Protein Fold Usages in Ribosomes: Another Glance to the Past
Abstract
:1. Introduction
- Ce texte cite une «certaine encyclopédie chinoise » où il est écrit que «Les animaux se divisent en: (a) appartenant à l’Empereur, (b) embaumés, (c) apprivoisés, (d) cochons de lait, (e) sirènes, (f) fabuleux, (g) chiens en libertés, (h) inclus dans la présente classification, (i) qui s’agitent comme des fous, (j) innombrables, (k) dessinés avec un pinceau très fin en poil de chameau, (l) et caetera, (m) qui viennent de casser la cruche, (n) qui de loin semblent des mouches» (Borges). Préface de «les mots et les choses» Michel Foucault.
1.1. About Usages in Complex Systems
1.2. “To Be or Not to Be” a Protein Fold
1.3. Folding or Misfolding: That’s a Question of Ribosome?
2. Results
2.1. Ribosomal Protein Fold Distribution
2.1.1. Overview
2.1.2. OB and SH3 Domains—The Small Barrel SRFs
2.1.3. The Premise of the Power-Law Behavior
2.1.4. Different Fold Usages in the LSU and SSU
2.2. Ribosomal Protein Folds Specific to Each Kingdom
2.2.1. Minimal Fold Content
2.2.2. Different Behavior of Kingdom Specific Folds in Bacteria and Archaea/Eukarya
2.3. Imitation Game: Fold Mimicry across Kingdoms
2.4. Fold Evolution/Convergence
2.5. The Inexorable Expansion of Fold Extensions
3. Discussion
3.1. What’s New from the Past?
3.2. Ancestral Evolutionary Mechanisms with Different Selective Pressure
3.3. Imitation Games at the Ribosome Age
3.4. Order First, Disorder Next?
4. Materials and Methods
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Kingdom | Proteins | Folds | Protein/Fold Ratio | Nucleotides | |
---|---|---|---|---|---|
Bacteria | LSU | 33 | 32 | 1.03 | 3036 † |
SSU | 19 | 20 | 0.95 | 1521 † | |
Total | 52 | 46 * | 1.13 | 4557 † | |
Archaea | LSU | 39 | 33 | 1.18 | 3175 † |
SSU | 26 | 25 | 1.04 | 1495 † | |
Total | 65 | 49 * | 1.32 | 4670 † | |
Eukarya | LSU | 44 | 36 | 1.22 | 3675 † |
SSU | 33 | 29 | 1.14 | 1800 † | |
Total | 77 | 54 * | 1.42 | 5475 † |
Specific Ribosomal Protein | Specific Ribosomal Protein Fold | Specific Ribosomal Protein | Universal Ribosomal Protein Fold | |
---|---|---|---|---|
Bacteria | bL9 | 3.40.5 RP L9; domain 1 & 3.10.430 RP L9; domain 2 | bL12 | 3.30.1390 RP L30; Chain: A |
bL17 | 3.90.1030 50s RP L17; Chain A | bL19 | 2.30.30 SH3 type barrels | |
bL20 | 1.10.1900 c-terminal domain of poly(a) binding domain | bL21 | 2.40.50 OB fold | |
bL25 | 2.40.240 RP L25; Chain P & 2.170.120 RNApol α Subunit; Chain A, domain 2 | bL27 | 2.40.50 OB fold | |
bL35 | 4.10.410 Factor Xa Inhibitor | bL28 | 2.30.170 RP L24e; Chain: T | |
bL36 | 2.60.120 Jelly Rolls | bL31 | 4.10.830 30s RP S14; Chain N | |
bS16 | 3.30.1320 S16 RP; Chain: A | bL32 | 1.20.5 Single α-helices involved in coiled-coils or other helix-helix interfaces | |
bS18 | 4.10.640 30s RP S18 | bL34 | 1.10.287 Helix Hairpins | |
bS20 | 1.20.58 Methane Monooxygenase Hydroxylase; Chain G, domain 1 | bS6 | 3.30.70 α-β Plaits | |
Archaea and Eukarya | eL8 | 3.30.1330 60s RP L30; Chain: A | eL14 | 2.30.30 SH3 type barrels |
eL15 | 3.40.1120 RP L15e | eL18 | 3.100.10 RP L15; Chain K; domain 2 | |
eL19 | 1.10.1650 50s RP L19e, Chain O, domain 1 | eL21 | 2.30.30 SH3 type barrels | |
eL20 | 3.10.20 UB roll | eL24 | 2.30.170 RP L24e; Chain: T | |
eL30 | 3.30.1330 60s RP L30; Chain: A | eL27 | 2.30.30 SH3 type barrels | |
eL31 | 3.10.440 RP L31e; Chain: W | eL32 | 3.30.70 α-β Plaits | |
eL33 | 2.40.10 Thrombin, subunit H | eL41 | 1.20.5 Single α-helices involved in coiled-coils or other helix-helix interfaces | |
eL34 | 6.20.340 His-Me finger endonuclease fold | eS4 (3 folds) | 2.30.30 SH3 type barrels & 2.40.50 OB fold & 3.10.290 Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region; Chain A | |
eL37 | 2.20.25 N-terminal domain TfIIb | eS8 | 3.10.290 Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region; Chain A | |
eL39 | 1.10.1620 Atp Synthase ε Chain; Chain: I | eS19 | 1.10.10 Arc Repressor Mutant, subunit A | |
eL40 | 4.10.1060 ZNF265 like | eS24 | 3.30.70 α-β Plaits | |
eL43 | 2.20.25 N-terminal domain TfIIb | eS28 | 2.40.50 OB fold | |
eS1 | 3.10.20 UB roll & 3.30.479 Tetrahydropterin Synthase; Chain A | |||
eS6 | 3.10.20 UB roll | |||
eS21 | 3.30.1230 Hypothetical Cytosolic Protein; Chain A | |||
eS27 | 2.20.25 N-terminal domain TfIIb | |||
eS31 | 6.20.50 N-terminal domain TfIIb | |||
Eukarya | eL22 | 3.30.1360 Gyrase A; domain 2 | eL6 | 2.30.30 SH3 type barrels |
eL29 | 6.10.140 Helix Hairpins | eL13 | 1.10.10 Arc Repressor Mutant, subunit A | |
eL38 | 3.30.720 Signal recognition particle alu RNA binding heterodimer, srp9/1 | eL36 | 1.10.10 Arc Repressor Mutant, subunit A | |
RACK1 | 2.130.10 Methylamine Dehydrogenase; Chain H | eS10 | 1.10.10 Arc Repressor Mutant, subunit A | |
eS26 | 3.30.1740 First Zn finger domain of poly(adp-ribose) polymerase-1 | eS25 | 1.10.10 Arc Repressor Mutant, subunit A | |
eS30 | 1.20.5 Single α-helices involved in coiled-coils or other helix-helix interfaces | |||
Eukarya specific ribosomal protein | Archaea and Eukarya specific ribosomal protein fold | |||
eS7 | 2.20.25 N-terminal domain TfIIb | |||
eS12 | 3.30.1330 60s RP L30; Chain: A |
Eukarya | Bacteria | |||
---|---|---|---|---|
Protein | CATH | Protein | CATH | |
LSU | eL15 | 3.40.1120 RP L15e | bL28 | 2.30.170 TP L24e; Chain T |
eL21 | 2.30.30 SH3 type barrels | bL27 | 2.40.50 OB fold | |
eL24 | 2.30.170 RP L24e; Chain T | bL19 | 2.30.30 SH3 type barrels | |
eL31 | 3.10.440 RP L31e; Chain W | bL17 | 3.90.1030 50s RP L17; Chain A | |
eL33 | 2.40.10 Thrombin, subunit H | bL20 | 1.10.1900 C-terminal domain of poly(a) binding protein | |
eL40 | 4.10.1060 ZNF265 like | bL36 | 2.60.120 Jelly Rolls | |
SSU | eS1 | 3.10.20 UB roll/3.30.479 Tetrahydropterin Synthase; Chain A | bS6/bS18 | 3.30.70 α-β Plaits/4.10.640 30s RP S18 |
eS4 | 2.30.30 SH3 type barrels | bS16 | 3.30.1320 S16 RP; Chain A | |
eS8 | 3.10.290 Structural Genomics Hypothetical 15.5Kd Protein In mrcA-pckA Intergenic Region; Chain A | bS20 | 1.20.58 Methane Monooxygenase Hydroxylase; Chain G, domain 1 | |
eS17 | 1.10.60 Diphtheria Toxin Repressor; domain 2 | uS2-dom | 3.40.50 Rossmann fold |
Urfolds/Metafolds | Universal 1 | B 2 | AE 3 | E 4 |
---|---|---|---|---|
SBBs | uL2, uL3, uL24, uS12, uS17 | bL19, bL21, bL27 | eL14, eL21, eL24, eL27, eL33, eS4, eS28 | eL6 |
βαββαβ | uL1 (domain1), uL5, uL6, L7/L12, uL10, uL13, uL16, uL23, uS3, uS5 (C terminal domain), uS8, uS9, uS10 | bL9 (C terminal domain), bS6 | eL30, eL32, eS24 | eL22 |
RLM | uL1 (domain 2), uL4, uS2 | |||
Perpendicularly stacked α helices | uS13, uS2 (coiled coil domain) | bL20 | eS17 | |
3 parallel α helices | uL29, uS15 | bL34, bS20 | eL19 |
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Tanoz, I.; Timsit, Y. Protein Fold Usages in Ribosomes: Another Glance to the Past. Int. J. Mol. Sci. 2024, 25, 8806. https://doi.org/10.3390/ijms25168806
Tanoz I, Timsit Y. Protein Fold Usages in Ribosomes: Another Glance to the Past. International Journal of Molecular Sciences. 2024; 25(16):8806. https://doi.org/10.3390/ijms25168806
Chicago/Turabian StyleTanoz, Inzhu, and Youri Timsit. 2024. "Protein Fold Usages in Ribosomes: Another Glance to the Past" International Journal of Molecular Sciences 25, no. 16: 8806. https://doi.org/10.3390/ijms25168806