A matter of life or death: modeling DNA damage and repair in bacteria

DNA damage is a hazard all cells must face, and evolution has created a number of mechanisms to repair damaged bases in the chromosome. Paradoxically, many of these repair mechanisms can create double-strand breaks in the DNA molecule which are fatal to the cell. This indicates that the connection between DNA repair and death is far from straightforward, and suggests that the repair mechanisms can be a double-edged sword. In this report, we formulate a mathematical model of the dynamics of DNA damage and repair, and we obtain analytical expressions for the death rate. We predict a counterintuitive relationship between survival and repair. We can discriminate between two phases: below a critical threshold in the number of repair enzymes, the half-life decreases with the number of repair enzymes, but becomes independent of the number of repair enzymes above the threshold. We are able to predict quantitatively the dependence of the death rate on the damage rate and other relevant parameters. We verify our analytical results by simulating the stochastic dynamics of DNA damage and repair. Finally, we also perform an experiment with Escherichia coli cells to test one of the predictions of our model.     

Cellular response to endoplasmic reticulum stress: a matter of life or death

The proper functioning of the endoplasmic reticulum (ER) is critical for numerous aspects of cell physiology. Accordingly, all eukaryotes react rapidly to ER dysfunction through a set of adaptive pathways known collectively as the ER stress response (ESR). Normally, this suite of responses succeeds in restoring ER homeostasis. However, in metazoans, persistent or intense ER stress can also trigger programmed cell death, or apoptosis. ER stress and the apoptotic program coupled to it have been implicated in many important pathologies but the regulation and execution of ER stress-induced apoptosis in mammals remain incompletely understood. Here, we review what is known about the ESR in both yeast and mammals, and highlight recent findings on the mechanism and pathophysiological importance of ER stress-induced apoptosis.     

A matter of life and death

Our ability to sustain some of the outward signs of life has rendered obsolete the legal system's definition of what it means to be alive.     

Shaping the T-cell repertoire: a matter of life and death

Thymocyte selection aims to shape a T-cell repertoire that, on the one hand, is able to recognize and respond to foreign peptides and, on the other hand, tolerizes the presence of self-peptides in the periphery. Deletion of T cells or their precursors that fail to fulfill these criteria is mainly mediated by the Bcl-2-regulated apoptosis pathway. Absence of T-cell receptor (TCR)-mediated signals or hyperactivation of the TCR by high-affinity self-peptide-major histocompatibility complexes can both trigger apoptotic cell death in developing thymocytes. Notably, TCR-signaling strength also defines survival and outgrowth of the fittest antigen-specific T-cell clones in the periphery. TCR threshold activity leading to such drastically opposing signaling outcomes (life or death) is modulated in part by cytokines and other factors, such as glucocorticoids, that fine-tune the Bcl-2 rheostat, thereby impacting on cell survival. This review aims to highlight the role of Bcl-2-regulated cell death for clonal T-cell selection.     

细胞命运,生死攸关

细胞凋亡是细胞生命活动中一种预定的、并受到严格控制的程序性死亡,它是细胞内一系列促凋亡因子和抗凋亡因子相互作用后获得平衡的结果。细胞凋亡的调控可以发生在表观遗传、转录、翻译、修饰、转运等不同水平,也可以发生在细胞不同的区域,如细胞核、胞质、线粒体、质膜等处。作者近年来发现的新的促/抗凋亡因子从多种不同的角度去诠释细胞凋亡网络的调控。例如,Caspase新的激活机制;凋亡蛋白磷酸化和泛素化修饰以及蛋白通过对中间纤维的影响来诱导线粒体介导的凋亡等等。另外,对凋亡信号如何从胞核流向胞质进而促发线粒体引起的凋亡途径也进行了描述。这些新的凋亡调控机理进一步证明了,细胞凋亡可以发生在细胞生长发育不同的时相和空间,并存在着一个极其复杂的信号传递网络,这一调控网络一旦失去平衡,细胞会引发肿瘤。     

Mitochondrial quality control: a matter of life and death for neurons

Neuronal survival critically depends on the integrity and functionality of mitochondria. A hierarchical system of cellular surveillance mechanisms protects mitochondria against stress, monitors mitochondrial damage and ensures the selective removal of dysfunctional mitochondrial proteins or organelles. Mitochondrial proteases emerge as central regulators that coordinate different quality control (QC) pathways within an interconnected network of mechanisms. A failure of this system causes neuronal loss in a steadily increasing number of neurodegenerative disorders, which include Parkinson's disease, spinocerebellar ataxia, spastic paraplegia and peripheral neuropathies. Here, we will discuss the role of the mitochondrial QC network for neuronal survival and neurodegeneration.     

A matter of bacterial life and death

Over 50 years ago, standard microbiological methods were established for determining whether bacterial cells were dead or alive. Recently there has been a flurry of reports suggesting that bacteria may exist in an eclipsed state, escaping detection by standard methods. Whether there really is such a state is of more than academic interest, considering the implications for public health. The ensuing debate has been unusually energetic for the normally cultured community of microbiologists.     

Caspases are not localized in mitochondria during life or death

Caspases are crucial for the initiation, propagation and execution of apoptosis. They normally exist as proenzymes, which can be activated through recruitment into activating complexes and by proteolytic cleavage by other caspases or proteases. Perturbation of organelles such as nuclei, endoplasmatic reticulum and mitochondria results in the activation of caspases. A number of caspases (-2, -3, -8 and -9) were published as being localized in the intermembrane space of mitochondria. However, in three different models of apoptosis (anti-Fas-induced cell death in murine hepatocytes, Fas ligand-induced apoptosis in Jurkat cells and apoptosis induced by growth factor withdrawal in Ba/F3 cells) we could not identify a mitochondrial location of caspases, neither under control nor under apoptotic conditions. In all three apoptotic models caspases were found in the cytosolic (caspases-2, -3, -6, -7, -8, -9) and nuclear subcellular fractions (caspases-2, -3). In another approach we treated isolated liver mitochondria with truncated Bid. Although tBid-dependent release of Cytochrome c, AIF, adenylate kinase, Smac/DIABLO and Omi/HtrA2 could be demonstrated, none of the caspases were detectable both in the supernatant and the mitochondrial fraction after treatment. Our results demonstrate that, in contrast to previous studies, no caspases-2, -3, -8 and -9 are associated with the mitochondrial fraction. These findings support the concept of a separate compartmentalization between proapoptotic cofactors in the mitochondria and silent precursor caspases in the cytosol.     

Modulating stress responses by the UPRosome: a matter of life and death

The accumulation of unfolded proteins in the endoplasmic reticulum (ER) triggers the unfolded protein response (UPR) through the activation of specialized sensors including inositol-requiring enzyme-1α (IRE1α). IRE1α signals by assembling a dynamic protein platform referred to as the UPRosome, where different modulator and adaptor proteins assemble to regulate the kinetics and amplitude of UPR effector responses. Conversely, chronic ER stress can cause apoptosis. Recent evidence indicates that several apoptosis-related proteins interact with IRE1α, regulating its prosurvival activities and performing a dual function in the regulation of cell death and adaptation to stress. Based on the increasing relevance of ER stress to the occurrence of diverse pathological conditions, strategies to target and modulate the assembly and composition of the UPRosome could have therapeutic benefits for disease intervention.     

IL-15 and IL-2: a matter of life and death for T cells in vivo

Interleukin (IL)-2 and IL-15 are redundant in stimulating T-cell proliferation in vitro. Their precise role in vivo in governing T-cell expansion and T-cell homeostasis is less clear. Each may have distinct functions and regulate distinct aspects of T-cell activation. The functional receptors for IL-2 and IL-15 consist of a private alpha-chain, which defines the binding specificity for IL-2 or IL-15, and shared IL-2 receptor beta- and gamma-chains. The gamma-chain is also a critical signaling component of IL-4, IL-7 and IL-9 receptors. Thus, the gamma-chain is called the common gamma or gamma-c. As these receptor subunits can be expressed individually or in various combinations resulting in the formation of receptors with different affinities, distinct signaling capabilities or both, we hypothesized that differential expression of IL-2 and IL-15 receptor subunits on cycling T cells in vivo may direct activated T cells to respond to IL-2 or IL-15, thereby regulating the homeostasis of T-cell response in vivo. By observing in vivo T-cell divisions and expression of IL-2 and IL-15 receptor subunits, we demonstrate that IL-15 is a critical growth factor in initiating T cell divisions in vivo, whereas IL-2 limits continued T-cell expansion via downregulation of the gamma-c expression. Decreased gamma-c expression on cycling T cells reduced sustained Bcl-2 expression and rendered cells susceptible to apoptotic cell death. Our study provides data that IL-2 and IL-15 regulate distinct aspects of primary T-cell expansion in vivo.     

A matter of life and death: self‐renewal in stem cells

If Narcissus could have self‐renewed even once on seeing his own reflection, he would have died a happy man. Stem cells, on the other hand, have an enormous capacity for self‐renewal; in other words, the ability to replicate and generate more of the same. In adult organisms, stem cells reside in specialized niches within each tissue. They replenish tissue cells that are lost during normal homeostasis, and on injury they repair damaged tissue. The ability of a stem cell to self‐renew is governed by the dynamic interaction between the intrinsic proteins it expresses and the extrinsic signals that it receives from the niche microenvironment. Understanding the mechanisms governing when to proliferate and when to differentiate is vital, not only to normal stem cell biology, but also to ageing and cancer. This review focuses on elucidating conceptually, experimentally and mechanistically, our understanding of adult stem cell self‐renewal. We use skin as a paradigm for discussing many of the salient points about this process, but also draw on the knowledge gained from these and other adult stem cell systems to delineate shared underlying principles, as well as highlight mechanistic distinctions among adult tissue stem cells. By doing so, we pinpoint important questions that still await answers.