Mitochondria are not required for death receptor-mediated cytosolic acidification during apoptosis

In addition to cell shrinkage, membrane blebbing, DNA fragmentation and phosphatidylserine exposure, intracellular acidification represents a hallmark of apoptosis. Although the mechanisms underlying cytosolic acidification during apoptosis remained largely elusive, a pivotal role of mitochondria has been proposed. In order to investigate the involvement of mitochondria in cytosolic acidification during apoptosis, we blocked the mitochondrial death pathway by overexpression of Bcl-2 and subsequently activated the death receptor pathway by anti-CD95 or TRAIL or the mitochondrial pathway by staurosporine. We show that Bcl-2 but not caspase inhibition prevented staurosporine-induced intracellular acidification. Thus, intracellular acidification in mitochondrial apoptosis is a Bcl-2-inhibitable, but caspase-independent process. In contrast, Bcl-2 only slightly delayed, but did not prevent intracellular acidification upon triggering of death receptors. The Na⁺/H⁺ exchanger NHE1 was partially degraded during apoptosis but only to a small extent and and at a delayed time point when cytosolic acidification was almost completed. We therefore conclude that cytosolic acidification is mitochondrially controlled in response to mitochondria-dependent death stimuli, but requires additional caspase-dependent mechanisms during death receptor-mediated apoptosis. Michaela Waibel, Stefan Kramer and Kirsten Lauber share equal first authorship.     

DNA fragmentation in apoptosis

Cleavage of chromosomal DNA into oligonucleosomal size fragments is an integral part of apoptosis.Elegant biochemical work identified the DNA fragmentation factor(DFF) as a major apoptotic endonuclease for DNA fragmentation in vitro Genetic studies in mice support the importence of DFF in DNA fragmentation and possibly in apoptosis in vivo.Recent work also suggests the existence of additional endonucleases for DNA degradation.Understanding the roles of individual endonucleases in apoptosis,and how they might coordinate to degrade DNA in different tissues during normal development and homeostasis,as well as in various diseased states,will be a major research focus in the near future.     

Caspase-12 and caspase-4 are not required for caspase-dependent endoplasmic reticulum stress-induced apoptosis

Alterations in cellular homeostasis that affect protein folding in the endoplasmic reticulum (ER) trigger a signaling pathway known as the unfolded protein response (UPR). The initially cytoprotective UPR will trigger an apoptotic cascade if the cellular insult is not corrected; however, the proteins required to initiate this cell death pathway are poorly understood. In this study, we show that UPR gene expression is induced in cells treated with ER stress agents in the presence or absence of murine caspase-12 or human caspase-4 expression and in cells that overexpress Bcl-x(L) or a dominant negative caspase-9. We further demonstrate that ER stress-induced apoptosis is a caspase-dependent process that does not require the expression of caspase-12 or caspase-4 but can be inhibited by overexpression of Bcl-x(L) or a dominant negative caspase-9. Additionally, treatment of human and murine cells with ER stress agents led to the cleavage of the caspase-4 fluorogenic substrate, LEVD-7-amino-4-trifluoromethylcoumarin, in the presence or absence of caspase-12 or caspase-4 expression, whereas Bcl-x(L) or a dominant negative caspase-9 overexpression inhibited LEVD-7-amino-4-trifluoromethylcoumarin cleavage. These data suggest that caspase-12 and caspase-4 are not required for the induction of ER stress-induced apoptosis and that caspase-4-like activity is not always associated with an initiating event.     

DNA fragmentation in apoptosis and homeostasis

Apoptosis is a highly regulated physiological process critical in development and tissue homeostasis. Abnormal apoptosis can lead to disease conditions including neurodegeneration, autoimmunity and cancer. DNA fragmentation is an integral part of apoptosis and has long been suspected to be of critical importance in cleaning up potentially antigenic DNA and genetic material capable of inducing neoplasmic transformation in neighboring cells. Direct evidence for this function of DNA fragmentation however, is still lacking. The identification of a heterodimeric DNA fragmentation factor 45 and 40 (DFF45 and DFF40, also called ICAD for Inhibitor of Caspase Activated DNase and CAD for Caspase Activated DNase respectively) as well as     

Both subtelomeric regions are required and sufficient for specific DNA fragmentation during macronuclear development in Stylonychia lemnae

Background  

Programmed DNA-reorganization and DNA-elimination events take place frequently during cellular differentiation. An extreme form of such processes, involving DNA reorganization, DNA elimination and DNA fragmentation, is found during macronuclear differentiation in hypotrichous ciliates. Ciliated protozoa can therefore serve as a model system to analyze the molecular basis of these processes during cellular differentiation in eukaryotic cells.     

Loss of Acinus inhibits oligonucleosomal DNA fragmentation but not chromatin condensation during apoptosis

Chromatin condensation and oligonucleosomal DNA fragmentation are the nuclear hallmarks of apoptosis. A proteolytic fragment of the apoptotic chromatin condensation inducer in the nucleus (Acinus), which is generated by caspase cleavage, has been implicated in mediating apoptotic chromatin condensation prior to DNA fragmentation. Acinus is also involved in mRNA splicing and a component of the apoptosis and splicing-associated protein (ASAP) complex. To study the role of Acinus for apoptotic nuclear alterations, we generated stable cell lines in which Acinus isoforms were knocked down by inducible and reversible RNA interference. We show that Acinus is not required for nuclear localization and interaction of the other ASAP subunits SAP18 and RNPS1; however, knockdown of Acinus leads to a reduction in cell growth. Most strikingly, down-regulation of Acinus did not inhibit apoptotic chromatin condensation either in intact cells or in a cell-free system. In contrast, although apoptosis proceeds rapidly, analysis of nuclear DNA from apoptotic Acinus knockdown cells shows inhibition of oligonucleosomal DNA fragmentation. Our results therefore suggest that Acinus is not involved in DNA condensation but rather point to a contribution of Acinus in internucleosomal DNA cleavage during programmed cell death.     

Caspase-3-like protease influences but is not essential for DNA fragmentation in Blastocystis undergoing apoptosis

Blastocystis hominis undergo apoptosis after treatment with a cytotoxic monoclonal antibody (MAb), 1D5, by mechanisms that are not fully understood, although our previous study demonstrated that caspase-3-like protease activity is involved. To elucidate the mechanism of MAb 1D5-induced apoptosis, we inhibited Blastocystis caspase-3-like protease to investigate if there would be a concomitant decrease in in situ DNA fragmentation. However, MAb 1D5-induced apoptosis, evidenced by DNA fragmentation, was not completely blocked by pretreating with specific caspase-3 inhibitor, Ac-DEVD-CHO, indicating that caspase-independent apoptotic pathways might also be involved. Our results also revealed that the treatment with MAb 1D5 resulted in the loss of mitochondrial membrane potential (deltapsim), independent of Ac-DEVD-CHO pretreatment. In conclusion, this study demonstrates that MAb 1D5-induced apoptosis in B. hominis is not wholly dependent on caspase-3-like protease activity and is associated with mitochondrial dysregulation. This is the first report showing evidence for complex apoptotic pathways in a unicellular parasite.     

Granzyme B-induced mitochondrial ROS are required for apoptosis

Caspases and the cytotoxic lymphocyte protease granzyme B (GB) induce reactive oxygen species (ROS) formation, loss of transmembrane potential and mitochondrial outer membrane permeabilization (MOMP). Whether ROS are required for GB-mediated apoptosis and how GB induces ROS is unclear. Here, we found that GB induces cell death in an ROS-dependent manner, independently of caspases and MOMP. GB triggers ROS increase in target cell by directly attacking the mitochondria to cleave NDUFV1, NDUFS1 and NDUFS2 subunits of the NADH: ubiquinone oxidoreductase complex I inside mitochondria. This leads to mitocentric ROS production, loss of complex I and III activity, disorganization of the respiratory chain, impaired mitochondrial respiration and loss of the mitochondrial cristae junctions. Furthermore, we have also found that GB-induced mitocentric ROS are necessary for optimal apoptogenic factor release, rapid DNA fragmentation and lysosomal rupture. Interestingly, scavenging the ROS delays and reduces many of the features of GB-induced death. Consequently, GB-induced ROS significantly promote apoptosis.To induce cell death, human granzyme B (GB) activates effector caspase-3 or acts directly on key caspase substrates, such as the proapoptotic BH3 only Bcl-2 family member Bid, inhibitor of caspase-activated DNase (ICAD), poly-(ADP-ribose) polymerase-1 (PARP-1), lamin B, nuclear mitotic apparatus protein 1 (NUMA1), catalytic subunit of the DNA-dependent protein kinase (DNA-PKcs) and tubulin.^{1, 2, 3} Consequently, caspase inhibitors have little effect on human GB-mediated cell death and DNA fragmentation.² GB causes reactive oxygen species (ROS) production, dissipation of the mitochondrial transmembrane potential (ΔΨm) and MOMP, which leads to the release of apoptogenic factors such as cytochrome c (Cyt c), HtrA2/Omi, endonuclease G (Endo G), Smac/Diablo and apoptosis-inducing factor, from the mitochondrial intermembrane space to the cytosol.^{4, 5, 6, 7, 8, 9, 10, 11} Interestingly, cells deficient for Bid, Bax and Bak are still sensitive to human GB-induced cell death,^{5, 11, 12, 13} suggesting that human GB targets the mitochondria in another way that needs to be characterized. Altogether, much attention has been focused on the importance of MOMP in the execution of GB-mediated cell death, leaving unclear whether ROS production is a bystander effect or essential to the execution of GB-induced apoptosis. The mitochondrial NADH: ubiquinone oxidoreductase complex I is a key determinant in steady-state ROS production. This 1 MDa complex, composed of 44 subunits,¹⁴ couples the transfer of two electrons from NADH to ubiquinone with the translocation of four protons to generate the ΔΨm. The importance of ROS has been previously demonstrated for caspase-3 and granzyme A (GA) pathways through the cleavage of NDUFS1 and NDUFS3, respectively.^{15, 16, 17, 18} GA induces cell death in a Bcl-2-insensitive and caspase- and MOMP-independent manner that has all the morphological features of apoptosis.^{1, 16, 17, 18, 19, 20} As GA and GB cell death pathways are significantly different, whether ROS are also critical for GB still need to be tested. Here, we show that GB induces ROS-dependent apoptosis by directly attacking the mitochondria in a caspase-independent manner to cleave NDUFS1, NDUFS2 and NDUFV1 in complex I. Consequently, GB inhibits electron transport chain (ETC) complex I and III activities, mitochondrial ROS production is triggered and mitochondrial respiration is compromised. Interestingly, MOMP is not required for GB to cleave the mitochondrial complex I subunits and ROS production. Moreover, GB action on complex I disrupts the organization of the respiratory chain and triggers the loss of the mitochondrial cristae junctions. We also show that GB-mediated mitocentric ROS are necessary for proper apoptogenic factor release from the mitochondria to the cytosol and for the rapid DNA fragmentation, both hallmarks of apoptosis. Moreover, GB-induced ROS are necessary for lysosomal membrane rupture. Thus, our work brings a new light to the GB pathway, showing that GB-mediated mitochondrial ROS are not adventitious waste of cell death, but essential mediators of apoptosis.     

Internucleosomal DNA fragmentation is not obligatory for castration induced rat ventral prostate cell apoptosis in vivo

Castrated male rats were treated with the reversible S1-phase cell cycle blocking drug, mimosine, and the effects of this drug on prostate cell apoptosis was characterized. At a single dose of mimosine (25 mg/kg/day), we found that the internucleosomal DNA fragmentation associated with apoptosis was partially suppressed in the rat ventral prostate at all early time points (24, 48 and 72 h) analyzed post-castration. This suppression was dose-dependent, and treatment with mimosine up to 150 mg/kg/day was sufficient to reduce the internucleosomal DNA fragmentation in the prostate by 90% at 72 h post-castration. Intriguingly, this drug did not suppress the induction of mRNAs for several apoptosis-associated gene products in the ventral prostate gland (bcl-2, p53, TGF-beta and SGP-2/clusterin). Moreover, this treatment did not suppress the histological appearance of apoptotic bodies in the ventral prostate detectable by fast green staining of thin sections of tissue. The apoptotic bodies present in mimosine-treated regressing ventral prostate tissues, however, were refractory to labeling by the in situ gap labeling method, further demonstrating lack of nuclear DNA fragmentation in the condensed nuclei of apoptotic cells. In summary, the cell cycle-blocking drug mimosine does not appear to affect the rate of apoptosis in the regressing rat ventral prostate gland. However, this drug was capable of suppressing the nuclear DNA fragmentation associated with androgen-regulated prostate cell apoptosis. These results support the concept that nuclear DNA fragmentation is not obligatory for apoptosis. Additionally, they imply that cell cycle movement from the G1/S-phase boundary might be important for the terminal DNA degradation associated with androgen-regulated prostate cell apoptosis.     

Detection of DNA fragmentation and endonucleases in apoptosis

DNA degradation during apoptosis is endonuclease mediated and proceeds through an ordered series of stages commencing with the production of large DNA pieces of 300 kb which are then degraded to fragments of 50 kb. The 50-kb fragments are further degraded, in some but not all cells, to smaller pieces (10-40 kb) releasing the small oligonucleosome fragments that are detected as a characteristic DNA ladder on conventional agarose gels. Methodology is presented for the detection of both DNA ladders and the initial stages of DNA fragmentation using pulsed-field gel electrophoresis. We have developed electrophoresis conditions that resolve large fragments of DNA and also retain the smaller fragments on the same gel. Methods for the detection of endonuclease activities responsible for the cleavage of DNA during apoptosis are also presented.     

The role of DNA fragmentation in apoptosis

The formation of distinct DNA fragments of oligonucleosomal size (180-200 bp lengths) is a biochemical hallmark of apoptosis in many cells. Recent observations also suggest large DNA fragments and even single-strand cleavage events occur during cell death. These observations have raised many questions. What are the types of DNA cleavage observed during apoptosis? What are the nucleases involved? And what is the role of these nucleolytic events in apoptosis?     

Drosophila Bcl-2 proteins participate in stress-induced apoptosis, but are not required for normal development

Many developing tissues require programmed cell death (PCD) for proper formation. In mice and C. elegans, developmental PCD is regulated by the Bcl-2 family of proteins. Two bcl-2 genes are encoded in the Drosophila genome (debcl/dBorg1/Drob-1/dBok and buffy/dBorg2) and previous RNAi-based studies suggested a requirement for these in embryonic development. However, we report here that, despite the fact that many tissues in fruit flies are shaped by PCD, deletion of the bcl-2 genes does not perturb normal development. We investigated whether the fly bcl-2 genes regulate non-apoptotic processes that require caspases, but found these to be bcl-2 gene-independent. However, irradiation of the mutants demonstrates that DNA damage-induced apoptosis, mediated by Reaper, is blocked by buffy and that debcl is required to inhibit buffy. Our results demonstrate that developmental PCD regulation in the fly does not rely upon the Bcl-2 proteins, but that they provide an added layer of protection in the apoptotic response to stress.     

Light and oxygen are not required for harpin-induced cell death

Nicotiana sylvestris leaves challenged by the bacterial elicitor harpin N(Ea) were used as a model system in which to determine the respective roles of light, oxygen, photosynthesis, and respiration in the programmed cell death response in plants. The appearance of cell death markers, such as membrane damage, nuclear fragmentation, and induction of the stress-responsive element Tnt1, was observed in all conditions. However, the cell death process was delayed in the dark compared with the light, despite a similar accumulation of superoxide and hydrogen peroxide in the chloroplasts. In contrast, harpin-induced cell death was accelerated under very low oxygen (<0.1% O(2)) compared with air. Oxygen deprivation impaired accumulation of chloroplastic reactive oxygen species (ROS) and the induction of cytosolic antioxidant genes in both the light and the dark. It also attenuates the collapse of photosynthetic capacity and the respiratory burst driven by mitochondrial alternative oxidase activity observed in air. Since alternative oxidase is known to limit overreduction of the respiratory chain, these results strongly suggest that mitochondrial ROS accumulate in leaves elicited under low oxygen. We conclude that the harpin-induced cell death does not require ROS accumulation in the apoplast or in the chloroplasts but that mitochondrial ROS could be important in the orchestration of the cell suicide program.     

Autophagy proteins are not universally required for phagosome maturation

Phagocytosis plays a central role in immunity and tissue homeostasis. After internalization of cargo into single-membrane phagosomes, these compartments undergo a maturation sequences that terminates in lysosome fusion and cargo degradation. Components of the autophagy pathway have recently been linked to phagosome maturation in a process called LC3-associated phagocytosis (LAP). In this process, autophagy machinery is thought to conjugate LC3 directly onto the phagosomal membrane to promote lysosome fusion. However, a recent study has suggested that ATG proteins may in fact impair phagosome maturation to promote antigen presentation. Here, we examined the impact of ATG proteins on phagosome maturation in murine cells using FCGR2A/FcγR-dependent phagocytosis as a model. We show that phagosome maturation is not affected in Atg5-deficient mouse embryonic fibroblasts, or in Atg5- or Atg7-deficient bone marrow-derived macrophages using standard assays of phagosome maturation. We propose that ATG proteins may be required for phagosome maturation under some conditions, but are not universally required for this process.     

Identical ends are not required for the equal encapsidation of plus- and minus-strand parvovirus LuIII DNA.

Sequence analyses of the left and right termini of LuIII virus show they are nonidentical imperfect palindromes of 122 and 211 nucleotides, respectively. The left terminus of the minus strand of LuIII DNA, uniquely in the flip conformation, can assume a T-shaped structure. The right terminus of the minus strand of LuIII DNA can assume a U-shaped structure, and it exists in either the flip or flop conformation. The termini of LuIII shared a high degree of sequence homology and showed conserved secondary structure with those of the rodent parvoviruses MVMp and H-1. LuIII, like adeno-associated virus, encapsidates equal amounts of plus- and minus-strand DNA. However, the sequence data for LuIII virus demonstrate that identical termini are not required for this encapsidation pattern.