utexas.edu) covariation
analyses have identi®ed numerous tertiary inter-
actions associated with potential U-turns.
Results and Discussion
The U-turn signature
Figure 1 is a schematic of tertiary interactions in
seven types of U-turns for which a 3D crystal or
NMR structure is available. Each nucleotide con-
stituent is shown with a distinct geometrical ®gure
(square, sugar; rectangle, base; circle, phosphate).
Nucleotides are numbered starting at position 0 for
the uridine (or guanosine) preceding the turn, so
that positions following the turn are ‡1, ‡2, etc.
The canonical U-turn motif involves two hydro-
gen bonds, as they appear in the crystal structure
of the Yeast tRNAPhe
anticodon loop (Figure 2,
Westhof et al., 1988). The crucial interaction stabi-
lizing the backbone reversal involves the uracil
base at position 0 and the phosphate group
immediately following position 2. Although not
absolutely required in the anticodon function
(Ashraf et al., 1999), this interaction is conserved in
all known U-turn structures and replaced with a
guanine-phosphate interaction in the GNRA loop
U-turn (Jucker & Pardi, 1995).
Another essential stabilizing hydrogen bond is
between the uridine 2H
OH at position 0 and the
purine N7 at position ‡2. An isosteric interaction
occurs in GNRA-type U-turns between the same
purine N7 and the 2H
hydroxyl of G0 (Jucker &
Pardi, 1995). Purine bases are conserved at position
‡2 in most of the U-turns studied (Figure 1),
suggesting that this structure/sequence constraint
should be a component of the U-turn signature.
The only exception to this rule is the anticodon U-
turn, where position ‡2 is approximately evenly
split between purines and pyrimidines in the
tRNA sequence alignment (Sprinzl et al., 1991).
Position ‡2 corresponds here to the central base of
the anticodon, and is thus subjected to an amino
acid coding constraint that may con¯ict with the
purine constraint.
Figure 1. Schematic of hydrogen bonds and base con-
servation in several U-turn structures. U-turn-speci®c
base-base, base-sugar and base-phosphate H bonds are
shown. The sequences shown (Y, pyrimidine; R, purine)
are either essential for structure or conserved in homolo-
gous molecules. (a) tRNA anticodon, 97 % consensus
sequence. (b) tRNA TÉC loop, 94 % consensus sequence.
(c) Hammerhead U-turn, sequence required for ribo-
zyme activity based on mutagenesis experiments
(Ruffner et al., 1990). (d) 23 S rRNA 1082-1086, 70 % con-
sensus sequence in Bacteria and chloroplasts, 89 % con-
sensus in eukaryotes. (e) 23 S rRNA 1065-1073, 93 %
consensus sequence in Bacteria and chloroplasts. (f)
GUAANA loop, consensus based on three similar NMR
and crystal structures, i.e. GUAAUA (Fountain et al.,
1996; Huang et al., 1996), GUAACA (Stallings & Moore,
1997) and GUAAAA (Puglisi & Puglisi, 1998). (g)
GNRA loop, original consensus sequence observed in
ribosomal RNA alignments (Woese et al., 1990) and
required for tertiary interactions (Heus & Pardi, 1991).
792 U-turns in rRNA
3. A ®nal constraint on U-turns has recently been
revealed in a study of the anticodon U-turn
(Auf®nger & Westhof, 1999). The authors observed
that the ®rst and last nucleotides of the anticodon
loop (positions 32:38, with sequences C:A, U:A,
U:U, C:C or U:C, see Figure 2) form a non-canoni-
cal base-pair that acts as an interface between the
end of the anticodon stem (base-pair 31:39) and the
U-turn at position 33. The hammerhead ribozyme
also features a Y:Y base-pair 5H
of a U-turn (Pley
et al., 1994a), although its conformation differs
from that of the tRNA 32:38 pair. Indeed, all U-
turns in Figure 1 contain a non-canonical pair at
the 5H
side of the turn.
An inspection of the anticodon U-turn in Figure 2
provides a possible explanation for the absence of
Watson-Crick pairs ¯anking the U-turn. The non-
canonical C32:A38 base-pair is shown in orange
while a hypothetical guanosine base (red) is posi-
tioned to form a Watson-Crick pair with C32. In
this scenario, the displacement of the C1H
atoms
between this guanosine base and A38 is about
9.3 AÊ . Here, the rotation of this guanosine base is
inadequate to connect properly to residue A36
without disrupting the whole loop conformation
(Auf®nger & Westhof, 1999). Intercalation of extra
residues between A36 and the hypothetical guano-
sine is also not possible.
There is an example where the UGA sequence
motif does not form a U-turn because the ¯anking
nucleotides form a normal Watson-Crick base-pair.
The solution structure for the 5H
-GGUG[UGAA]-
CACC oligonucleotide, representative of the
tetraloop positions 1516-1519 in 16 S rRNA, does
not make a U-turn (Butcher et al., 1997). The base
juxtapositions ¯anking most U-turns are Y:H
(H ˆ A, C or U), except in GUAANA loops
(Figure 1(f)), where it is a sheared G:A pair
(Fountain et al., 1996; Huang et al., 1996; Stallings
& Moore, 1997; Puglisi & Puglisi, 1998). Therefore,
we favor U-turn candidates ¯anked by Y:H or G:A
base juxtapositions, although the conformation for
these non-canonical pairs is not the same.
The U-turn signature emerging from this anal-
ysis is presented in Figure 3. This sequence motif
does not include the GNRA-type U-turn, for which
the GNRA sequence requirement is well estab-
lished (Woese et al., 1990; Heus & Pardi, 1991). The
UNR-type U-turn typically features a conserved
Figure 2. Stereo representation of the Yeast tRNAPhe
anticodon loop (Westhof et al., 1988), from A31 to U39. Resi-
due 37 has been omitted for clarity. The anticodon is blue and the closing base-pair is purple. The turning uridine
base (33) is black. Hydrogen bonds between U3-3 and A36 stabilizing the U-turn are shown with broken lines. The
non-canonical 32:38 base-pair ¯anking the U-turn is orange, with its bifurcated hydrogen bond (Auf®nger & Westhof,
1999) shown with a broken line. A hypothetical guanosine base (red) has been positioned to form a Watson-Crick
pair with C32, showing the effect of a canonical base-pair at this position. The C1H
atom of this hypothetical guano-
sine base is displaced by 9.26 AÊ from the C1H
of A38. Exposed H bond donors and acceptors in the three bases and
sugars following the turn are shown with ``hard'' spheres.
Figure 3. Consensus sequence and structure for UNR-
type U-turns.
U-turns in rRNA 793
4. Table 1. U-turn candidates in 16 S and 23 S rRNA
Category rRNA LT LC UP TC
A. Canonical GNRA hairpin loops 16 S H 159-162 1 None
16 S H 297-300 1 None
16 S H 727-730 1 None
16 S H 898-901 1 None
16 S H 1077-1080 1 None
16 S H 1266-1269 1 None
23 S H 463-466 1 None
23 S H 630-633 1 None
23 S H 1223-1226 1 None
23 S H 2375-2378 1 None
23 S H 2595-2598 1 None
23 S H 2659-2662 1 ‡2: [2661(2550:2558)]
23 S H 2857-2860 1 None
B. GNRA in larger hairpin loops 16 S H 1315-1322 2 None
23 S H 306-311 2 None
23 S H 745-752 4 À2: [746(2057:2611)]
23 S H 780-784 1 None
C. GNRA in internal and multi-
stem loops
16 S M 765-768 1 None
16 S M 1108-1112 1 ‡1: [1109(933:1384)]
23 S M 215-223 6 À1: [219(234:430)];
‡1: [221(265:427)]
23 S M 475-483 2 None
23 S I 511-515 2 None
23 S M 818-821 1 None
23 S I 1565-1572 4 None
23 S M 1668-1681 7 None
D. UNR in trinucleotide hairpin
loops
23 S H 1083-1085 1 ‡1: [1084(1054:1105)];
‡2: [1085(1055:1104)]
23 S H 1926-1928 1 ‡2: (1834:1928)
E. UNR at position 2 flanked by
Y:R or Y:Y base-pairs
16 S I 13-16 2 À1: (13:920); 0: (14:1398);
‡1: (15:1397); ‡2: (16:920)
16 S H 322-331 2 None
16 S H 618-622 2 None
16 S H 1090-1095 2 None
23 S H 567-574 2 ‡6: (574:2034)
23 S H 1065-1073 2 ‡5: [1071(1091:1100)];
‡6: [1072(1092:1099)]
F. UNR in hairpin loops flanked
by G:A base-pairs
16 S H 260-266 2 None
16 S H 691-696 2 None
23 S H 714-717 1 None
23 S H 1093-1098 2 None
6. purine base at position ‡2 (a constraint that does
not apply to the anticodon U-turn) and a ¯anking
Y:A, Y:Y or G:A pair at position À1 (this position
should not be occupied by a canonical Watson-
Crick base-pair). The base-pairing partner of pos-
ition À1 does not necessarily belong to the same
loop as the U-turn and can be a distant nucleotide
(e.g. in the 16 S rRNA 1211 motif, the ¯anking
base-pair is 1047:1210, see Figure 1). Tertiary
contacts at positions À1, ‡1, ‡2, and ‡3 will be
investigated.
GNRA patterns
Conserved GNRA patterns occur at 25 positions
in the 16 S and 23 S rRNAs. We de®ne here ``con-
served'' as present in a minimum of 80 % of the
bacterial sequences. GNRA patterns are found
under the following forms.
Canonical GNRA hairpin loops
The canonical form of the GNRA U-turn is the
four-nucleotide hairpin loop, with 13 occurrences
overall (Figure 4 and Table 1, category A). Some of
these candidates have been con®rmed experimen-
tally, including the 23 S rRNA 2659:2662 tetraloop
at the tip of the sarcin-ricin loop (Szewczak &
Moore, 1995; Correll et al., 1998). Comparative
analysis of this loop suggests a base-triple
interaction between position ‡2 (2661) and
the base-pair 2550:2558 (see the CRW site,
http://www.rna.icmb.utexas.edu). Whereas this
base-triple covariation is not consistent with the
loop-loop interaction observed in the recent 50 S
subunit crystal structure (Ban et al., 1999),
rearrangements remain possible and should be
considered in future studies of rRNA dynamics.
The recent low-resolution crystal structure of the
70 S ribosome also suggests an interaction between
the canonical GNRA loop at position 16 S:898-901
and the 790 helix of 23 S rRNA (Cate et al., 1999).
Two tetraloops with GNRA/GNRG sequence vari-
ations were also included (16 S:727-730 and
23 S:630-633), since both sequences can fold in the
same way (Murphy & Cech, 1994). This is con-
®rmed for the 16 S rRNA loop 727-730 in the
S15,S6,S18 rRNA crystal structure (Agalarov et al.,
2000).
GNRA in larger hairpin loops
Four conserved GNRA motifs occur within hair-
pin loops that contain more than four nucleotides
(Table 1 and Figure 4, category B). While one of
these (23 S:306) is located within a 6 nt loop and is
¯anked on both sides with nucleotides that can
form a non-canonical base-pair, the GNRA
sequence is placed asymmetrically in the other
hairpin loops. In these cases, the loop needs to be
distorted to accommodate a GNRA structure.
Although this is theoretically possible, there is no
experimental precedent. The example at positions
780-784 in 23 S rRNA would have a bulged
K (G or U) following the GNRA structure, while
the two remaining GNRA motifs occur in loops of
size eight, at the second or fourth loop position.
GNRA in internal and multi-stem loops
Eight conserved GNRA sequences occur in
internal or multi-stem loops (Figure 4 and Table 1,
category C). GNRA tetraloop conformations have
never been observed experimentally in such situ-
ations; therefore, these should be considered tenta-
tive. The GNRA sequence is involved in a putative
tertiary interaction in at least one of these loops (see
the CRW site, http://www.rna.icmb.utexas.edu).
The strongest example occurs in the 1108 loop of
16 S rRNA, where position 1109 (‡1) covaries with
the 933:1384 base-pair, while in the 215 loop of 23 S
rRNA, base triple covariations occur at positions ‡1
and À1. Two other internal loops display signi®cant
levels of GNRA/GNRG variation: 16 S rRNA
765-768 (3.4 % GAAG) and 23 S rRNA 818-821
(33 % GAAG) (see above).
UNR patterns
UNR patterns conserved in more than 90 % of
the bacterial sequences are found at 44 sites in 16 S
and 23 S rRNA. We eliminate 11 of these sites that
are ¯anked by Watson-Crick pairs with multiple
compensatory base changes, since we do not
expect U-turns to be enclosed by standard base-
pairs. The remaining 33 sites are ¯anked by
unpaired nucleotides or by a highly conserved
Watson-Crick base juxtaposition (e.g. 95 % U:A)
that could possibly form a non-canonical base-pair.
While the majority of candidates occur in hairpin
or multi-stem loops, where UNR-type U-turns
have already been observed experimentally, three
occur in internal loops (Table 1), an unexpected
and structurally less likely situation. Candidates of
the UNR type were classi®ed into categories D
through J (Table 1).
UNR in trinucleotides hairpin loops
Two trinucleotide hairpin loops contain the UNR
motif directly closed by a single base-pair which is
highly conserved (Figure 4 and Table 1, category
D). The 23 S rRNA base-pair 1082:1086 is U:A in
nearly 100 % of the bacterial and chloroplast
sequences and C:G in almost all of the eukaryotic
sequences (Table 2). Such an atypical base-pairing
constraint can be associated to various confor-
mations of non-canonical base-pairs (Gautheret &
Gutell, 1997). Indeed, a reverse Watson-Crick base-
pair at position 1082:1086 and a U-turn in the
UAA hairpin were identi®ed in the crystal struc-
ture of the L11 binding region of 23 S rRNA (Conn
et al., 1999; Wimberly et al., 1999). The 1926 triloop
also has the UAA sequence; here, the closing base-
pair is a conserved C:G in Bacteria and chloro-
plasts (Table 2). While reverse Watson-Crick U:A
796 U-turns in rRNA
7. and C:G base-pairs do not form identical isosteric
conformations (Gautheret & Gutell, 1997), a pre-
cedent for this type of exchange is the tRNA 15:48
reverse Watson-Crick base-pair. Given similar
sequence constraints in both loops, we expect their
3D structure to be similar as well. Since the bases
‡1 and ‡2 in the 23 S rRNA 1083-1085 loop are
involved in tertiary contacts with base-pairs
1054:1105 and 1055:1104 in the crystal structure of
the L11 binding region of 23 S rRNA (Conn et al.,
1999), we anticipated tertiary interactions at pos-
itions 1927 or 1928. Interestingly, our comparative
analysis revealed a covariation between positions
1928 and 1834 (see Figure 4 and the CRW site,
http://www.rna.icmb.utexas.edu/).
UNR at position 2 flanked by Y:R or
Y:Y base-pairs
Six UNR sites have the UNR pattern at position
2 of a hairpin or internal loop, and ¯anked by a
Y:R or Y:Y juxtaposition (Figure 4 and Table 1, cat-
egory E). This arrangement is similar to the tRNA
anticodon U-turn, except for the difference in loop
sizes. Tertiary contacts at position ‡1 to ‡3 have
been predicted for loop 16 S:13 (see the CRW site,
http://www.rna.icmb.utexas.edu/), with covaria-
tions at positions 13:920 (À1), 14:1398 (U-turn
position), 15:1397 (‡1) and 16:920 (‡2). Although
the U-turn position has not been implicated in
long-range tertiary interactions, contacts with
position À1 are possible, as shown in the hammer-
head ribozyme (Pley et al., 1994a) and TcC-loop of
tRNA (Quigley & Rich, 1976). In addition, two of
the U-turn candidates in this category have tertiary
interactions at positions 5 and 6 (23 S rRNA
position 567 and 1065, see Table 1 and Figure 4).
UNR in hairpin loops flanked by G:A base-pairs
Four UNR motifs are ¯anked by a G:A base jux-
taposition (Figure 4 and Table 1, category F). Hexa-
nucleotide loops with the GUAANA sequence
consensus fall in this category, forming a well
characterized three-dimensional motif (Fountain
et al., 1996; Huang et al., 1996; Stallings & Moore,
1997; Puglisi & Puglisi, 1998), with a sheared G:A
closing base-pair and a U-turn forming at the con-
served uridine base. Nucleotides AAU located 3H
to
the U-turn in the 23 S rRNA 1093 loop form ter-
tiary contacts with the 1065-1073 loop (Conn et al.,
1999). Likewise, the 23 S rRNA 713 loop is
involved in an important tertiary interaction brid-
ging the 30 S and 50 S ribosomal subunits (Culver
et al., 1999). The 16 S rRNA hairpin loop 691-696
begins with a G and ends with an A and is similar
to the previous two motifs in size and loop closure.
Interestingly, this loop is protected by tRNA
(Moazed & Noller, 1989b) and the association of
subunits (Powers et al., 1993; Merryman et al.,
1999). The fourth motif, 16 S rRNA 260-266, has a
seven-nucleotide loop with a weak covariation in
the Bacteria between positions 260 and 265. This
would create a ®ve-nucleotide hairpin loop with a
G:G, G:A or A:A closing base-pair. These pairing
types can adopt a sheared base-pair conformation
similar to the G:A pair in the other motif.
Sequence variations in the 23 S rRNA 713 loop
are particularly interesting (Table 3). Archaea and
eukaryotes have a central GAAA sequence closed
by a Watson-Crick base-pair (G:C or C:G), while
Bacteria and chloroplasts have a central UNAN
sequence closed by a G:A juxtaposition. Both com-
binations (Watson-Crick pair ‡ GNRA sequence or
G:A pair ‡ UNRN sequence) can form a U-turn at
position 2 of the loop, and thus retain the ability to
form the tertiary interaction with the 30 S riboso-
mal subunit.
UNR in internal and multi-stem loops flanked by
C:G pairs
Three internal and multi-stem loops display con-
served UNA sequences adjacent to a conserved
C:G pair in Bacteria (see Figure 4 and Table 1, cat-
egory G, and the CRW site for base-pair frequen-
cies). It is unlikely that reverse Watson-Crick C:G
pairs form in these cases, since the pairs are
¯anked by other secondary structure base-pairs.
Although other non-canonical conformations are
still possible, these three sites are weak U-turn can-
didates. An additional site in this category, found
at 23 S rRNA position 202, has been eliminated,
since it is part of a ``loop E'' motif (Leontis &
Westhof, 1998), which does not contain a U-turn.
Table 2. Base-pair frequencies for 23 S rRNA positions
1082:1086 and 1925:1929 (only frequencies over 1 % are
shown)
Kingdom Most frequent sequence
A. 1082:1086
(eu)Bacteria U:A (98.8 %) C:G (1.0 %)
(1 phylogenetic event)a
Chloroplast U:A (98.0 %) U:C (2.0 %)
Archaea C:G (59.5 %) U:A (40.5 %)
(3 phylogenetic events)a
Eucarya C:G (98.6 %)
B. 1925:1929
(eu)Bacteria C:G (99.2 %)
Chloroplast C:G (100.0 %)
Archaea U:G (100.0 %)
Eucarya C:G (99.4 %)
a
Concerted base changes occurring between closely related
organisms (see Materials and Methods).
Table 3. Sequence variations at 23 S rRNA positions
713-718
Kingdom Most frequent sequence
(eu)Bacteria GUAANA (96 %)
Chloroplast GUNANA (85 %)
Archaea CGAAAG (40 %) GGAAAC
(35 %) CUUACG (8 %)
Eucarya GGAAAC (80 %) CGAAAG
(5 %)
U-turns in rRNA 797
8. UNR in loops flanked by other base-pairs
Five UNR sequences are ¯anked by other base
juxtapositions (Figure 4 and Table 1, category H).
Two of these are ¯anked by a secondary structure
base-pair (23 S:1951 and 16 S:1065), but atypical
sequence constraints in these pairs are compatible
with a non-canonical pairing (Table 4). In addition,
the 23 S rRNA 1951 U-turn candidate is associated
to a base-triple type covariation between positions
(1950:1956) and 1954 (Figure 4 and the CRW
site, http://www.rna.icmb.utexas.edu/). The 16 S
Figure 4 (legend shown on page 800)
798 U-turns in rRNA
9. rRNA 787-795 loop contains two overlapping U-
turn signatures: the 95 % consensus for 788-790 is
UYA, while the 83 % consensus for 789-791 is
UAG. The structure of this nine-nucleotide hairpin
resembles the tRNA TcC-loop (Gu et al., 1994),
with a closing A:C base-pair reducing the loop size
to seven. The U-turn occurring at position U55 in
tRNA would be homologous to position U789 in
16 S rRNA (Gu et al., 1994). In addition, in vitro
selection experiments indicate that U789, rather
than U788 is required for ribosome function (Lee
et al., 1997). Therefore, while sequence conservation
alone would favor a U-turn at 788, this turn is
more likely at position 789. Nucleotides within this
Figure 4 (legend shown on page 800)
U-turns in rRNA 799
10. Figure 4. Potential U-turns shown on the E. coli secondary structures for the small subunit (a), the large subunit 5H
half (b) and the large subunit 3H
half (c) of ribosomal RNA. Loops containing potential U-turns are shown as nucleo-
tides, and the remainder of the structure is shown as gray circles. Each U-turn position is shown as a red nucleotide.
Green nucleotides show positions involved in tertiary interactions. U-turn positions involved in tertiary interactions
have red nucleotides enclosed in green boxes. Tentatively proposed interactions in proximity to U-turns are blue. Yel-
low boxes highlight hairpin loops and their loop type identi®ers; orange boxes highlight internal and multi-stem
loops and their loop type identi®ers. U-turn categories are de®ned as in Table 1: A, canonical GNRA hairpin loops;
B, GNRA in larger hairpin loops; C, GNRA in internal and multi-stem loops; D, UNR in trinucleotide hairpin
loops; E, UNR at position 2 ¯anked by Y:R or Y:Y base-pairs;, UNR in internal and multi-stem loops ¯anked
by C:G base-pairs; H, UNR in loops ¯anked by other base-pairs; I, UNR in loops without ¯anking base-pairs;
J, ambiguous UNR/GNRA exchanges.
800 U-turns in rRNA
11. loop are protected by ribosomal subunit associ-
ation, suggesting that this U-turn motif is involved
in tertiary interactions (Powers et al., 1993;
Merryman et al., 1999).
UNR in loops without flanking base-pair
Flanking base-pairs are unknown or ambiguous
for ten of the U-turn candidates (Figure 4 and
Table 1, category I). Four of these potential U-turns
are associated with predicted tertiary interactions
at position ‡1 to ‡3 relative to the turn (summar-
ized in Table 1). The 116 loop in 16 S rRNA con-
tains two predicted interactions: a base triple at
positions 121(124:237) or 121(125:236) (Babin et al.,
1999) and the two base-pairs 118:288 and 119:287
(see putative tertiary interactions on the CRW site).
The latter interaction is supported by U.V. cross-
linking (Stiege et al., 1986). Proposed tertiary inter-
actions at positions 2112:2169 and 2113:2170
(Figure 4 and the CRW site) in the rRNA E site
(23 S rRNA 2162 loop) (Moazed & Noller, 1989a)
are also supported by crosslinking studies (Doring
et al., 1991). These tertiary interactions correspond
to positions ‡2 and ‡3 after the proposed U-turn.
Tertiary base covariations are also observed at the
3H
end of the 23 S rRNA 1339 loop (pseudoknot
1343-1344:1403-1404, see the CRW cite) and in the
23 S rRNA 2583 loop (1782:2586). Both of these
proposed interactions are supported experimen-
tally, the former by site-directed mutagenesis (Kooi
et al., 1993), and the latter by U.V. crosslinks
between positions 2584-2588 and 1777-1792 (Stiege
et al., 1983). The 23 S:2497 loop has putative
tertiary interactions 5H
to the turn at positions À1
and À2 (2499:2453 and 2498:2454).
Ambiguous UNR/GNRA exchanges
Exchanges between UNR and GNRA sequences
occur at two hairpin loop sites (16 S:863 and
16 S:1013, see Figure 4). This is similar to the
sequence variation at the 23 S:713 hairpin loop
(Table 3). This type of variation could result from a
selective pressure for U-turns at these sites. The
16 S:863 loop has another characteristic associated
with U-turns: two positions 3H
to this putative U-
turn form tertiary pseudoknot base-pairs to 16 S
rRNA positions 570-571 (Gutell et al., 1986; Vila
et al., 1994). However, in both cases the UNR
sequence is not ¯anked by a G:A or Y:H mismatch,
but instead by canonical base-pair exchanges (e.g.
G:C to A:U). The structures for these two sites are
uncertain, since these pairing types have not been
observed ¯anking a U-turn.
Conclusion
Comparative sequence analysis enables us to dis-
tinguish randomly occurring U-turn signatures
from candidates that are supported by sequence
conservation and speci®c patterns of base-pair
exchanges. We have identi®ed 58 UNR and GNRA
U-turn candidates in a variety of structural settings
in the 16 S and 23 S rRNAs. Since the sequence
and structural information that de®nes a U-turn is
minimal and the sequence constraint rules that we
have used to identify U-turns may be associated
with other structural motifs, some of our predicted
U-turns may be incorrect. Alternatively, these U-
turn signatures may be associated with structural
conformations that alternate between U-turns and
these other structural motifs. Used as working
hypotheses, putative U-turns and the associated
tertiary interactions can be used for modeling
(prior to re®nement) and interpretation (after
re®nement) of the X-ray crystal structures of the
ribosome.
Materials and Methods
We have used the alignments of small and large sub-
unit rRNA sequences maintained by us at the University
of Texas (R.R.G., unpublished results). The small subunit
rRNA alignment contains 5826 Bacteria, 182 chloroplast,
264 Archaea and 1054 Eukaryotic sequences. The large
subunit rRNA alignment contains 326 Bacteria, 103
chloroplast, 41 Archaea and 263 Eukaryotic sequences.
Secondary structure diagrams for representatives of the
main phylogenetic groupings are inferred with compara-
tive sequence analysis (Gutell et al., 1993; Gutell, 1994)
and are available from our Austin, Texas CRW site (The
Comparative RNA Web Site: http://www.rna.icmb.u-
texas.edu/, R.R.G., unpublished results).
Base frequencies were computed independently in the
Bacteria, chloroplast, Archaea and Eukaryotic align-
ments. When not otherwise speci®ed, base or base-pair
frequencies refer only to Bacteria sequences. Base num-
bering always refers to Escherichia coli 16 S or 23 S rRNA
sequences (GeneBank accession no. J01695). The phyloge-
netic events for base-pairs in Tables 2 and 4 were
derived from the CRW site (http://www.rna.icmb.
utexas.edu/). Here, the numbers of mutual changes that
have occurred throughout evolution for each pair in our
comparative structure model are accessible, as well as
Table 4. Sequence variations at base-paired positions
16 S rRNA 1064:1192 and 23 S rRNA 1950:1956 (all
frequencies over 1 % are shown, see the CRW web site
for a detailed analysis)
Kingdom Most frequent sequence
A. 16 S 1064:1192
(eu)Bacteria G:C (97 %) G:U (2 %)
Archaea G:C (100 %)
Eucarya C:U (89 %) U:C (4 %) U:A (2 %)
(4 phylogenetic events)a
B. 23 S 1950:1956
(eu)Bacteria G:U (94 %) U:A (5 %)
(2 phylogenetic events)a
Archaea G:U (59 %) U:G (17 %) A:A
(15 %) U:A (10 %) (no
phylogenetic event)a
Eucarya C:A (89 %) G:U (3 %) U:G (3 %)
U:U (3 %) (2 phylogenetic
events)a
a
Concerted base changes occurring between closely related
organisms (see Materials and Methods).
U-turns in rRNA 801
12. details of the base-pair types and speci®c phylogenetic
location for each mutual change. A ``phylogenetic event''
was recorded when both positions in the pair varied
between two consecutive organisms. This approximation
is simplistic but conservative, since all but the most
recent events are neglected.
tRNA base frequencies, were derived from the 1997
version of M. Sprinzl's tRNA alignments (Sprinzl et al.,
1991). All nuclear tRNAs and tDNAs were included in
our base counts. The Yeast tRNAPhe
numbering is used
throughout.
The Figures and Tables for this article are available
online at the main CRW site (http://www.rna.icmb.u-
texas.edu/, go to ``RNA Structure Analysis/U-Turn'') or
by using the speci®c URL (http://www.rna.icmb.utexa-
s.edu/ANALYSIS/U-TURN/).
Acknowledgments
This work was supported in part from the NIH grants
awarded to R.G. (NIH - GM48207) and startup funds
from the Institute for Cellular and Molecular Biology at
the University of Texas at Austin.
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Edited by J. A. Doudna
(Received 25 February 2000; received in revised form 22 May 2000; accepted 22 May 2000)
U-turns in rRNA 803