Serum cytochrome c to indicate the extent of ongoing tumor cell death

Despite the significant implication of apoptosis in tumorigenesis, there is no biomarker to assess the extent of ongoing apoptosis in vivo for hematological malignancies. We investigated the potential of serum cytochrome c (cyto-c) as a biomarker for apoptosis. Cyto-c and lactate dehydrogenase (LD) were released into the culture medium from apoptotic cells induced by tumor necrosis factor-related apoptosis-inducing ligand in a time-dependent manner in vitro, with different kinetic patterns. Only one-third of 153 patients with hematological malignancies showed high levels of serum cyto-c (>20 ng/ml). Although serum cyto-c level was roughly correlated to serum LD activity, their different kinetic patterns from serial measurements indicated that serum cyto-c rather than LD is a more sensitive indicator for tracking changes of tumor status. Furthermore, serum cyto-c level stratified patients with acute adult T-cell leukemia into favorable and unfavorable subgroups with 5-year survival rates of 67%vs. 11%. In conclusion, serum cyto-c may provide a fast real-time biomarker for tracking changes of tumor status involved in apoptotic cell death, but lacking disease or cell-type specificity.     

Electron transfer between hemes in mammalian cytochrome c oxidase

Fast intraprotein electron transfer reactions associated with enzymatic catalysis are often difficult to synchronize and therefore to monitor directly in non-light-driven systems. However, in the mitochondrial respiratory enzyme cytochrome oxidase aa(3), the kinetics of the final electron transfer step into the active site can be determined: reverse electron flow between the close-lying and chemically identical hemes a(3) and a can be initiated by flash photolysis of CO from reduced heme a(3) under conditions where heme a is initially oxidized. To follow this reaction, we used transient absorption spectroscopy, with femtosecond time resolution and a time window extending to 4 ns. Comparison of the picosecond heme a(3)-CO photodissociation spectra under different redox states of heme a shows significant spectral interaction between both hemes, a phenomenon complicating the interpretation of spectral studies with low time resolution. Most importantly, we show that the intrinsic electron equilibration, corresponding to a DeltaG(0) of 45-55 meV, occurs in 1.2 +/- 0.1 ns. This is 3 orders of magnitude faster than the previously established equilibration phase of approximately 3 mus, which we suggest to reflect a change in redox equilibrium closely following CO migration out of the active site. Our results allow testing a number of conflicting predictions regarding this reaction between both experimental and theoretical studies. We discuss the potential physiological relevance of fast equilibration associated with this low-driving-force redox reaction.     

Modulation of endothelial cell shape and growth by retinoids

Physiologic concentrations of retinol (1 X 10(-6) M) caused capillary and aortic endothelial cells (EC) to undergo a morphologic change, characterized by a rounder cell body, increased refractility at cell edges, and longer cytoplasmic processes distributed in a bipolar fashion. Computer image analysis of retinoid-treated EC revealed that both retinoic acid and retinol affected cellular area. Twenty-four hours following retinoic acid treatment, EC occupied a greater area than control (P less than 0.03) or retinol-treated EC (P less than 0.02). By Day 7, however, retinoic acid-treated EC occupied equivalent cellular areas as compared to control cells (P = 0.8). In contrast, by Day 7, retinol-treated EC occupied a smaller cellular area than control (P less than 0.002) or retinoic acid-treated EC (P less than 0.001). Proliferation studies revealed that within the first 72 hr of retinol treatment, basal EC growth was inhibited by 33% and the cells exhibited a lowered responsiveness to basic fibroblast growth factor (bFGF). In contrast, EC treated with retinoic acid and pericytes treated with each of the retinoids were not inhibited. The inhibitory effect of the 72 hr retinol treatment was reversible. Following 3 days exposure to retinol, EC given fresh media without retinoid underwent a population doubling in a subsequent 3-day period. However, in the continued presence of retinol, EC were 100% growth-inhibited. After a 3-day pretreatment with retinol, with or without continued retinol treatment, EC were refractile to the mitogenic action of bFGF in a subsequent 3-day period. These results demonstrate that retinol inhibits the basal and growth factor-stimulated growth of EC and causes a significant shape alteration of EC, supporting our hypothesis that vitamin A may be one of the signals that modify the growth and phenotype of EC.     

Rapid extracellular release of cytochrome c is specific for apoptosis and marks cell death in vivo

Diverse death stimuli including anticancer drugs trigger apoptosis by inducing the translocation of cytochrome c from the outer mitochondrial compartment into the cytosol. Once released, cytochrome c cooperates with apoptotic protease-activating factor-1 and deoxyadenosine triphosphate in caspase-9 activation and initiation of the apoptotic protease cascade. The results of this study show that on death induction by chemotherapeutic drugs, staurosporine and triggering of the death receptor CD95, cytochrome c not only translocates into the cytosol, but furthermore can be abundantly detected in the extracellular medium. The cytochrome c release from the cell is a rapid and apoptosis-specific process that occurred within 1 hour after induction of apoptosis, but not during necrosis. Interestingly, elevated cytochrome c levels were observed in sera from patients with hematologic malignancies. In the course of cancer chemotherapy, the serum levels of cytochrome c in the majority of the patients grew rapidly as a result of increased cell death. These data suggest that monitoring of cytochrome c in the serum of patients with tumors might serve as a useful clinical marker for the detection of the onset of apoptosis and cell turnover in vivo.     

Mitochondrial DNA mutations may contribute to aging via cell death caused by peptides that induce cytochrome c release

Mice wherein the wild-type mitochondrial DNA polymerase (pol gamma) is replaced by a proofreading-deficient version are born with mutation frequencies in mitochondrial DNA (mtDNA) much higher than are ever normally seen in old rodents or humans. These mice, however, are phenotypically normal at birth, raising the question regarding how the much lower frequencies observed in normal aging could possibly contribute to the aging process. In contrast, transgenic mice with cardiac-specific expression of a proofreading-deficient poly gamma from birth onwards accumulate mtDNA mutations to levels normally seen in aging. But these mice develop dilated cardiomyopathy suggesting that age-related mtDNA mutations are pathogenic. Using computer simulation, we show that both findings are predicted based on the hypotheses that (1) rare lethal mutations that cause apoptosis underlie the pathogenesis of mutagenesis in mtDNA and (2) most sporadic mtDNA mutations are phenotypically recessive and therefore nonpathogenic. Biochemical evidence is presented that mitochondria with mtDNA mutations generate a peptide that causes the release of cytochrome c, providing a mechanism for the increased apoptosis observed in aging. Simulation also predicts that normal, age-related accumulation of mtDNA mutations causes significant levels of cell death. These findings suggest that mtDNA mutations play an important role in the aging process and that their pathogenic mechanism is linked to apoptosis.     

Single-molecule study of DNA unlinking by eukaryotic and prokaryotic type-II topoisomerases

Type-II topoisomerases are responsible for untangling DNA during replication by removing supercoiled and interlinked DNA structures. Using a single-molecule micromanipulation setup, we follow the real-time decatenation of two mechanically braided DNA molecules by Drosophila melanogaster topoisomerase (Topo) II and Escherichia coli Topo IV. Although Topo II relaxes left-handed (L) and right-handed (R-) braids similarly at a rate of approximately 2.9 s-1, Topo IV has a marked preference for L-braids, which it relaxes completely and processively at a rate of approximately 2.4 s-1. However, Topo IV can unlink R-braids at about half that rate when they supercoil to form L-plectonemes. These results imply that the preferred substrate for unlinking by Topo IV has the symmetry of an L-crossing and shed new light on the decatenation of daughter strands during DNA replication, which are usually assumed to be linked in an R-braid.     

Modulation of cell death by Bcl-xL through caspase interaction

The caspases are cysteine proteases that have been implicated in the execution of programmed cell death in organisms ranging from nematodes to humans. Many members of the Bcl-2 family, including Bcl-x_L, are potent inhibitors of programmed cell death and inhibit activation of caspases in cells. Here, we report a direct interaction between caspases and Bcl-x_L. The loop domain of Bcl-x_L is cleaved by caspases in vitro and in cells induced to undergo apoptotic death after Sindbis virus infection or interleukin 3 withdrawal. Mutation of the caspase cleavage site in Bcl-x_L in conjunction with a mutation in the BH1 homology domain impairs the death-inhibitory activity of Bcl-x_L, suggesting that interaction of Bcl-x_L with caspases may be an important mechanism of inhibiting cell death. However, once Bcl-x_L is cleaved, the C-terminal fragment of Bcl-x_L potently induces apoptosis. Taken together, these findings indicate that the recognition/cleavage site of Bcl-x_L may facilitate protection against cell death by acting at the level of caspase activation and that cleavage of Bcl-x_L during the execution phase of cell death converts Bcl-x_L from a protective to a lethal protein.     

Modulation of granulocyte survival and programmed cell death by cytokines and bacterial products.

Mature circulating polymorphonuclear cells (PMN) have the shortest half-life among leukocytes and undergo rapid programmed cell death in vitro. In this study, we have examined the possibility that inflammatory signals (cytokines and bacterial products) can regulate PMN survival. PMN in culture were found to rapidly die, with percentages of survival at 24, 48, 72, and 96 hours of 97.3% +/- 1.9%, 36.8% +/- 5.3%, 14.5% +/- 3.1%, and 4.2% +/- 2.9%, respectively (mean +/- SE of 20 different donors). PMN incubated with interleukin-1 beta (IL-1 beta), tumor necrosis factor, granulocyte-macrophage colony-stimulating factor (CSF), granulocyte-CSF, and interferon-gamma (IFN-gamma), but not with prototypic chemoattractants (fMLP, recombinant C5a, and IL-8), showed a marked increase in survival, with values ranging at 72 hours of incubation from 89.5% +/- 5.8% for IL-1 beta to 47.6% +/- 6.4% for IFN-gamma. The calculated half-life was 35 hours for untreated and 115 hours for IL-1-treated PMN. PMN activated with lipopolysaccharide (LPS) or inactivated streptococci also showed a longer survival compared with untreated cells (94.4% +/- 3.2% and 95.5% +/- 2.4%, respectively, at 72 hours). PMN surviving in response to LPS or IL-1 beta retained the capacity to produce superoxide anion when treated with phorbol esters or fMLP. All inducers of PMN survival protect these cells from programmed cell death because they reduced cells with morphologic features of apoptosis and the fragmentation of DNA in multiples of 180 bp. Thus, certain cytokines and bacterial products can prolong PMN survival by interfering with the physiologic process of apoptosis. Prolongation of survival may be important for the regulation of host resistance and inflammation, and may represent a crucial permissive step for certain cytokines and microbial products that activate gene expression and function in PMN.     

A peptide inhibitor of cytochrome c/inositol 1,4,5-trisphosphate receptor binding blocks intrinsic and extrinsic cell death pathways

Apoptotic stimuli augment intracellular calcium concentration through inositol 1,4,5-trisphosphate receptors (IP3R) on endoplasmic reticulum calcium stores. We previously discovered an apoptotic cascade wherein cytochrome c binds to IP3R early in apoptosis, resulting in dysregulated calcium release. Here we show that cytochrome c binding to IP3R depends on a cluster of glutamic acid residues within the C terminus of the channel. A cell permeant peptide derived from this sequence displaces cytochrome c from IP3R and abrogates cell death induced by staurosporine treatment of HeLa cells and Fas ligand stimulation of Jurkat cells. Small-molecule inhibitors of cytochrome c/IP3R interactions may prove useful in treating disorders associated with inappropriate intrinsic and extrinsic apoptotic signaling.     

Oxidation of ferrocytochrome c by mitochondrial cytochrome c oxidase.

Attempts to rationalize the kinetics of cytochrome c oxidation catalyzed by solubilized mitochondrial cytochrome c oxidase (ferrocytochrome c:oxygen oxidoreductase, EC 1.9.3.1) have been based on assumptions of productive complex formation (Michaelis-Menten approach). However, the range of substrate concentrations used has not, in general, been sufficient to establish a general rate equation. Data adequate to derive such a rate expression are presented, as well as a method for estimation of constants which appear in the rate law deduced and reported herein. It is shown that either of two types of mechanisms, one assuming productive complex formation, as opposed to the other postulating dead-end complex formation, accurately predict the rate equation as deduced from experiment.     

Solution structure and dynamics of the complex between cytochrome c and cytochrome c peroxidase determined by paramagnetic NMR

The physiological complex of yeast cytochrome c peroxidase and iso-1-cytochrome c is a paradigm for biological electron transfer. Using paramagnetic NMR spectroscopy, we have determined the conformation of the protein complex in solution, which is shown to be very similar to that observed in the crystal structure [Pelletier H, Kraut J (1992) Science 258:1748-1755]. Our results support the view that this transient electron transfer complex is dynamic. The solution structure represents the dominant protein-protein orientation, which, according to our estimates, is occupied for >70% of the lifetime of the complex, with the rest of the time spent in the dynamic encounter state. Based on the observed paramagnetic effects, we have delineated the conformational space sampled by the protein molecules during the dynamic part of the interaction, providing experimental support for the theoretical predictions of the classical Brownian dynamics study [Northrup SH, Boles JO, Reynolds JCL (1988) Science 241:67-70]. Our findings corroborate the dynamic behavior of this complex and offer an insight into the mechanism of the protein complex formation in solution.     

Amino acids determining enzyme-substrate specificity in prokaryotic and eukaryotic protein kinases

The binding between a PK and its target is highly specific, despite the fact that many different PKs exhibit significant sequence and structure homology. There must be, then, specificity-determining residues (SDRs) that enable different PKs to recognize their unique substrate. Here we use and further develop a computational procedure to discover putative SDRs (PSDRs) in protein families, whereby a family of homologous proteins is split into orthologous proteins, which are assumed to have the same specificity, and paralogous proteins, which have different specificities. We reason that PSDRs must be similar among orthologs, whereas they must necessarily be different among paralogs. Our statistical procedure and evolutionary model identifies such residues by discriminating a functional signal from a phylogenetic one. As case studies we investigate the prokaryotic two-component system and the eukaryotic AGC (i.e., cAMP-dependent PK, cGMP-dependent PK, and PKC) PKs. Without using experimental data, we predict PSDRs in prokaryotic and eukaryotic PKs, and suggest precise mutations that may convert the specificity of one PK to another. We compare our predictions with current experimental results and obtain considerable agreement with them. Our analysis unifies much of existing data on PK specificity. Finally, we find PSDRs that are outside the active site. Based on our results, as well as structural and biochemical characterizations of eukaryotic PKs, we propose the testable hypothesis of "specificity via differential activation" as a way for the cell to control kinase specificity.     

Analysis of an evolutionarily conserved antigenic site on mammalian cytochrome c using synthetic peptides.

Two synthetic peptides inclusive of the NH2-terminal N-acetyl-Gly-Asp-Val-Glu tetrapeptide of mammalian cytochrome c (cyt c) were used in this study to address the question of whether mammals can respond immunologically to an evolutionarily conserved region of a protein. These peptides were assessed for their capacity (i) to act as immunogens for the production of anti-self cyt c antisera and (ii) to bind rabbit anti-rodent cyt c antibody. The findings from these studies indicate the existence of an immunogenic determinant in an evolutionarily conserved region of cyt c that contains residues 1-4. This determinant can induce anti-self cyt c antibodies whether presented as a peptide on a carrier protein or in the context of the intact molecule as polymerized mammalian cyt c.     

弓形虫致密颗粒抗原GRA8的原核和真核表达质粒的构建

目的 构建弓形虫RH株致密颗粒抗原GRA8的原核和真核重组表达质粒。方法 参照GRA8序列分别设计引物。采用PCR从弓形虫RH株基因组DNA中分别扩增出编码GRA8的基因片段，克隆至pMD18-T载体；菌落PCR鉴定阳性克隆并测序分析；各组阳性克隆的质粒分别亚克隆至原核表达质粒pGEX-4T-2和真核表达载体pVAXl，分别转化大肠杆菌BL21和JM109,PCR和酶切鉴定转化菌落的插入序列；将构建的原核表达菌株经IPTG诱导，SDS—PAGE和免疫印迹分析融合蛋白的表达；将构建的真核重组表达质粒免疫小鼠，观察其诱导的抗体应答。结果 PCR扩增出GRA8基因的特异片段。各组阳性克隆的序列正确，并分别被亚克隆到原核表达质粒pGEX-4T-2和真核表达载体pVAXl上，构建了弓形虫致密颗粒抗原GRA8的原核和真核重组表达质粒；原核表达质粒在大肠杆菌中表达了GRA8的融合蛋白；真核重组表达质粒诱导小鼠产生了抗弓形虫抗原的抗体。结论以pGEX-4T-2和pVAX1为载体，分别成功构建了GRA8的原核和真核重组表达质粒     

Mitochondrial stress protein recognition of inactivated dehydrogenases during mammalian cell death

The mammalian renal toxicant tetrafluoroethylcysteine (TFEC) is metabolized to a reactive intermediate that covalently modifies the lysine residues of a select group of mitochondrial proteins, forming difluorothioamidyl lysine protein adducts. Cellular damage is initiated by this process and cell death ensues. NH₂-terminal sequence analysis of purified mitochondrial proteins containing difluorothioamidyl lysine adducts identified the lipoamide succinyltransferase and dihydrolipoamide dehydrogenase subunits of the α-ketoglutarate dehydrogenase complex (αKGDH), a key regulatory component of oxidative metabolism, as targets for TFEC action. Adduct formation resulted in marked inhibition of αKGDH enzymatic activity, whereas the related pyruvate dehydrogenase complex was unmodified by TFEC and its activity was not inhibited in vivo. Covalent modification of αKGDH subunits also resulted in interactions with mitochondrial chaperonin HSP60 in vivo and with HSP60 and mitochondrial HSP70 in vitro. These observations confirm the role of mammalian stress proteins in the recognition of abnormal proteins and provide supporting evidence for reactive metabolite-induced cell death by modification of critical protein targets.     

Modulation of hematopoietic stem/progenitor cell engraftment by transforming growth factor beta

OBJECTIVE: To investigate if cell cycle progression plays a role in modulating the engraftment potential of mouse hematopoietic stem and progenitor cells (HSPC). MATERIALS AND METHODS: HSPC were isolated from adult mouse bone marrow, cultured in vitro under conditions promoting cell cycle arrest, and subsequently were evaluated for cell cycle status, clonogenic activity, and transplant potential. RESULTS In the presence of steel factor (STL) as a survival cytokine, transforming growth factor beta (TGF-beta) increased the G0/G1 fraction of cycling progenitor cells (Rh(high)) after a 20-hour culture. Clonogenic activity of quiescent long-term repopulating (Rh(low)) HSPC was unaffected by this culture, whereas clonogenic potential of Rh(high) cells decreased by about 30%. In competitive repopulation assays, Rh(low) cells cultured in STL + TGF-beta engrafted better than cells cultured in STL alone. However, culture in STL + TGF-beta did not overcome the failure of Rh(high) cells to engraft after transplant. We also utilized a two-stage culture system to first induce proliferation of Rh(low) HSPC by a 48-hour culture in STL + interleukin 6 + Flt-3 ligand, followed by shifting the culture to STL + TGF-beta for 24 hours to induce cycle arrest. A competitive repopulation assay demonstrated a relative decrease in repopulating potential in cultures that were cycle arrested compared to those that were not. CONCLUSION: Cell cycle progression by itself cannot account for the decrease in repopulating potential that is observed after ex vivo expansion. Other determinants of engraftment must be identified to facilitate the transplantation of cultured HSPC.     

NMR basis for interprotein electron transfer gating between cytochrome c and cytochrome c oxidase

The final interprotein electron transfer (ET) in the mammalian respiratory chain, from cytochrome c (Cyt c) to cytochrome c oxidase (CcO) is investigated by (1)H-(15)N heteronuclear single quantum coherence spectral analysis. The chemical shift perturbation in isotope-labeled Cyt c induced by addition of unlabeled CcO indicates that the hydrophobic heme periphery and adjacent hydrophobic amino acid residues of Cyt c dominantly contribute to the complex formation, whereas charged residues near the hydrophobic core refine the orientation of Cyt c to provide well controlled ET. Upon oxidation of Cyt c, the specific line broadening of N-H signals disappeared and high field (1)H chemical shifts of the N-terminal helix were observed, suggesting that the interactions of the N-terminal helix with CcO are reduced by steric constraint in oxidized Cyt c, while the chemical shift perturbations in the C-terminal helix indicate notable interactions of oxidized Cyt c with CcO. These results suggest that the overall affinity of oxidized Cyt c for CcO is significantly, but not very much weaker than that of reduced Cyt c. Thus, electron transfer is gated by dissociation of oxidized Cyt c from CcO, the rate of which is controlled by the affinity of oxidized Cyt c to CcO for providing an appropriate electron transfer rate for the most effective energy coupling. The conformational changes in Lys13 upon CcO binding to oxidized Cyt c, shown by (1)H- and (1)H, (15)N-chemical shifts, are also expected to gate intraprotein ET by a polarity control of heme c environment.     

The mechanism of proton pumping by cytochrome c oxidase

Cytochrome c oxidase catalyzes the reduction of oxygen to water that is accompanied by pumping of four protons across the mitochondrial or bacterial membrane. Triggered by the results of recent x-ray crystallographic analyses, published data concerning the coupling of individual electron transfer steps to proton pumping are reanalyzed: Conversion of the conventional oxoferryl intermediate F to the fully oxidized form O is connected to pumping of only one proton. Most likely one proton is already pumped during the double reduction of O, and only three protons during conversion of the “peroxy” forms P to O via the oxoferryl form F. Based on the available structural, spectroscopic, and mutagenesis data, a detailed mechanistic model, carefully considering electrostatic interactions, is presented. In this model, each of the four reductions of heme a during the catalytic cycle is coupled to the uptake of one proton via the D-pathway. These protons, but never more than two, are temporarily stored in the regions of the heme a and a₃ propionates and are driven to the outside (“pumped”) by electrostatic repulsion from protons entering the active site during turnover. The first proton is pumped by uptake of one proton via the K-pathway during reduction, the second and third proton during the P → F transition when the D-pathway and the active site become directly connected, and the fourth one upon conversion of F to O. Atomic structures are assigned to each intermediate including F′ with an alternative route to O.     

Dioxygen activation and bond cleavage by mixed-valence cytochrome c oxidase

Elucidating the structures of intermediates in the reduction of O₂ to water by cytochrome c oxidase is crucial to understanding both oxygen activation and proton pumping by the enzyme. In the work here, the reaction of O₂ with the mixed-valence enzyme, in which only heme a₃ and Cu_B in the binuclear center are reduced, has been followed by time-resolved resonance Raman spectroscopy. The results show that O=O bond cleavage occurs within the first 200 μs after reaction initiation; the presence of a uniquely stable Fe—O—O(H) peroxy species is not detected. The product of this rapid reaction is a heme a₃ oxoferryl (Fe^IV=O) species, which requires that an electron donor in addition to heme a₃ and Cu_B must be involved. The available evidence suggests that the additional donor is an amino acid side chain. Recent crystallographic data [Yoshikawa, S., Shinzawa-Itoh, K., Nakashima, R., Yaono, R., Yamashita, E., Inoue, N., Yao, M., Fei, M. J., Libeu, C. P., Mizushima, T., et al. Science, in press; Ostermeier, C., Harrenga, A., Ermler, U. & Michel, H. (1997) Proc. Natl. Acad. Sci. USA 94, 10547–10553] show that one of the Cu_B ligands, His240, is cross-linked to Tyr244 and that this cross-linked tyrosyl is ideally positioned to participate in dioxygen activation. We propose a mechanism for O—O bond cleavage that proceeds by concerted hydrogen atom transfer from the cross-linked His—Tyr species to produce the product oxoferryl species, Cu_B²⁺—OH⁻, and the tyrosyl radical. This mechanism provides molecular structures for two key intermediates that drive the proton pump in oxidase; moreover, it has clear analogies to the proposed O—O bond forming chemistry that occurs during O₂ evolution in photosynthesis.