Isoprostane nomenclature: Inherent problems may cause setbacks for the development of the isoprostanoid field

Do we have to bother about the isoprostane nomenclature? The widely accepted IUPAC isoprostane nomenclature provides an unambiguous and systematic terminology to name all theoretical possible isoprostanes. However, the currently accepted nomenclature system provides an unnatural framework which is not well suited to address certain biologically relevant questions. Artificial categorization of isoprostanoids into prostanoid families disrupts prostaglandin-ring core structures needed to describe biogenetic precursor–product relationships. In addition, the IUPAC system defines isoprostanoid families which comprise chemically heterogeneous isoprostanoids which largely differ in their physicochemical properties from those of the corresponding prostaglandins. As a result of this, alternative nomenclature systems such as the phytoprostane nomenclature system overcoming some inherent problems of the IUPAC nomenclature are still in use. However, different naming of isoprostanoids especially the classification of prostanoid family names has created considerable confusion. Therefore, a cautionary note on the current use of different nomenclature systems is necessary.     

Current development in non-enzymatic lipid peroxidation products,isoprostanoids and isofuranoids,in novel biological samples

Abstract

Isoprostanoids and isofuranoids are lipid mediators that can be formed from omega-3 and omega-6 polyunsaturated fatty acids (PUFAs). F₂-isoprostanes formed from arachidonic acid, especially 15-F_2t-isoprostane, are commonly measured in biological tissues for decades as the biomarker for oxidative stress and diseases. Recently, other forms of isoprostanoids derived from adrenic, eicosapentaenoic, and docosahexaenoic acids namely F₂-dihomo-isoprostanes, F₃-isoprostanes, and F₄-neuroprostanes respectively, and isofuranoids including isofurans, dihomo-isofurans, and neurofurans are reported as oxidative damage markers for different metabolisms. The most widely used samples in measuring lipid peroxidation products include but not limited to the blood and urine; other biological fluids, specialized tissues, and cells can also be determined. In this review, measurement of isoprostanoids and isofuranoids in novel biological samples by gas chromatography (GC)–mass spectrometry (MS), GC–MS/MS, liquid chromatography (LC)–MS, and LC–MS/MS will be discussed.     

Analysis of oxidative stress and wound-inducible dinor isoprostanes F(1) (phytoprostanes F(1)) in plants

Isoprostanes F(2) are arachidonate autoxidation products in mammals that have been shown to be induced during several human disorders associated with enhanced free-radical generation. Isoprostanes F(2) represent not only extremely reliable markers of oxidative stress in vivo, but they also exert potent biological effects. Therefore, it has been postulated that isoprostanoids are mediators of oxidant injury in vivo. Higher plants, however, do not synthesize arachidonic acid or isoprostanes. Here we show that a series of isoprostane F(2) analogs termed phytoprostanes F(1) (previously dinor isoprostanes F(1)) are formed by an analogous pathway from alpha-linolenate in plants. High-performance liquid chromatography and gas chromatography-mass spectrometry methods using [(18)O](3)phytoprostanes F(1) as internal standard have been developed to quantify phytoprostanes F(1). In fresh peppermint (Mentha piperita) leaves, phytoprostanes F(1) were found in free form (76 ng/g of dry weight) and at about 150-fold higher levels esterified in lipids. It is notable that these levels of phytoprostanes F(1) are more than two orders of magnitude higher than the basal levels of isoprostanes F(2) in mammalian tissues. Furthermore, wounding, as well as butyl hydroperoxide or cupric acetate stress triggered a dramatic increase of free and esterified phytoprostanes F(1). Thus phytoprostanes F(1) may represent a sensitive measure of oxidative damage in plants similar to isoprostanes in mammals. However, one of the most exciting issues to be clarified is the possibility that linolenate-derived phytoprostanes F(1) exert biological activities in plants and/or animals.     

Recent progress in developing FRET-based intracellular sensors for the detection of small molecule nutrients and ligands

Intracellular sensors for nutrients such as sugars, metabolic precursors and signaling ligands such as amino acids will help to elucidate the complex roles of these small molecules in biology. In this update, several recently developed sensors, originating from the Frommer laboratory, which combine bacterial periplasmic-binding protein-based specificity for ligand targeting with fluorescent protein-derived resonance energy transfer for signal transduction are reviewed. The insight gained from designing these sensors, along with the preliminary results gathered from their first application, serve to illustrate the impact that they can have on improving our fundamental understanding of biology.     

Apoplastic ascorbate metabolism and its role in the regulation of cell signalling

The apoplast has crucial functions in plant biology. It comprises all the compartments beyond the plasmalemma, including the cell wall. As the reservoir of information on the biotic and abiotic environment surrounding the cell and a major conduit of information between cells, the apoplast has functions in stress perception and the subsequent appropriate control of growth and defence. The oxidative burst phenomenon, caused by environmental challenges and pathogen attack in particular, oxidises the apoplast. Ascorbic acid (AA), the major and probably the only antioxidant buffer in the apoplast, becomes oxidised in these conditions. The apoplastic enzyme ascorbate oxidase (AO) also regulates the reduction/oxidation (redox) state of the apoplastic ascorbate pool. We propose that a key function of the oxidative burst and of AO is to modify the apoplastic redox state in such a way as to modify receptor activity and signal transduction to regulate defence and growth.     

Increased availability of endogenous and dietary oleic acid contributes to the upregulation of cardiac fatty acid oxidation

In the present study, we tested the hypothesis that cardiac substrate utilization is affected by oleic acid originating from the endogenous conversion of stearate by stearoyl-CoA desaturase and from the diet. Here, we show that the cardiac oleate content is increased in tristearate (TS)- and trioleate (TO)-fed rats when compared with chow-fed rats. TS or TO feeding increases mitochondrial fatty acid oxidation via activation of expression of the oxidative genes, activation of the AMP-activated protein kinase pathway, and a decrease in glucose uptake. These results suggest that oleic acid, both dietary and de novo synthesized, affects substrate utilization in the heart. Furthermore, our data show that the endogenous synthesis of oleate in the heart can compensate for a deficiency of this fatty acid in the diet.     

Hepatic response to aluminum toxicity: dyslipidemia and liver diseases

Aluminum (Al) is a metal toxin that has been implicated in the etiology of a number of diseases including Alzheimer's, Parkinson's, dialysis encephalopathy, and osteomalacia. Al has been shown to exert its effects by disrupting lipid membrane fluidity, perturbing iron (Fe), magnesium, and calcium homeostasis, and causing oxidative stress. However, the exact molecular targets of aluminum's toxicity have remained elusive. In the present review, we describe how the use of a systems biology approach in cultured hepatoblastoma cells (HepG2) allowed the identification of the molecular targets of Al toxicity. Mitochondrial metabolism is the main site of the toxicological action of Al. Fe-dependent and redox sensitive enzymes in the tricarboxylic acid (TCA) cycle and oxidative phosphorylation (OXPHOS) are dramatically decreased by Al exposure. In an effort to compensate for diminished mitochondrial function, Al-treated cells stabilize hypoxia inducible factor-1α (HIF-1α) to increase ATP production by glycolysis. Additionally, Al toxicity leads to an increase in intracellular lipid accumulation due to enhanced lipogenesis and a decrease in the β-oxidation of fatty acids. Central to these effects is the alteration of α-ketoglutarate (KG) homeostasis. In Al-exposed cells, KG is preferentially used to quench ROS leading to succinate accumulation and HIF-1α stabilization. Moreover, the channeling of KG to combat oxidative stress leads to a reduction of l-carnitine biosynthesis and a concomitant decrease in fatty acid oxidation. The fluidity and interaction of these metabolic modules and the implications of these findings in liver-related disorders are discussed herein.     

Exploring the Chemistry and Biology of Vanadium-dependent Haloperoxidases

Nature has developed an exquisite array of methods to introduce halogen atoms into organic compounds. Most of these enzymes are oxidative and require either hydrogen peroxide or molecular oxygen as a cosubstrate to generate a reactive halogen atom for catalysis. Vanadium-dependent haloperoxidases contain a vanadate prosthetic group and utilize hydrogen peroxide to oxidize a halide ion into a reactive electrophilic intermediate. These metalloenzymes have a large distribution in nature, where they are present in macroalgae, fungi, and bacteria, but have been exclusively characterized in eukaryotes. In this minireview, we highlight the chemistry and biology of vanadium-dependent haloperoxidases from fungi and marine algae and the emergence of new bacterial members that extend the biological function of these poorly understood halogenating enzymes.     

Oxygen consumption and expression of the adenine nucleotide translocator in cells lacking mitochondrial DNA

It has been shown previously that human rho degrees cells, deprived of mitochondrial DNA and consequently of functional oxidative phosphorylation, maintain a mitochondrial membrane potential, which is necessary for their growth. The goal of our study was to determine the precise origin of this membrane potential in three rho degrees cell lines originating from the human HepG2, 143B, and HeLa S3 cell lines. Residual cyanide-sensitive oxygen consumption suggests the persistence of residual mitochondrial respiratory chain activity, about 8% of that of the corresponding parental cells. The fluorescence emitted by the three rho degrees cell lines in the presence of a mitochondrial specific fluorochrome was partially reduced by a protonophore, suggesting the existence of a proton gradient. The mitochondrial membrane potential is maintained both by a residual proton gradient (up to 45 to 50% of the potential) and by other ion movements such as the glycolytic ATP(4-) to mitochondrial ADP(3-) exchange. The ANT2 gene, encoding isoform 2 of the adenine nucleotide translocator, is overexpressed in rho degrees HepG2 and 143B cells strongly dependent on glycolytic ATP synthesis, as compared to the corresponding parental cells, which present a more oxidative metabolism. In rho degrees HeLa S3 cells, originating from the HeLa S3 cell line, which already displays a glycolytic energy status, ANT2 gene expression was not higher as in parental cells. Mitochondrial oxygen consumption and ANT2 gene overexpression vary in opposite ways and this suggests that these two parameters have complementary roles in the maintenance of the mitochondrial membrane potential in rho degrees cells.     

Cyclooxygenases and lipoxygenases are used by the fungus Podospora anserina to repel nematodes

Oxylipins are secondary messengers used universally in the living world for communication and defense. The paradigm is that they are produced enzymatically for the eicosanoids and non-enzymatically for the isoprostanoids. They are supposed to be degraded into volatile organic compounds (VOCs) and to participate in aroma production. Some such chemicals composed of eight carbons are also envisoned as alternatives to fossil fuels. In fungi, oxylipins have been mostly studied in Aspergilli and shown to be involved in signalling asexual versus sexual development, mycotoxin production and interaction with the host for pathogenic species. Through targeted gene deletions of genes encoding oxylipin-producing enzymes and chemical analysis of oxylipins and volatile organic compounds, we show that in the distantly-related ascomycete Podospora anserina, isoprostanoids are likely produced enzymatically. We show the disappearance in the mutants lacking lipoxygenases and cyclooxygenases of the production of 10-hydroxy-octadecadienoic acid and that of 1-octen-3-ol, a common volatile compound. Importantly, this was correlated with the inability of the mutants to repel nematodes as efficiently as the wild type. Overall, our data show that in this fungus, oxylipins are not involved in signalling development but may rather be used directly or as precursors in the production of odors against potential agressors.

Mitochondria in health and disease: perspectives on a new mitochondrial biology

The integrity of mitochondrial function is fundamental to cell life. It follows that disturbances of mitochondrial function will lead to disruption of cell function, expressed as disease or even death. In this review, I consider recent developments in our knowledge of basic aspects of mitochondrial biology as an essential step in developing our understanding of the contributions of mitochondria to disease. The identification of novel mechanisms that govern mitochondrial biogenesis and replication, and the delicately poised signalling pathways that coordinate the mitochondrial and nuclear genomes are discussed. As fluorescence imaging has made the study of mitochondrial function within cells accessible, the application of that technology to the exploration of mitochondrial bioenergetics is reviewed. Mitochondrial calcium uptake plays a major role in influencing cell signalling and in the regulation of mitochondrial function, while excessive mitochondrial calcium accumulation has been extensively implicated in disease. Mitochondria are major producers of free radical species, possibly also of nitric oxide, and are also major targets of oxidative damage. Mechanisms of mitochondrial radical generation, targets of oxidative injury and the potential role of uncoupling proteins as regulators of radical generation are discussed. The role of mitochondria in apoptotic and necrotic cell death is seminal and is briefly reviewed. This background leads to a discussion of ways in which these processes combine to cause illness in the neurodegenerative diseases and in cardiac reperfusion injury. The demands of mitochondria and their complex integration into cell biology extends far beyond the provision of ATP, prompting a radical change in our perception of mitochondria and placing these organelles centre stage in many aspects of cell biology and medicine.     

Bacterial hemoglobins and flavohemoglobins for alleviation of nitrosative stress in Escherichia coli

Escherichia coli MG1655 cells expressing novel bacterial hemoglobin and flavohemoglobin genes from a medium-copy-number plasmid were grown in shake flask cultures under nitrosative and oxidative stress. E. coli cells expressing these proteins display enhanced resistance against the NO(.) releaser sodium nitroprusside (SNP) relative to that of the control strain bearing the parental plasmid. Expression of bacterial hemoglobins originating from Campylobacter jejuni (CHb) and Vitreoscilla sp. (VHb) conferred resistance on SNP-challenged cells. In addition, it has been shown that NO(.) detoxification is also a common feature of flavohemoglobins originating from different taxonomic groups and can be transferred to a heterologous host. These observations have been confirmed in a specific in vitro NO(.) consumption assay. Protein extracts isolated from E. coli strains overexpressing flavohemoglobins consumed authentic NO(.) more readily than protein extracts from the wild-type strain. Oxidative challenge to the cells evoked nonuniform responses from the various cell cultures. Improved oxidative-stress-sustaining properties had also been observed when the flavohemoglobins from E. coli, Klebsiella pneumoniae, Deinococcus radiodurans, and Pseudomonas aeruginosa were expressed in E. coli.     

Mutational bias suggests that replication termination occurs near the dif site, not at Ter sites

In bacteria, Ter sites bound to Tus/Rtp proteins halt replication forks moving only in one direction, providing a convenient mechanism to terminate them once the chromosome had been replicated. Considering the importance of replication termination and its position as a checkpoint in cell division, the accumulated knowledge on these systems has not dispelled fundamental questions regarding its role in cell biology: why are there so many copies of Ter, why are they distributed over such a large portion of the chromosome, why is the tus gene not conserved among bacteria, and why do tus mutants lack measurable phenotypes? Here we examine bacterial genomes using bioinformatics techniques to identify the region(s) where DNA polymerase III‐mediated replication has historically been terminated. We find that in both Escherichia coli and Bacillus subtilis, changes in mutational bias patterns indicate that replication termination most likely occurs at or near the dif site. More importantly, there is no evidence from mutational bias signatures that replication forks originating at oriC have terminated at Ter sites. We propose that Ter sites participate in halting replication forks originating from DNA repair events, and not those originating at the chromosomal origin of replication.     

Comparative biology and pathology of oxidative stress in Alzheimer and other neurodegenerative diseases: beyond damage and response

In this review, we consider comparative aspects of the biology and pathology of oxygen radicals in neurodegenerative disease and how these findings have influenced our concept of oxidative stress. The common definition of oxidative stress is a breach of antioxidant defenses by oxygen radicals leading to damage to critical molecules and disrupted physiology. Inherent in this definition is that oxidative stress is an unstable situation, for if there is net damage, viability of the system decreases with time, leading to disequilibria and death. While this circumstance defines acute conditions, such as stroke and head trauma which result in dysfunction and death, it does not fit physiological situations or chronic diseases closely aligned to normal physiology. Therefore, we propose that oxidative modifications in Alzheimer disease may actually serve as a homeostatic response to stress resulting in a shift of neuronal priority from normal function to basic survival. This phenomenon is comparable to normal physiological conditions of metabolic decrease, such as those seen in hibernation and estivation. Thus, Alzheimer disease could be seen as part of normal aging that includes additional pathology due to inadequate homeostatic response.     

Oxidative stress: a theoretical model or a biological reality?

Although oxidative stress has been extensively studied the last fifteen years, many physicians and biologists are still sceptical concerning its interest in biology and medicine. This is probably due, in part, to the fact that this subject is a matter of biophysics, and the first studies reported were written using a physical language that inspired these people used to a more concrete problematic very little. Another problem is the difficulty to detect the species mediating oxidative stress, and to determine their role in biological processes. This review is aimed at presenting oxidative stress, as well as reactive oxygen species and free radicals--the molecules that mediate it--in a clear form able to convince all researchers involved in life sciences that these short-lived intermediates are indissociable from any aerobic organism. Moreover, if reactive oxygen species and free radicals are undoubtedly involved in many pathologies, they have physiological functions too.     

Oligonucleotide aptamers that recognize small molecules.

Nucleic acid receptors ('aptamers'), which recognize a large variety of organic molecules of low molecular weight, have been isolated from combinatorial nucleic acid libraries by in vitro selection methods. Structural studies of nucleic acid-small molecule complexes provide insight into both the principles of molecular recognition by this class of biopolymers and the architecture of tertiary motifs in nucleic acid folding. Aptamers that recognize small molecules are increasingly applied as tools in molecular biology, from the detection of oxidative damage in DNA to conditional gene expression and from their use as modules for the engineering of allosteric ribozymes to biosensors.