Mesophiles vs. Thermophiles: Untangling the Hot Mess of Intrinsically Disordered Proteins and Growth Temperature of Bacteria
Abstract
:1. Introduction
1.1. Intrinsically Disordered Proteins and Their Abundance
1.2. Identification of IDP Groups
1.3. Quasi-Independent Contrasts
2. Results and Discussion
2.1. Overall IDP Abundance in Different Proteomes
2.2. Overall IDP Abundance in Orthologs
2.3. Abundance in Different IDP Classes and Proteins with Different Molecular Functions
2.4. Analysis of Aligned Ortholog Clusters
2.5. Phylogeny Impact on FOD/OGT Relationship
3. Materials and Methods
3.1. Data Sources and Availability
3.2. Protein Clustering
- Proteins from at least 10 different species per cluster;
- At least one candidate IDP (identification described in the disorder calculation subsection);
3.3. Disorder Calculations
- 3.
- RAPID disorder score ≥ 0.5;
- 4.
- Total number of residues × RAPID disorder score ≥ 100;
- 5.
- IDP type 3, 4, or 5 (strong polyampholytes or positive/negative strong polyelectrolytes);
3.4. Cluster Disorder Alignment
3.5. Quasi-Independent Contrast Calculation
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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IDP Class | Thermophilic FOD | Mesophilic FOD |
---|---|---|
Weak polyampholytes/polyelectrolytes | 0.303 ± 0.054; n = 21 | 0.192 ± 0.007; n = 609 |
Boundary proteins | 0.181 ± 0.007; n = 422 | 0.176 ± 0.002; n = 7830 |
Strong polyampholytes | 0.358 ± 0.014; n = 180 | 0.357 ± 0.004; n = 2145 |
Negative strong polyelectrolytes | - | - |
Positive strong polyelectrolytes | 0.682 ± 0.016; n = 13 | 0.706 ± 0.005; n = 256 |
IDP Function Tag | Thermophilic FOD | Mesophilic FOD |
---|---|---|
Activator | - | 0.339 ± 0.010; n = 33 |
Nuclease | - | 0.110 ± 0.003; n = 18 |
Chaperone | 0.090 ± 0.010; n = 18 | 0.114 ± 0.003; n = 516 |
DNA-binding | 0.276 ± 0.032; n = 35 | 0.264 ± 0.008; n = 477 |
Elongation factor | 0.125 ± 0.034; n = 33 | 0.070 ± 0.005; n = 367 |
Excision nuclease | 0.053 ± 0.005; n = 7 | 0.054 ± 0.001; n = 192 |
Hydrolase | 0.064 ± 0.005; n = 14 | 0.108 ± 0.009; n = 209 |
Initiation factor | 0.217 ± 0.026; n = 3 | 0.209 ± 0.004; n = 56 |
Isomerase | 0.090 ± 0.024; n = 3 | 0.076 ± 0.001; n = 91 |
Ligase | 0.060 ± 0.008; n = 12 | 0.058 ± 0.002; n = 336 |
Lyase | 0.077 ± 0.005; n = 11 | 0.076 ± 0.001; n = 230 |
Multifunctional enzyme | 0.055 ± 0.000; n = 1 | 0.052 ± 0.001; n = 13 |
Oxidoreductase | 0.102 ± 0.018; n = 13 | 0.073 ± 0.002; n = 245 |
Peroxidase | 0.082 ± 0.007; n = 3 | 0.097 ± 0.004; n = 59 |
Protease | 0.082 ± 0.008; n = 7 | 0.080 ± 0.001; n = 284 |
RNA-binding | 0.165 ± 0.033; n = 17 | 0.126 ± 0.005; n = 388 |
Receptor | 0.095 ± 0.000; n = 1 | 0.112 ± 0.016; n = 10 |
Repressor | 0.331 ± 0.086; n = 4 | 0.263 ± 0.017; n = 51 |
Ribosomal protein | 0.467 ± 0.018; n = 110 | 0.437 ± 0.004; n = 1859 |
Rotamase | 0.191 ± 0.030; n = 4 | 0.209 ± 0.010; n = 36 |
Serine protease | 0.062 ± 0.000; n = 1 | 0.063 ± 0.001; n = 49 |
Sigma factor | 0.142 ± 0.011; n = 18 | 0.149 ± 0.003; n = 154 |
Topoisomerase | 0.075 ± 0.007; n = 6 | 0.087 ± 0.001; n = 151 |
Transferase | 0.087 ± 0.012; n = 27 | 0.073 ± 0.003; n = 713 |
Translocase | 0.049 ± 0.004; n = 7 | 0.076 ± 0.004; n = 127 |
rRNA-binding | 0.294 ± 0.010; n = 96 | 0.284 ± 0.002; n = 1700 |
tRNA-binding | 0.338 ± 0.015; n = 55 | 0.297 ± 0.005; n = 686 |
Protein Name | FOD (Thermophilic) | FOD (Mesophilic) | Absolute FOD Difference | Cluster Members |
---|---|---|---|---|
Rubredoxin | 0.085 | 0.389 | 0.304 | A0A291P6P4, A0A410H536, A0A1B2LXP3… |
Acyl carrier | 0.534 | 0.392 | 0.142 | A0A291P5S3, A0A410H1W4, A0A386X534… |
Spore protein | 0.647 | 0.786 | 0.139 | A0A0D8BNT0, A0A0D8BRQ7, M5R4X2… |
LRSP * bL19 | 0.357 | 0.239 | 0.118 | A0A1U9K6D3, A0A1B9NF78, A0A1B0ZK26… |
SRSP bS21 | 0.596 | 0.484 | 0.112 | A0A0D5YVA4, A0A1Z4BT12, A0A1L3J4J5… |
SRSP uS14 | 0.476 | 0.370 | 0.106 | A0A0P0DDQ1, A0A0D5YRD0, A0A0S2I2L9… |
LRSP bL28 | 0.512 | 0.610 | 0.098 | A0A0D8BU85, M5QWZ7, A0A1D7QW46… |
Cupin | 0.385 | 0.287 | 0.097 | A0A0K2SHK7, A0A0D5NPB9, A0A4P6K4Z4… |
LRSP uL24 | 0.323 | 0.414 | 0.090 | A0A0D8BQ30, M5QVZ2, A0A1D7QZW9… |
SRSP uS14 | 0.501 | 0.417 | 0.083 | A0A291PBX7, A0A7C9NQP7, A0A3T1DHB4… |
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Kruglikov, A.; Xia, X. Mesophiles vs. Thermophiles: Untangling the Hot Mess of Intrinsically Disordered Proteins and Growth Temperature of Bacteria. Int. J. Mol. Sci. 2024, 25, 2000. https://doi.org/10.3390/ijms25042000
Kruglikov A, Xia X. Mesophiles vs. Thermophiles: Untangling the Hot Mess of Intrinsically Disordered Proteins and Growth Temperature of Bacteria. International Journal of Molecular Sciences. 2024; 25(4):2000. https://doi.org/10.3390/ijms25042000
Chicago/Turabian StyleKruglikov, Alibek, and Xuhua Xia. 2024. "Mesophiles vs. Thermophiles: Untangling the Hot Mess of Intrinsically Disordered Proteins and Growth Temperature of Bacteria" International Journal of Molecular Sciences 25, no. 4: 2000. https://doi.org/10.3390/ijms25042000
APA StyleKruglikov, A., & Xia, X. (2024). Mesophiles vs. Thermophiles: Untangling the Hot Mess of Intrinsically Disordered Proteins and Growth Temperature of Bacteria. International Journal of Molecular Sciences, 25(4), 2000. https://doi.org/10.3390/ijms25042000