The Ancient History of Peptidyl Transferase Center Formation as Told by Conservation and Information Analyses
Abstract
:1. Introduction
2. Material and Methods
2.1. Download of Complete 23S Ribosomal RNAs from Public Databases
2.2. Retrieving PTCs from 23S Ribosomal RNA Sequences
2.3. Multiple Alignment, Filtering, and Production of PTC Datasets
2.4. Information Theory Analysis of PTCs
2.5. Mapping Conservation into 2D and 3D PTC Structures
2.6. 3D Modeling of the Different PTC Sequences and Structural Comparisons
3. Results
3.1. PTC Datasets: Production and Taxonomic Analysis
3.2. Multiple Alignment and Sequence Conservation of PTC Datasets
3.3. Mapping 100% Conserved Sites into the 3D Structure of the PTC
3.4. Identity Elements, Entropy Variation, Information Variation
3.5. Mapping Identity Elements and Information Clusters into the 2D Structure of the PTC
3.6. Mapping Proto-tRNAs into the 2D Structure of the PTC
3.7. Mapping Identity Elements and Information Clusters into the 3D Structure of the PTC
3.8. Structural Alignment of PTC Datasets to T. Thermophilus
4. Discussion
Supplementary Materials
Author Contributions
Funding
Conflicts of Interest
References
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Dataset Name | Clades | Number of PTC Sequences | Alignment Size (Gaps) | Positions 100% Conserved |
---|---|---|---|---|
PTC-all | Bacteria Archaea Eukarya | 1424 | 201 (10) | 42 |
PTC-Bac | Bacteria * | 1301 | 195 (8) | 62 |
PTC-Arc | Archaea * | 118 | 186 (7) | 83 |
PTC-Pro | Proteobateria * | 564 | 186 (7) | 110 |
PTC-Fir | Firmicutes ** | 237 | 184 (4) | 122 |
PTC-Act | Actinobacteria | 153 | 179 (0) | 132 |
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Prosdocimi, F.; Zamudio, G.S.; Palacios-Pérez, M.; Torres de Farias, S.; V. José, M. The Ancient History of Peptidyl Transferase Center Formation as Told by Conservation and Information Analyses. Life 2020, 10, 134. https://doi.org/10.3390/life10080134
Prosdocimi F, Zamudio GS, Palacios-Pérez M, Torres de Farias S, V. José M. The Ancient History of Peptidyl Transferase Center Formation as Told by Conservation and Information Analyses. Life. 2020; 10(8):134. https://doi.org/10.3390/life10080134
Chicago/Turabian StyleProsdocimi, Francisco, Gabriel S. Zamudio, Miryam Palacios-Pérez, Sávio Torres de Farias, and Marco V. José. 2020. "The Ancient History of Peptidyl Transferase Center Formation as Told by Conservation and Information Analyses" Life 10, no. 8: 134. https://doi.org/10.3390/life10080134