Figure 1.
Schematic representation of mechanisms of (A) between-pathways Synthetic Lethality, (B) within-pathway Synthetic Lethality, and (C) within-reversible-pathway Synthetic Lethality.
S: substrate, I: intermediate, P: product, C1–4: components of a protein complex. Red crosses define single mutations. For details see text.
Figure 2.
Normalized proportion of negative genetic interactions within one KEGG pathway.
The proportion is related to the number of all possible pairwise interactions S(S−1)/2, where S is the size of the KEGG pathway. Negative interactions between components of a molecular complex were excluded (compare the fourth and the fifth columns). We counted the normalized number of negative genetic interactions within one pathway using recent data on the genome-wide screening of genetic interactions in yeast from [5], using the most stringent filter on the epistasis measure ε. Definitions of yeast signaling and metabolic pathways were taken from KEGG database [30]. Only KEGG pathways with a normalized proportion of ≥1% are shown. DNA repair KEGG pathways are highlighted in bold.
Figure 3.
Abstract representation of the recombinational DNA repair pathway.
The scheme represents a simplified version of the pathway depicted in Figure S1 in Text S1 using the same abbreviations. Dynamic states S, I, P represent DNA damage substrate (S), toxic intermediate (I), and the product of repair (P). F1 (e.g. Rad51), F2 (e.g. Rad54), R1 (e.g. Srs2), R2 (e.g. Mph1) are enzymes in the main pathway, and F3-EC represent enzymes in the compensatory pathway. ks signify the kinetic rates of the model state transition steps. The two types of synthetic lethality (SL) are indicated: Red Xs – classic scenario of between-pathway SL (e.g. BRCA1 or BRCA2 mutant and PARP inhibition); Green Xs – within-reversible-pathway SL between two mutations in genes acting in a single non-essential pathway leading to the accumulation of a toxic intermediate (e.g. srs2 rad54 double mutant). For more discussion see also Section S1 in Text S1.
Figure 4.
Pathway steady states for various combinations of parameters in the mathematical model of DNA repair with reversible steps and a toxic intermediate.
The classification of pathway steady states depends on the values of three control parameters, representing the ratios of some kinetic rates of the model (for more details see Section S2A in Text S1): The diagrams visualize the values of the control parameters where thickness of the solid arrows shows the relative value of the corresponding kinetic rate and the dashed arrows represent kinetic rates which values are irrelevant for a given scenario. Color coding shows partial orderings of the parameters important for a given pathway state (thickness of edges of the same color should be compared but not between color.
Figure 5.
Visualization of the steady states for the toy model in dependence of various parameters.
The phase diagrams (r2×r1 plane) show the qualitative behavior for small, intermediate and large values of the model parameters. Red color corresponds to the state for which Ps>0.5 (DNA is repaired with probability >50%). If Ps<0.5 then the color is chosen as green if the probability of trapping in the intermediate state (I) is bigger than the propability of the initial unrepaired state (S), and as blue in the opposite case. The case k1 = 0 (F1↓) is represented separately on the right. In this case, another parameter is used instead of r1 for the phase plane. The case k−1 = 0 (R1↓) is treated separately on the top and only the r2 value is varied. The 14 model simulations listed in Figure 6 are shown by the circled numbers in the position of the chosen parameters.
Figure 6.
Modeling possible scenarios of single and double synthetic lethal mutations.
Pathway steady states depicted as Normal states (N) as Normal Robust (NR) and Normal Fragile (NF); Mutant states (M) as compensated state dependent on compensatory pathway EC(C); death from DNA damage (DD) and death from toxicity (DT). Dynamic plots show prediction of model for evolution of substrate (S), intermediate (I) and product (P) amounts over time corresponding to the choice of kinetic parameters shown on the Model diagram. (X-axis)-time, (Y-axis)-substances level. F1, F2, R1, R2, and EC refer to the enzymes catalyzing the two forward and two backward reactions as well as the compensatory pathway, respectively (see Figure 3). (↓)-complete knock-down or mutational loss of function; (↑)-over-expression. A deletion mutant was simulated by setting the corresponding kinetic rate constant to zero. An overexpression mutant was simulated by setting the corresponding kinetic rate constant sufficiently high to have a qualitative effect onto the steady state or the dynamics in the simulations. Some double mutants are not shown due to their triviality (such as F1↓F2↓) or difficulties with interpretation (such as F1↓R1↓). For more modeling scenarios see Figure S5 in Text S1.
Figure 7.
Modeling possible scenarios of single and double synthetic lethal mutations (continued).
Pathway steady states depicted as Normal states (N) as Normal Robust (NR) and Normal Fragile (NF); Mutant states (M) as compensated state dependent on compensatory pathway EC(C); death from DNA damage (DD) and death from toxicity (DT). Dynamic plots show prediction of model for evolution of substrate (S), intermediate (I) and product (P) amounts over time corresponding to the choice of kinetic parameters shown on the Model diagram. (X-axis)-time, (Y-axis)-substances level. F1, F2, R1, R2, and EC refer to the enzymes catalyzing the two forward and two backward reactions as well as the compensatory pathway, respectively (see Figure 3). (↓)-complete knock-down or mutational loss of function; (↑)-over-expression. A deletion mutant was simulated by setting the corresponding kinetic rate constant to zero. An overexpression mutant was simulated by setting the corresponding kinetic rate constant sufficiently high to have a qualitative effect onto the steady state or the dynamics in the simulations. Some double mutants are not shown due to their triviality (such as F1↓F2↓) or difficulties with interpretation (such as F1↓R1↓). For more modeling scenarios see Figure S5 in Text S1.
Figure 8.
Examples of molecular processes with alternative pathways and potential to kinetic trap.
A) Multiple post-translational protein modifications (phosphorylation followed by ubiquitination; acetylation followed by phosphorylation; sumotargeted ubiquitination, etc.). M1 and M2 represent two types of post-translational modifications. MOD1–4 represent enzymes catalyzing the reactions. Kinetic trapping of an intermediate modification can drastically disturb the balance between signaling pathways (e.g. #23 in Figure 2) B) Protein folding control by chaperones. Protein folding is controlled by chaperones (#18 in Figure 2) and may generate partially unfolded proteins as toxic intermediates which are subject to degradation [55]. Regulation of protein folding homeostasis is essential for protein pool control [56]; C) Lack of balance between production and detoxification of ROS leads to significant increases or drop in ROS levels that can be detrimental for cell signaling [57]–[59] (#19 in Figure 2). D) Coordinated sumoylation-desumoylation is important for proper signal propagation [60]–[62]. E) Glycan biosynthesis and protein glycosylation depend on the availability of common carrier dolichol phosphate (P-DOL). Correct recycling of P-DOL is important for sustaining the pool and utilization of this carrier in other glycans biosynthesis pathways. Kinetic trapping can consume the pool of P-DOL and perturb cell signaling [63], [64] (#2, 3 and 26 in Figure 2) F) Protein ubiquitylation is not only a tagging signal for degradation, but also involved in signaling. The correct tuning between two functions of ubiquitylation depends on the type and the length of ubiquitin (UB) polymer transferred to the protein and at the ubiquitylation site [65]. Monoubiquitylated proteins participate in signal transduction [66], [67], whereas K48-polyubiquitylated proteins are redirected to the proteasome for proteolysis. Thus, the balance between protein homeostasis and ubiquitin-dependent signaling is essential [68].