On the Mechanism of Action of H2O2 in the Cellular Stress

We propose a hypothesis according to which the reactive and reduced species of oxygen could be the intracellular inducers of the stress (or “heat-shock”) response. This hypothesis is based on the following observations on Drosphila cells: -a) the return to normoxia after 24 h anaerobiosis is suficient to induce the synthesis of the ‘heat shock’ proteins without elevation of temperature together with a rapid increase of O₂ consumption; -b) hydrogen peroxide introduced in the culture medium induces the early transcrip-tional activation of the ‘heat shock’ genes (maximal after 5 minutes); -c) hydrogen peroxide added to cellular extracts in vitro (thus acting as an intracellular metabolite) activates instantaneously the binding capacity of a ‘heat shock’ factor to a DNA ‘heat shock’ regulatory element. Thus, hydrogen peroxide, and possibly other reactive reduced species ofoxygen, could trigger the onset of the stress (or ‘heat shock’) response.     

Na,K-ATPase: A murzyme facilitating thermodynamic equilibriums at the membrane-interface

The redox metabolic paradigm of murburn concept advocates that diffusible reactive species (DRS, particularly oxygen-centric radicals) are mainstays of physiology, and not mere pathological manifestations. The murburn purview of cellular function also integrates the essential principles of bioenergetics, thermogenesis, homeostasis, electrophysiology, and coherence. In this context, any enzyme that generates/modulates/utilizes/sustains DRS functionality is called a murzyme. We have demonstrated that several water-soluble (peroxidases, lactate dehydrogenase, hemogoblin, etc.) and membrane-embedded (Complexes I–V in mitochondria, Photosystems I/II in chloroplasts, rhodopsin/transducin in rod cells, etc.) proteins serve as murzymes. The membrane protein of Na,K-ATPase (NKA, also known as sodium-potassium pump) is the focus of this article, owing to its centrality in neuro-cardio-musculo electrophysiology. Herein, via a series of critical queries starting from the geometric/spatio-temporal considerations of diffusion/mass transfer of solutes in cells to an update on structural/distributional features of NKA in diverse cellular systems, and from various mechanistic aspects of ion-transport (thermodynamics, osmoregulation, evolutionary dictates, etc.) to assays/explanations of inhibitory principles like cardiotonic steroids (CTS), we first highlight some unresolved problems in the field. Thereafter, we propose and apply a minimalist murburn model of trans-membrane ion-differentiation by NKA to address the physiological inhibitory effects of trans-dermal peptide, lithium ion, volatile anesthetics, confirmed interfacial DRS + proton modulators like nitrophenolics and unsaturated fatty acid, and the diverse classes of molecules like CTS, arginine, oximes, etc. These explanations find a pan-systemic connectivity with the inhibitions/uncouplings of other membrane proteins in cells.     

Aerobic respiration: proof of concept for the oxygen-centric murburn perspective

Abstract

The inner mitochondrial membrane protein complexes (I–V) and prokaryotic respiratory machinery are examined for a deeper understanding of their structure–function correlations and dynamics. In silico analysis of the structure of complexes I–IV, docking studies and erstwhile literature confirm that they carry sites which are in close proximity to DROS (diffusible reactive oxygen species) generating redox centers. These findings provide supportive evidence for the newly proposed oxygen-centric chemical-coupling mechanism (murburn concept), wherein DROS catalyzes the esterification of inorganic phosphate to ADP. Further, in a reductionist system, we demonstrate that a DROS (like superoxide) can effectively esterify inorganic phosphate to ADP. The impact of these findings and the interactive dynamics of classical inhibitors (rotenone and cyanide), uncouplers (dinitrophenol and uncoupling protein) and other toxins (atractyloside and oligomycin) are briefly discussed.

Highlights

? Earlier perception: Complexes (I–IV) pump protons and Complex V make ATP (aided by protons)

? Herein: Respiratory molecular machinery is probed for new structure–function correlations

? Analyses: Quantitative arguments discount proton-centric ATP synthesis in mitochondria and bacteria

? In silico data: ADP-binding sites and O₂/ diffusible reactive oxygen species (DROS)-accessible channels are unveiled in respiratory proteins

? In vitro data: Using luminometry, ATP synthesis is demonstrated from ADP, Pi and superoxide

? Inference: Findings agree with decentralized ADP–Pi activation via oxygen-centric murburn scheme

Communicated by Ramaswamy H. Sarma     

Morphological homeostasis by autophagy

With cellular organelles coming in all shapes and sizes, the principle ‘form follows function’ is readily discernible through the cytologist’s lens. Architecturally, one might ask whether there is feedback in this organization. Does a cell ‘know’ when it has constructed membrane into the stacks of the Golgi, the cisternae of the mitochondria or the tubules of the endoplasmic reticulum? Proofreading can occur in vivo as both errors in nucleic acids and misfolds in proteins are recognized by the cell. Are there analogous systems which maintain/regulate the architectural integrity of organelles? Our recent paper entitled “Generation of cubic membranes from controlled homotypic interactions of membrane proteins in the endoplasmic reticulum” suggests that autophagy may play such a role.     

Murburn posttranslational modifications of proteins: Cellular redox processes and murzyme-mediated metabolo-proteomics

Murburn concept constitutes the thesis that diffusible reactive species or DRS are obligatorily involved in routine metabolic and physiological activities. Murzymes are defined as biomolecules/proteins that generate/modulate/sustain/utilize DRS. Murburn posttranslational modifications (PTMs) result because murburn/murzyme functionalism is integral to cellular existence. Cells must incorporate the inherently stochastic nature of operations mediated by DRS. Due to the earlier/inertial stigmatic perception that DRS are mere agents of chaos, several such outcomes were either understood as deterministic modulations sponsored by house-keeping enzymes or deemed as unregulated nonenzymatic events resulting out of “oxidative stress”. In the current review, I dispel the myths around DRS-functions, and undertake systematic parsing and analyses of murburn modifications of proteins. Although it is impossible to demarcate all PTMs into the classical or murburn modalities, telltale signs of the latter are evident from the relative inaccessibility of the locus, non-specificities and mechanistic details. It is pointed out that while many murburn PTMs may be harmless, some others could have deleterious or beneficial physiological implications. Some details of reversible/irreversible modifications of amino acid residues and cofactors that may be subjected to phosphorylation, halogenation, glycosylation, alkylation/acetylation, hydroxylation/oxidation, etc. are listed, along with citations of select proteins where such modifications have been reported. The contexts of these modifications and their significance in (patho)physiology/aging and therapy are also presented. With more balanced explorations and statistically verified data, a definitive understanding of normal versus pathological contexts of murburn modifications would be obtainable in the future.     

Structural studies on bacterial system used in the recognition and uptake of the macromolecule alginate

Alginate is an acidic heteropolysaccharide produced by brown seaweed and certain kinds of bacteria. The cells of Sphingomonas sp. strain A1, a gram-negative bacterium, have several alginate-degrading enzymes in their cytoplasm and efficiently utilize this polymer for their growth. Sphingomonas sp. strain A1 cells can directly incorporate alginate into their cytoplasm through a transport system consisting of a “pit” on their cell surface, substrate-binding proteins in their periplasm, and an ATP-binding cassette transporter in their inner membrane. This review deals with the structural and functional aspects of bacterial systems necessary for the recognition and uptake of alginate.     

New secreted toxins and immunity proteins encoded within the Type VI secretion system gene cluster of Serratia marcescens

Protein secretion systems are critical to bacterial virulence and interactions with other organisms. The Type VI secretion system (T6SS) is found in many bacterial species and is used to target either eukaryotic cells or competitor bacteria. However, T6SS‐secreted proteins have proven surprisingly elusive. Here, we identified two secreted substrates of the antibacterial T6SS from the opportunistic human pathogen, Serratia marcescens. Ssp1 and Ssp2, both encoded within the T6SS gene cluster, were confirmed as antibacterial toxins delivered by the T6SS. Four related proteins encoded around the Ssp proteins (‘Rap’ proteins) included two specifically conferring self‐resistance (‘immunity’) against T6SS‐dependent Ssp1 or Ssp2 toxicity. Biochemical characterization revealed specific, tight binding between cognate Ssp–Rap pairs, forming complexes of 2:2 stoichiometry. The atomic structures of two Rap proteins were solved, revealing a novel helical fold, dependent on a structural disulphide bond, a structural feature consistent with their functional localization. Homologues of the Serratia Ssp and Rap proteins are found encoded together within other T6SS gene clusters, thus they represent founder members of new families of T6SS‐secreted and cognate immunity proteins. We suggest that Ssp proteins are the original substrates of the S. marcescens T6SS, before horizontal acquisition of other T6SS‐secreted toxins. Molecular insight has been provided into how pathogens utilize antibacterial T6SSs to overcome competitors and succeed in polymicrobial niches.     

Lipid Rafts Disruption Increases Ochratoxin A Cytotoxicity to Hepatocytes

Lipid rafts are microdomains in plasma membrane and can mediate cytotoxicity. In this study, the role of lipid rafts in ochratoxin A‐induced toxicity was investigated using Hepatoblastoma Cell Line HepG‐2 cells. Disruption of cholesterol‐containing lipid rafts enhanced Ochratoxin A (OTA) toxicity, as shown by increased lactate dehydrogenase leakage, increased reactive oxygen species level and reduction of superoxide dismutase activity in a time‐dependent manner. Isobaric tags for relative and absolute quantitation‐based proteomics of the cell membranes showed that nearly 85.5% proteins were downregulated by OTA, indicating that OTA inhibited the membrane protein synthesis. Most of altered proteins were involved in Gene Ontology “transport”, “cell adhesion” and “vesicle‐mediated transport”. In conclusion, lipid rafts play a key role in OTA‐induced cytotoxicity. This study provides insight into how OTA toxicity is regulated by the plasma membrane, especially the lipid rafts.     

Chemistries and colors of bioluminescent reactions: a review

Many different organisms, ranging from bacteria and fungi to fireflies and fish, are endowed with the ability to emit light, but the bioluminescent systems are not evolutionarily conserved: genes coding for the luciferase proteins (Lase) are not homologous, and the luciferins are also different, falling into many unrelated chemical classes. Biochemically, all known Lase are oxygenases that utilize molecular oxygen to oxidize a substrate (a luciferin; literally the ‘light-bearing’ molecule), with formation of a product molecule in an electronically excited state. The color of the light may differ, even though the same luciferin/Lase system underlies the reaction. Filters or differences in Lase structure are responsible in some cases; in others a secondary emitter associated with a second protein is involved. In the coelenterates a green fluorescent protein, whose chromophore is derived from the primary amino-acid sequence, results in a red shift of the emission. In the bacteria accessory proteins causing either blue- or red-shifts have been isolated from different species; the chromophores are noncovalently bound. Although radiationless energy transfer has been implicated in the excitation of such accessory emitters, this may not be so in all cases.     

Involvement of Lysophosphatidic Acid,Sphingosine 1-Phosphate and Ceramide 1-Phosphate in the Metabolization of Phosphatidic Acid by Lipid Phosphate Phosphatases in Bovine Rod Outer Segments

The aim of the present research was to evaluate the generation of [2-3H]diacylglycerol ([2-3H]DAG) from [2-3H]-Phosphatidic acid ([2-3H]PA) by lipid phosphate phosphatases (LPPs) at different concentrations of lysophosphatidic acid (LPA), sphingosine 1-phosphate (S1P), and ceramide 1-phosphate (C1P) in purified ROS obtained from dark-adapted retinas (DROS) or light-adapted retinas (BLROS) as well as in ROS membrane preparations depleted of soluble and peripheral proteins. Western blot analysis revealed the presence of LPP3 exclusively in all membrane preparations. Immunoblots of entire ROS and depleted ROS did not show dark-light differences in LPP3 levels. LPPs activities were diminished by 53% in BLROS with respect to DROS. The major competitive effect on PA hydrolysis was exerted by LPA and S1P in DROS and by C1P in BLROS. LPPs activities in depleted ROS were similar to the activity observed in entire DROS and BLROS, respectively. LPA, S1P and C1P competed at different extent in depleted DROS and BLROS. Sphingosine and ceramide inhibited LPPs activities in entire and depleted DROS. Ceramide also inhibited LPPs activities in entire and in depleted BLROS. Our findings are indicative of a different degree of competition between PA and LPA, S1P and C1P by LPPs depending on the illumination state of the retina.     

Soy isoflavones and cellular mechanics

Soy isoflavones are diphenolic compounds that are frequently used for alternative treatment of ageing symptoms in both genders. They operate at principally two hierarchical levels of functional organization – cellular and molecular, while these ‘types’ of action appear to have indefinite borders. Soy isoflavone action at the cellular level involves inter alia the effects on cell mechanics. This epigenetic and modular determinant of cell function and fate is defined by: the anchorage to extracellular matrix (ECM) and neighboring cells, cytoskeleton organization, membrane tension and vesicle trafficking. Soy isoflavones have been reported to: (i) generally fashion an inert cell phenotype in some cancers and enhance the cell anchorage in connective tissues, via the effects on ECM proteins, focal adhesion kinases-mediated events and matrix metalloproteinases inhibition; (ii) affect cytoskeleton integrity, the effects being related to Ca²⁺ ions fluxes and involving cell retraction or differentiation/proliferation-related variations in mechanical status; (iii) increase, remain “silent” or decrease membrane tension/fluidity, which depends on polarity and a number and arrangement of functional groups in applied isoflavone; (iv) provoke inhibitory effects on vesicle trafficking and exo-/endocytosis, which are usually followed by changed cell morphology. Here we present and discuss the abundance of effects arising from cells’ “encounter” with soy isoflavones, focusing on different morphofunctional definers of cell mechanics.     

Diacylglyceride lipase activity in rod outer segments depends on the illumination state of the retina

We have demonstrated that the competition between phosphatidic acid (PA) and lysophosphatidic acid (LPA), sphingosine 1-phosphate (S1P) and ceramide 1-phosphate (C1P) for lipid phosphate phosphatases (LPP) generates different levels of diacylglycerol (DAG) depending on the illumination state of the retina. The aim of the present research was to determine the diacylglyceride lipase (DAGL) activity in purified rod outer segments (ROS) obtained from dark-adapted retinas (DROS) or light-adapted retinas (BLROS) as well as in ROS membrane preparations depleted of soluble and peripheral proteins. [2-(3)H]monoacylglycerol (MAG), the product of DAGL, was evaluated from [2-(3)H]DAG generated by LPP action on [2-(3)H]PA in the presence of either LPA, S1P or C1P. MAG production was inhibited by 55% in BLROS and by 25% when the enzymatic assay was carried out in ROS obtained from dark-adapted retinas and incubated under room light (LROS). The most important events occurred in DROS where co-incubation of [2-(3)H]PA with LPA, S1P or C1P diminished MAG production. A higher level of DAGL activity was observed in LROS than in BLROS, though this difference was not apparent in the presence of LPA, S1P or C1P. DAGL activity in depleted DROS was diminished with respect to that in entire DROS. LPA, S1P and C1P produced a similar decrease in MAG production in depleted DROS whereas only C1P significantly diminished MAG generation in depleted BLROS. Sphingosine and ceramide inhibited MAG production in entire DROS and stimulated its generation in BLROS. Sphingosine and ceramide stimulated MAG generation in both depleted DROS and BLROS. Under our experimental conditions the degree of MAG production depended on the illumination state of the retina. We therefore suggest that proteins related to phototransduction phenomena are involved in the effects observed in the presence of S1P/sphingosine or C1P/ceramide.     

Cytochrome P450 reductase: a harbinger of diffusible reduced oxygen species

The bi-enzymatic system of cytochrome P450 (CYP, a hemoprotein) and cytochrome P450 reductase (CPR, a diflavoenzyme) mediate the redox metabolism of diverse indigenous and xenobiotic molecules in various cellular and organ systems, using oxygen and NADPH. Curiously, when a 1:1 ratio is seen to be optimal for metabolism, the ubiquitous CYP:CPR distribution ratio is 10 to 100:1 or higher. Further, the NADPH equivalents consumed in these in vitro or in situ assemblies usually far exceeded the amount of substrate metabolized. We aimed to find the rationale to explain for these two oddities. We report here that CPR is capable of activating molecular oxygen on its own merit, generating diffusible reduced oxygen species (DROS). Also, in the first instance for a flavoprotein, CPR is shown to deplete peroxide via diffusible radical mediated process, thereby leading to the formation of water (but without significant evolution of oxygen). We also quantitatively demonstrate that the rate of oxygen activation and peroxide depletion by CPR accounts for the major reactivity in the CYP+CPR mixture. We show unambiguously that CPR is able to regulate the concentration of diffusible reduced oxygen species in the reaction milieu. These findings point out that CPR mediated processes are bound to be energetically 'wasteful' and potentially 'hazardous' owing to the unavoidable nature of the CPR to generate and deplete DROS. Hence, we can understand that CPR is distributed at low densities in cells. Some of the activities that were primarily attributed to the heme-center of CYP are now established to be a facet of the flavins of CPR. The current approach of modeling drugs to minimize "uncoupling" on the basis of erstwhile hypothesis stands questionable, considering the ideas brought forth in this work.     

Mitochondria-targeted drug delivery in cancers

Mitochondria are considered one of the most important subcellular organelles for targeting and delivering drugs because mitochondria are the main location for various cellular functions and energy (i.e., ATP) production, and mitochondrial dysfunctions and malfunctions cause diverse diseases such as neurodegenerative disorders, cardiovascular disorders, metabolic disorders, and cancers. In particular, unique mitochondrial characteristics (e.g., negatively polarized membrane potential, alkaline pH, high reactive oxygen species level, high glutathione level, high temperature, and paradoxical mitochondrial dynamics) in pathological cancers have been used as targets, signals, triggers, or driving forces for specific sensing/diagnosing/imaging of characteristic changes in mitochondria, targeted drug delivery on mitochondria, targeted drug delivery/accumulation into mitochondria, or stimuli-triggered drug release in mitochondria. In this review, we describe the distinctive structures, functions, and physiological properties of cancer mitochondria and discuss recent technologies of mitochondria-specific “key characteristic” sensing systems, mitochondria-targeted “drug delivery” systems, and mitochondrial stimuli-specific “drug release” systems as well as their strengths and weaknesses.     

SMP domain proteins in membrane lipid dynamics

Synaptotagmin-like mitochondrial-lipid-binding (SMP) domain proteins are evolutionarily conserved family of proteins in eukaryotes that localize between the endoplasmic reticulum (ER) and either the plasma membrane (PM) or other organelles. They are involved in tethering of these membrane contact sites through interaction with other proteins and membrane lipids. Recent structural and biochemical studies have demonstrated that SMP domain proteins transport a wide variety of lipid species by the ability of the SMP domain to harbor lipids through its unique hydrophobic cavity. Growing evidence suggests that SMP domain proteins play critical roles in cell physiology by their actions at membrane contact sites. In this review, we summarize the functions of SMP domain proteins and their direct roles in lipid transport across different membrane compartments. We also discuss their physiological functions in organisms as well as “bypass” pathways that act in parallel with SMP domain proteins at membrane contact sites.     

Three-finger proteins from the Ly6/uPAR family: Functional diversity within one structural motif

The discovery in higher animals of proteins from the Ly6/uPAR family, which have structural homology with snake “three-finger” neurotoxins, has generated great interest in these molecules and their role in the functioning of the organism. These proteins have been found in the nervous, immune, endocrine, and reproductive systems of mammals. There are two types of the Ly6/uPAR proteins: those associated with the cell membrane by GPI-anchor and secreted ones. For some of them (Lynx1, SLURP-1, SLURP-2, Lypd6), as well as for snake α-neurotoxins, the target of action is nico- tinic acetylcholine receptors, which are widely represented in the central and peripheral nervous systems, and in many other tissues, including epithelial cells and the immune system. However, the targets of most proteins from the Ly6/uPAR family and the mechanism of their action remain unknown. This review presents data on the structural and functional properties of the Ly6/uPAR proteins, which reveal a variety of functions within a single structural motif.     

Diacylglyceride lipase activity in rod outer segments depends on the illumination state of the retina

We have demonstrated that the competition between phosphatidic acid (PA) and lysophosphatidic acid (LPA), sphingosine 1-phosphate (S1P) and ceramide 1-phosphate (C1P) for lipid phosphate phosphatases (LPP) generates different levels of diacylglycerol (DAG) depending on the illumination state of the retina. The aim of the present research was to determine the diacylglyceride lipase (DAGL) activity in purified rod outer segments (ROS) obtained from dark-adapted retinas (DROS) or light-adapted retinas (BLROS) as well as in ROS membrane preparations depleted of soluble and peripheral proteins. [2-³H]monoacylglycerol (MAG), the product of DAGL, was evaluated from [2-³H]DAG generated by LPP action on [2-³H]PA in the presence of either LPA, S1P or C1P. MAG production was inhibited by 55% in BLROS and by 25% when the enzymatic assay was carried out in ROS obtained from dark-adapted retinas and incubated under room light (LROS). The most important events occurred in DROS where co-incubation of [2-³H]PA with LPA, S1P or C1P diminished MAG production. A higher level of DAGL activity was observed in LROS than in BLROS, though this difference was not apparent in the presence of LPA, S1P or C1P. DAGL activity in depleted DROS was diminished with respect to that in entire DROS. LPA, S1P and C1P produced a similar decrease in MAG production in depleted DROS whereas only C1P significantly diminished MAG generation in depleted BLROS. Sphingosine and ceramide inhibited MAG production in entire DROS and stimulated its generation in BLROS. Sphingosine and ceramide stimulated MAG generation in both depleted DROS and BLROS. Under our experimental conditions the degree of MAG production depended on the illumination state of the retina. We therefore suggest that proteins related to phototransduction phenomena are involved in the effects observed in the presence of S1P/sphingosine or C1P/ceramide.     

Metabolic scaling theory in plant biology and the three oxygen paradoxa of aerobic life

Alfred Russell Wallace was a field naturalist with a strong interest in general physiology. In this vein, he wrote that oxygen (O₂), produced by green plants, is “the food of protoplasm, without which it cannot continue to live”. Here we summarize current models relating body size to respiration rates (in the context of the metabolic scaling theory) and show that oxygen-uptake activities, measured at 21 vol.% O₂, correlate closely with growth patterns at the level of specific organs within the same plant. Thus, whole plant respiration can change ontogenetically, corresponding to alterations in the volume fractions of different tissues. Then, we describe the evolution of cyanobacterial photosynthesis during the Paleoarchean, which changed the world forever. By slowly converting what was once a reducing atmosphere to an oxidizing one, microbes capable of O₂-producing photosynthesis modified the chemical nature and distribution of the element iron (Fe), slowly drove some of the most ancient prokaryotes to extinction, created the ozone (O₃) layer that subsequently shielded the first terrestrial plants and animals from harmful UV radiation, but also made it possible for Earth’s forest to burn, sometimes with catastrophic consequences. Yet another paradox is that the most abundant protein (i.e., the enzyme Rubisco, Ribulose-1,5-biphosphate carboxylase/oxygenase) has a greater affinity for oxygen than for carbon dioxide (CO₂), even though its function is to bind with the latter rather than the former. We evaluate this second “oxygen paradox” within the context of photorespiratory carbon loss and crop yield reduction in C3 vs. C4 plants (rye vs. maize). Finally, we analyze the occurrence of reactive oxygen species (ROS) as destructive by-products of cellular metabolism, and discuss the three “O₂-paradoxa” with reference to A. R. Wallace’s speculations on “design in nature”.     

Das Triplett aus zwei Monophyla und einem Paraphylum als Baustein des phylogenetischen Systems

The triplet consisting of two monophyletic taxa and one paraphyletic taxon as constructive element of the phylogenetic system Evolution has produced very many novelties (apomorphies). Most of them are small and relatively inconstant, these are more or less indicative of the phylogenetic relationships between closely related species. They cannot be the constitutive character of a supraspecific taxon that exists since a long time and comprises many diversified species. Such a taxon of higher rank can only be characterized by an improbable, rare novelty that has developed only once and has been preserved in all descendent species. Two consecutive apomorphies of this persistent type (‘fixed apomorphies’) characterize three supraspecific taxa, the triplet “A”, “B” and “A minus B” (Fig. 1). The group “A minus B” is rejected in Hennig's theory because it is ‘paraphyletic’, but it is not an artefact created by the systematicist. It is an inevitable mathematical consequence of the differentiatison of the group “B” within the group “A”. Being the result of a subtraction, it is necessarily associated with the two monophyletic partners in the triplet, as it is delimited on one side by the synapomorphy of the group “A”, of which it is a part, and on the other side by the autapomorphy of the separate group “B”. Traditional classifications often include paraphyletic groupings that are inconsistent with phylogenetics, e. g. the Reptilia and the Apterygota. The fault in such cases is that these groups are extended beyond the limits of a triplet and cover more than a single interval between consecutive monophyletic taxa. Paraphyletic groups are admitted in the phylogenetic system only for bridging the gaps in our cladistic information. According to HENNIG'S theory, all supraspecific taxa should be arranged two by two as sister-groups originating from one ancestral species and comprising all descendents of that species. The fixed evolutionary novelties which characterize higher supraspecific taxa are, however, rare and scattered. It is highly improbable that they have developed in sister species, therefore the taxa marked by them cannot be sister-groups (except in very rare cases). In HENNIG'S earlier papers, e. g. in his system of Lepidoptera (1953: 46–49), the alleged ‘sister-groups' are, in reality, the groups “B” and “A minus B” of a triplet (see Fig. 2). In his revised concept (1957 and later), two autapomorphic groups which are most closely related in the recent fauna (“B” and “C” in Fig. 3) are called ‘sister-groups’. But these have originated independently from different ancestors in a plesiomorphic complex of extinct species and are more closely related to parts of this complex than to each other. True sister-groups (“Bx” and “Cx” in Fig. 4) would be formed if these related plesiomorphic species were included, but this extension of the ’backward‘ border of the taxon is not justified by synapomorphy (in the terms of logic, it is a ’metabasis‘), and it would make the classification of fossil species impossible, unless these show at least one synapomorphy with either “B” or “C”. In the system of the recent fauna the sister-groups are identical with the autapomorphic groups, because the plesiomorphic species are extinct. The natural system based on synapomorphies and autapomorphies is the triplet-system as outlined in Figure 6. It is not a new type of classification, but its theoretical foundation was missing, and precise instructions were needed for its use in phylogenetics. The information obtained by HENNIG'S method is entirely preserved in this system and can be retrieved from it, and both recent and extinct species can be classified together. The disadvantage of the triplet-system is that it contains twice as many taxa as HENNIG'S classification. This complexity will limit its use in the practice of taxonomy, but it may be simplified by transforming the system into a sequence of paraphyletic taxa terminating in a single monophylum.     

TNF-alpha potentiates protein-tyrosine nitration through activation of NADPH oxidase and eNOS localized in membrane rafts and caveolae of bovine aortic endothelial cells

A major source of reactive oxygen species (ROS) in endothelial cells is the NADPH oxidase enzyme complex. The selective distributions of any enzyme within cells have important implications in regulating enzyme effectiveness through facilitation of access to local substrates and/or product targets. Because membrane rafts provide a spatially preferable environment for a variety of enzyme systems, we sought to determine whether NADPH oxidase is present and functional in this plasma membrane compartment in endothelial cells. We found that, in resting endothelial cells, NADPH oxidase subunits were preassembled and the enzyme functional in membrane rafts, specifically in caveolae. Stimulation with TNF-alpha induced additional recruitment of the p47(phox) regulatory subunit to raft-localized NADPH oxidase and enhanced ROS production within raft domains. TNF-alpha also induced nitric oxide production through activation of endothelial nitric oxide synthase (eNOS) present in the same membrane compartment. The dual activation of superoxide and nitric oxide-generating systems provided a spatially favorable environment for nitration of tyrosine-containing proteins localized to rafts. Perturbation of membrane raft structural integrity with cholesterol-sequestering compounds caused the delocalization of NADPH oxidase subunits and eNOS from the rafts and inhibited TNF-alpha-induced ROS production and protein tyrosine nitration. Together, these data provide evidence that membrane rafts and caveolae play a role in the spatial regulation of NADPH oxidase and subsequent ROS/reactive nitrogen species in endothelial cells.