The Mutational Robustness of the Genetic Code and Codon Usage in Environmental Context: A Non-Extremophilic Preference?
Abstract
:1. Introduction
2. Materials and Methods
2.1. Data Aquisition
2.2. Distortion as a Measure for Code Performance
2.3. Background Mutation Model
2.4. Multi-Linear Regressions
3. Results
3.1. Environmental Factors Mainly Increase Expected Distortions
3.2. Robustness of Enviromental Effects with Regard to Ti/Tv-Ratio
3.3. The Effect of GC-Content on Physicochemical Fidelities
4. Discussion
4.1. Selection in Extremophiles can Decrease Mutational Robustness
4.2. GC-Content and Its Effect on Distortions
4.3. Limitations of the Current Model and Future Prospects
4.4. Implications of the Non-Extremophile Optimality of the Genetic Code and Codon Usage
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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D | Parameter | Unstandardized Coeff. | Βstd | t | p | F(5,397) | R2 | p | |
---|---|---|---|---|---|---|---|---|---|
β | SE | ||||||||
Hyd. | Intercept | 1.525 | 0.018 | - | 82.653 | 0.000 | 471.286 | 0.854 | 0.000 |
Temp. | 0.001 | 0.000 | 0.160 | 7.967 | 0.000 | ||||
NaCl | −0.001 | 0.000 | −0.100 | −5.247 | 0.000 | ||||
pH | 0.003 | 0.001 | 0.060 | 2.944 | 0.003 | ||||
GC | 0.440 | 0.067 | 1.300 | 6.529 | 0.000 | ||||
GC2 | −0.115 | 0.063 | −0.360 | −1.810 | 0.071 | ||||
Pol. | Intercept | 1.447 | 0.018 | - | 79.729 | 0.000 | 61.372 | 0.430 | 0.000 |
Temp. | 0.000 | 0.000 | 0.120 | 3.024 | 0.003 | ||||
NaCl | 0.002 | 0.000 | 0.360 | 9.426 | 0.000 | ||||
pH | 0.002 | 0.001 | 0.090 | 2.327 | 0.020 | ||||
GC | −0.416 | 0.066 | −2.470 | −6.275 | 0.000 | ||||
GC2 | 0.314 | 0.062 | 1.980 | 5.026 | 0.000 | ||||
Vol. | Intercept | 28.919 | 0.353 | - | 82.024 | 0.000 | 18.882 | 0.193 | 0.000 |
Temp. | 0.013 | 0.001 | 0.420 | 9.060 | 0.000 | ||||
NaCl | 0.007 | 0.004 | 0.080 | 1.744 | 0.082 | ||||
pH | −0.006 | 0.018 | −0.010 | −0.327 | 0.744 | ||||
GC | −0.898 | 1.288 | −0.330 | −0.697 | 0.486 | ||||
GC2 | 0.830 | 1.213 | 0.320 | 0.684 | 0.494 | ||||
pI | Intercept | 1.130 | 0.023 | - | 49.960 | 0.000 | 130.303 | 0.617 | 0.000 |
Temp. | 0.001 | 0.000 | 0.320 | 10.067 | 0.000 | ||||
NaCl | 0.002 | 0.000 | 0.210 | 6.857 | 0.000 | ||||
pH | 0.002 | 0.001 | 0.060 | 1.954 | 0.051 | ||||
GC | 0.023 | 0.083 | 0.090 | 0.282 | 0.778 | ||||
GC2 | −0.177 | 0.078 | −0.730 | −2.273 | 0.024 |
D | Parameter | Unstandardized Coeff. | Βstd | t | p | F(3,3870) | R2 | p | |
---|---|---|---|---|---|---|---|---|---|
β | SE | ||||||||
Hyd. | Intercept | 1.531 | 0.005 | - | 284.970 | 0.000 | 5706.573 | 0.815 | 0.000 |
Temp. | 0.001 | 0.000 | 0.150 | 21.510 | 0.000 | ||||
GC | 0.468 | 0.021 | 1.370 | 22.490 | 0.000 | ||||
GC2 | −0.148 | 0.020 | −0.450 | −7.480 | 0.000 | ||||
Pol. | Intercept | 1.436 | 0.006 | - | 259.990 | 0.000 | 557.517 | 0.301 | 0.000 |
Temp. | 0.000 | 0.000 | 0.160 | 11.920 | 0.000 | ||||
GC | −0.324 | 0.021 | −1.790 | −15.140 | 0.000 | ||||
GC2 | 0.228 | 0.020 | 1.320 | 11.210 | 0.000 | ||||
Vol. | Intercept | 26.972 | 0.107 | - | 252.380 | 0.000 | 241.166 | 0.157 | 0.000 |
Temp. | 0.014 | 0.001 | 0.330 | 22.310 | 0.000 | ||||
GC | 6.031 | 0.413 | 1.890 | 14.590 | 0.000 | ||||
GC2 | −5.249 | 0.394 | −1.730 | −13.320 | 0.000 | ||||
pI | Intercept | 1.128 | 0.007 | - | 155.120 | 0.000 | 1098.377 | 0.460 | 0.000 |
Temp. | 0.001 | 0.000 | 0.170 | 14.370 | 0.000 | ||||
GC | 0.175 | 0.028 | 0.650 | 6.230 | 0.000 | ||||
GC2 | −0.328 | 0.027 | −1.270 | −12.220 | 0.000 |
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Radványi, Á.; Kun, Á. The Mutational Robustness of the Genetic Code and Codon Usage in Environmental Context: A Non-Extremophilic Preference? Life 2021, 11, 773. https://0-doi-org.brum.beds.ac.uk/10.3390/life11080773
Radványi Á, Kun Á. The Mutational Robustness of the Genetic Code and Codon Usage in Environmental Context: A Non-Extremophilic Preference? Life. 2021; 11(8):773. https://0-doi-org.brum.beds.ac.uk/10.3390/life11080773
Chicago/Turabian StyleRadványi, Ádám, and Ádám Kun. 2021. "The Mutational Robustness of the Genetic Code and Codon Usage in Environmental Context: A Non-Extremophilic Preference?" Life 11, no. 8: 773. https://0-doi-org.brum.beds.ac.uk/10.3390/life11080773