| Literature DB >> 29267315 |
Mohieddin Jafari1, Naser Ansari-Pour2, Sadegh Azimzadeh3, Mehdi Mirzaie4.
Abstract
It is nearly half a century past the age of the introduction of the Central Dogma (CD) of molecular biology. This biological axiom has been developed and currently appears to be all the more complex. In this study, we modified CD by adding further species to the CD information flow and mathematically expressed CD within a dynamic framework by using Boolean network based on its present-day and 1965 editions. We show that the enhancement of the Dogma not only now entails a higher level of complexity, but it also shows a higher level of robustness, thus far more consistent with the nature of biological systems. Using this mathematical modeling approach, we put forward a logic-based expression of our conceptual view of molecular biology. Finally, we show that such biological concepts can be converted into dynamic mathematical models using a logic-based approach and thus may be useful as a framework for improving static conceptual models in biology.Entities:
Mesh:
Year: 2017 PMID: 29267315 PMCID: PMC5739447 DOI: 10.1371/journal.pone.0189922
Source DB: PubMed Journal: PLoS One ISSN: 1932-6203 Impact factor: 3.240
Fig 1(A) The 1965 and the present-day Central Dogma editions in molecular biology (B) The initial four-node Central Dogma wiring diagram formed by DNA, mRNA, Protein and Activator. (C) The present-day seven-node Central Dogma wiring diagram formed by DNA, mRNA, Protein, Activator, miRNA, DegProtein and DegRNA. The directed edge “—o” represents a functional relationship with both activatory and inhibitory effects (D) Network representation of Boolean rules corresponding to the simple 1965 model. (E) Network representation of Boolean rules corresponding to the present-day updated model. For simplicity, the first version of each model is shown.
Boolean rules governing the state of the 4-node network of the 1965 proposed central dogma depicted in Fig 1B derived from [1, 2].
The symbols “&”, “|” and “!” represent “AND”, “OR” and “NOT” operators.
| Node | V1: Activatory gene expression | V2: Inhibitory gene expression | |
|---|---|---|---|
| The chemical molecules which facilitate active protein production during or after translation | Activator | ||
| The genes transcribed to coding RNA | DNA | ||
| The coding RNA | DNA & Protein | DNA &! Protein | |
| The functional active protein | (mRNA & Activator) | Protein | ||
Boolean rules governing the state of the 7-node network of the present-day central dogma depicted in Fig 1C derived from [1–3, 7–11, 20, 21].
The symbols “&”, “|” and “!” represent “AND”, “OR” and “NOT” operators.
| Node | V1: Activatory | V2: mRNA expression inhibition | V3: miRNA expression Inhibition | V4: Gene silencing | V5: Gene silencing & mRNA expression inhibition | V6: Gene silencing & miRNA expression inhibition | V7: miRNA & mRNA expression inhibition | V8: Inhibitory | |
|---|---|---|---|---|---|---|---|---|---|
| The chemical molecules or residue which facilitate active protein generation before or after translation | Protein | Activator | ||||||||
| All biochemical modifications that are involved in negative regulation of protein amount | Protein &! DegProtein | ||||||||
| The protein complex which degrades RNA species | miRNA & Protein &! DegProtein | ||||||||
| The non-silenced genes which is detectable by RNA polymerase | (miRNA & Protein) | DNA | ( | (miRNA & Protein) | DNA | ( | |||||
| A RNA species which is involved in regulation of gene silencing (for simplification, all other RNA species which has negative effect on protein production is shown with the same label) | (DNA & Protein | mRNA) &! DegRNA | (DNA & | (DNA & Protein | mRNA) &! DegRNA | (DNA & | (DNA & Protein | mRNA) &! DegRNA | (DNA & | |||
| The mature messenger RNA that is ready for translation (for simplification, all other RNA species which has positive effect on protein production is shown with the same label) | DNA & Protein &! DegRNA | DNA & | DNA & Protein &! DegRNA | DNA & Protein &! DegRNA | DNA & | ||||
| The functional active protein | (mRNA & Activator | Protein) &! DegProtein | ||||||||
The probabilistic version of the combined Boolean network of the present-day central dogma.
The symbols “&”, “|” and “!” represent “AND”, “OR” and “NOT” operators.
| Protein | Activator | 1 | |
| Protein &! DegProtein | 1 | |
| miRNA & Protein &! DegProtein | 1 | |
| (miRNA & Protein) | DNA | 0.1 | |
| (!miRNA & Protein) | DNA | 0.9 | |
| (DNA & Protein | mRNA) &! DegRNA | 0.8 | |
| (DNA &! Protein | mRNA) &! DegRNA | 0.2 | |
| DNA & Protein &! DegRNA | 0.8 | |
| DNA &! Protein &! DegRNA | 0.2 | |
| (mRNA & Activator | Protein) &! DegProtein | 1 |
The attractors of the Boolean model as depicted in Fig 1B obtained from the synchronous update method.
In each version of the model, the number of single SSs and the corresponding normalized basin of attractions are demonstrated. The color gradient from red, yellow to green illustrate the lowest to the highest values, respectively. A to K attractors are encoded in the following order: Activator/DNA/mRNA/Protein. The D*, H* and K* denote specific states pertaining to this Central Dogma modeling.
| Central Dogma 1965 | Description | No. SSs with one state | A | B | C | D* | E | F | G | H* | I | J | K* |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 0000 | 1000 | 1001 | 0001 | 0100 | 1100 | 1111 | 0111 | 0110 | 1101 | 0101 | |||
| Activatory gene expression | 8 | 12.5 | 6.25 | 18.75 | 12.5 | 12.5 | 6.25 | 18.75 | 12.5 | - | - | - | |
| Inhibitory gene expression | 7 | 12.5 | 6.25 | 18.75 | 12.5 | - | - | - | - | 12.5 | 25 | 12.5 | |
| Activator/DNA/mRNA/Protein | |||||||||||||
The attractors of the Boolean model depicted in Fig 1C obtained from the synchronous update method.
In each version of the model, demonstrated are the number of single SSs, SSs with multiple states (limit cycles) and corresponding normalized basin of attractions. The color gradient from red, yellow to green illustrate the lowest to highest values. The attractors A to I are encoded in the following order: Activator/DegProtein/DegRNA/DNA/miRNA/mRNA/Protein.
| Present-day Central Dogma | System name | No. of SS with one state | No. of SS with multiple states | A | B | C | D | E | F | G | H | I |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 0000000 | 1000000 | 0001000 | 1001000 | 0001110 | 0001100 | 1001100 | 1001000 > 1001010 > 1001111 > 1111101 | 1001000 > 1001110 > 1001111 > 1111101 | ||||
| Activatory | 4 | 0 | 12.5 | 21.88 | 12.5 | 53.12 | - | - | - | - | - | |
| mRNA expression inhibition | 3 | 1 | 12.5 | 21.88 | - | - | 12.5 | - | - | 53.12 | - | |
| miRNA expression inhibition | 4 | 0 | 12.5 | 21.88 | - | - | - | 12.5 | 53.12 | - | - | |
| Gene silencing | 4 | 0 | 12.5 | 17.19 | 12.5 | 57.81 | - | - | - | - | - | |
| Gene silencing & mRNA expression inhibition | 3 | 1 | 12.5 | 17.19 | - | - | 12.5 | - | - | 57.81 | - | |
| Gene silencing & miRNA expression inhibition | 4 | 0 | 12.5 | 17.19 | - | - | - | 12.5 | 57.81 | - | - | |
| miRNA & mRNA expression inhibition | 3 | 1 | 12.5 | 21.88 | - | - | 12.5 | - | - | - | 53.12 | |
| Inhibitory | 3 | 1 | 12.5 | 17.19 | - | - | 12.5 | - | - | - | 57.81 | |
| Activator/DegProtein/DegRNA/DNA/miRNA/mRNA/Protein | ||||||||||||
The attractors of the Boolean model depicted in Fig 1C obtained from the asynchronous updating method.
Each version of the model illustrated the presence of simple attractors, the complex (loose) attractor and corresponding edge numbers in the latter. The binary digits (0 and 1) of the attractors (A to H) from left to right indicate the state of the components Activator, DegProtein, DegRNA, DNA, miRNA, mRNA and protein.
| Present-day Central Dogma | System name | Simple attractor | Complex (loose) attractor | ||||||
|---|---|---|---|---|---|---|---|---|---|
| A | B | C | D | E | F | G | H | ||
| 0000000 | 1000000 | 0001000 | 1001000 | 0001110 | 1001100 | 0001100 | 1111111,1011111,1101111,1001111,1111011,1011011,1101011,1001011,1111101,1011101,1101101,1001101,1111001,1011001,1101001,1001001,1111110,1011110,1101110,1001110,1111010,1011010,1101010,1001010,1111100,1011100,1101100,1001100,1111000,1011000,1101000,1001000 | ||
| Activatory | ✓ | ✓ | ✓ | ✓ | |||||
| mRNA expression inhibition | ✓ | ✓ | ✓ | 32 | |||||
| miRNA expression inhibition | ✓ | ✓ | ✓ | ✓ | |||||
| Gene silencing | ✓ | ✓ | ✓ | ✓ | |||||
| Gene silencing & mRNA expression inhibition | ✓ | ✓ | ✓ | 32 | |||||
| Gene silencing & miRNA expression inhibition | ✓ | ✓ | ✓ | ✓ | |||||
| miRNA & mRNA expression inhibition | ✓ | ✓ | ✓ | 32 | |||||
| Inhibitory | ✓ | ✓ | ✓ | 32 | |||||
| Activator/DegProtein/DegRNA/DNA/miRNA/mRNA/Protein | |||||||||
Fig 2Network visualization of the complex (loose) attractor in the present-day model.
Node size and color are proportional to betweenness and closeness centrality measures respectively.
The absorption probabilities for the Markov chain corresponding to the Boolean model depicted in Fig 1C in all versions.
These probabilities were estimated based on 1000 iterations. The last column represents the absorption probabilities of the probabilistic Boolean network of the present-day Central Dogma (See Table 2).
| Activator/DegProtein/DegRNA/DNA/miRNA/mRNA/Protein | V1 | V2 | V3 | V4 | V5 | V6 | V7 | V8 | Mixture V1_V8 |
|---|---|---|---|---|---|---|---|---|---|
| 0.125 | 0.125 | 0.125 | 0.125 | 0.125 | 0.125 | 0.125 | 0.125 | 0.125 | |
| 0.125 | 0.125 | 0.064 | |||||||
| 0.125 | 0.125 | 0.036 | |||||||
| 0.125 | 0.125 | 0.125 | 0.125 | 0.009 | |||||
| 0.219 | 0.219 | 0.219 | 0.172 | 0.172 | 0.172 | 0.219 | 0.172 | 0.177 | |
| 0.531 | 0.047 | 0.578 | 0.047 | 0.047 | 0.047 | 0.301 | |||
| 0.047 | 0.063 | 0.057 | |||||||
| 0.531 | 0.578 | 0.057 | |||||||
| 0.047 | 0.063 | 0.014 | |||||||
| 0.203 | 0.234 | 0.203 | 0.234 | 0.014 | |||||
| 0.234 | 0.234 | 0.234 | 0.234 | 0.012 | |||||
The robustness analysis of the reconstructed models of the central dogma.
| Model Versions | Hamming distance | P-value | Gini Index | P-value of the Gini Index |
|---|---|---|---|---|
| 0.271 | 0.19 | 0.588 | 0.52 | |
| 0.275 | 0.1 | 0.575 | 0.61 | |
| 0.162 | <0.001 | 0.918 | <0.001 | |
| 0.149 | <0.001 | 0.908 | <0.001 | |
| 0.151 | <0.001 | 0.904 | <0.001 | |
| 0.151 | 0.01 | 0.918 | <0.001 | |
| 0.144 | 0.01 | 0.904 | <0.001 | |
| 0.148 | <0.001 | 0.908 | <0.001 | |
| 0.146 | <0.001 | 0.921 | <0.001 | |
| 0.145 | <0.001 | 0.921 | <0.001 | |