The p53 protein is well-known for its tumour suppressor function. The p53-MDM2 negative feedback loop constitutes the core module of a network of regulatory interactions activated under cellular ...stress. In normal cells, the level of p53 proteins is kept low by MDM2, i.e. MDM2 negatively regulates the activity of p53. In the case of DNA damage,the p53-mediated pathways are activated leading to cell cycle arrest and repair of the DNA. If repair is not possible due to excessive damage, the p53-mediated apoptotic pathway is activated bringing about cell death. In this paper, we give an overview of our studies on the p53-MDM2 module and the associated pathways from a systems biology perspective. We discuss a number of key predictions, related to some specific aspects of cell cycle arrest and cell death, which could be tested in experiments.
The cell cycle is an orderly sequence of events which ultimately lead to the
division of a single cell into two daughter cells. In the case of DNA damage by
radiation or chemicals, the damage ...checkpoints in the $G_{1}$ and $G_{2}$
phases of the cell cycle are activated. This results in an arrest of the cell
cycle so that the DNA damage can be repaired. Once this is done, the cell
continues with its usual cycle of activity. We study a mathematical model of
the DNA damage checkpoint in the $G_{2}$ phase which arrests the transition
from the $G_{2}$ to the $M$ (mitotic) phase of the cell cycle. The tumor
suppressor protein p53 plays a key role in activating the pathways leading to
cell cycle arrest in mammalian systems. If the DNA damage is severe, the p53
proteins activate other pathways which bring about apoptosis, i.e., programmed
cell death. Loss of the p53 gene results in the proliferation of cells
containing damaged DNA, i.e., in the growth of tumors which may ultimately
become cancerous. There is some recent experimental evidence which suggests
that the mutation of a single copy of the p53 gene (in the normal cell each
gene has two identical copies) is sufficient to trigger the formation of
tumors. We study the effect of reducing the gene copy number of the p53 and two
other genes on cell cycle arrest and obtain results consistent with
experimental observations.
A common survival strategy of microorganisms subjected to stress involves the generation of phenotypic heterogeneity in the isogenic microbial population enabling a subset of the population to ...survive under stress. In a recent study, a mycobacterial population of M. smegmatis was shown to develop phenotypic heterogeneity under nutrient depletion. The observed heterogeneity is in the form of a bimodal distribution of the expression levels of the Green Fluorescent Protein (GFP) as reporter with the gfp fused to the promoter of the rel gene. The stringent response pathway is initiated in the subpopulation with high rel activity.In the present study, we characterize quantitatively the single cell promoter activity of the three key genes, namely, mprA, sigE and rel, in the stringent response pathway with gfp as the reporter. The origin of bimodality in the GFP distribution lies in two stable expression states, i.e., bistability. We develop a theoretical model to study the dynamics of the stringent response pathway. The model incorporates a recently proposed mechanism of bistability based on positive feedback and cell growth retardation due to protein synthesis. Based on flow cytometry data, we establish that the distribution of GFP levels in the mycobacterial population at any point of time is a linear superposition of two invariant distributions, one Gaussian and the other lognormal, with only the coefficients in the linear combination depending on time. This allows us to use a binning algorithm and determine the time variation of the mean protein level, the fraction of cells in a subpopulation and also the coefficient of variation, a measure of gene expression noise.The results of the theoretical model along with a comprehensive analysis of the flow cytometry data provide definitive evidence for the coexistence of two subpopulations with overlapping protein distributions.
The cell cycle is an orderly sequence of events which ultimately lead to the division of a single cell into two daughter cells. In the case of DNA damage by radiation or chemicals, the damage ...checkpoints in the \(G_{1}\) and \(G_{2}\) phases of the cell cycle are activated. This results in an arrest of the cell cycle so that the DNA damage can be repaired. Once this is done, the cell continues with its usual cycle of activity. We study a mathematical model of the DNA damage checkpoint in the \(G_{2}\) phase which arrests the transition from the \(G_{2}\) to the \(M\) (mitotic) phase of the cell cycle. The tumor suppressor protein p53 plays a key role in activating the pathways leading to cell cycle arrest in mammalian systems. If the DNA damage is severe, the p53 proteins activate other pathways which bring about apoptosis, i.e., programmed cell death. Loss of the p53 gene results in the proliferation of cells containing damaged DNA, i.e., in the growth of tumors which may ultimately become cancerous. There is some recent experimental evidence which suggests that the mutation of a single copy of the p53 gene (in the normal cell each gene has two identical copies) is sufficient to trigger the formation of tumors. We study the effect of reducing the gene copy number of the p53 and two other genes on cell cycle arrest and obtain results consistent with experimental observations.
A prominent feature of gene transcription regulatory networks is the presence
in large numbers of motifs, i.e, patterns of interconnection, in the networks.
One such motif is the feed forward loop ...(FFL) consisting of three genes X, Y
and Z. The protein product of x of X controls the synthesis of protein product
y of Y. Proteins x and y jointly regulate the synthesis of z proteins from the
gene Z. The FFLs, depending on the nature of the regulating interactions, can
be of eight different types which can again be classified into two categories:
coherent and incoherent. In this paper, we study the noise characteristics of
FFLs using the Langevin formalism and the Monte Carlo simulation technique
based on the Gillespie algorithm. We calculate the variances around the mean
protein levels in the steady states of the FFLs and find that, in the case of
coherent FFLs, the most abundant FFL, namely, the Type-1 coherent FFL, is the
least noisy. This is however not so in the case of incoherent FFLs. The results
suggest possible relationships between noise, functionality and abundance.
Phenotypic heterogeneity in an isogenic, microbial population enables a subset of the population to persist under stress. In mycobacteria, stresses like nutrient and oxygen deprivation activate the ...stress response pathway involving the two-component system MprAB and the sigma factor, SigE. SigE in turn activates the expression of the stringent response regulator, rel. The enzyme polyphosphate kinase 1 (PPK1) regulates this pathway by synthesizing polyphosphate required for the activation of MprB. The precise manner in which only a subpopulation of bacterial cells develops persistence, remains unknown. Rel is required for mycobacterial persistence. Here we show that the distribution of rel expression levels in a growing population of mycobacteria is bimodal with two distinct peaks corresponding to low (L) and high (H) expression states, and further establish that a positive feedback loop involving the mprAB operon along with stochastic gene expression are responsible for the phenotypic heterogeneity. Combining single cell analysis by flow cytometry with theoretical modeling, we observe that during growth, noise-driven transitions take a subpopulation of cells from the L to the H state within a "window of opportunity" in time preceding the stationary phase. We find evidence of hysteresis in the expression of rel in response to changing concentrations of PPK1. Our results provide, for the first time, evidence that bistability and stochastic gene expression could be important for the development of "heterogeneity with an advantage" in mycobacteria.
A prominent feature of gene transcription regulatory networks is the presence in large numbers of motifs, i.e, patterns of interconnection, in the networks. One such motif is the feed forward loop ...(FFL) consisting of three genes X, Y and Z. The protein product of x of X controls the synthesis of protein product y of Y. Proteins x and y jointly regulate the synthesis of z proteins from the gene Z. The FFLs, depending on the nature of the regulating interactions, can be of eight different types which can again be classified into two categories: coherent and incoherent. In this paper, we study the noise characteristics of FFLs using the Langevin formalism and the Monte Carlo simulation technique based on the Gillespie algorithm. We calculate the variances around the mean protein levels in the steady states of the FFLs and find that, in the case of coherent FFLs, the most abundant FFL, namely, the Type-1 coherent FFL, is the least noisy. This is however not so in the case of incoherent FFLs. The results suggest possible relationships between noise, functionality and abundance.
PDF