bluuebunny/crossref_metadata_2025 huggingface dataset:
Design and applications of methods for fluorescence detection of iron in biological systems
Authors: Espósito B. P. , Breuer W. , Cabantchik Z. I.
Published: June 2004

Fluorescence metalosensors provide a means to detect iron in biological systems that is versatile, economical, sensitive and of a high-throughput nature. They rely on relatively high-affinity iron-binding carriers conjugated to highly fluorescent probes that undergo quenching after metal complexation. Metal specificity is determined by probes containing either an iron-binding moiety of high affinity (type A) or of relatively lower affinity (type B) used in combination with a strong specific iron chelator. Due to the heterogeneous nature of biological systems, the apparent metal-binding affinity and complexation stoichiometry ought to be specifically defined. Fluoresceinated moieties coupled to metal-binding cores detect Fe at sub-micromolar concentrations and even sub-microlitre volumes (i.e. cells). Although an ideal probe should also be specific for a particular oxidation state of iron, in physiological conditions that property might be difficult to attain. Quantification of labile iron in cells has relied on the ability of permeant iron chelators to restore the fluorescence of probes quenched by intracellular Fe. Modern design of probes aims to (a) improve probe targeting to specific cell compartments and (b) create probes that respond to metal binding by signal enhancement.
Plant copper chaperones
Authors: Wintz H. , Vulpe C.
Published: June 2004

Copper chaperones, soluble copper-binding proteins, are essential for ensuring proper distribution of copper to cellular compartments and to proteins requiring copper prosthetic groups. They are found in all eukaryotic organisms. Orthologues of the three copper chaperones characterized in yeast, ATX1, CCS and COX17, are present in Arabidopsis thaliana. Plants are faced with unique challenges to maintain metal homoeostasis, and thus their copper chaperones have evolved by diversifying and gaining additional functions. In this paper we present our current knowledge of copper chaperones in A. thaliana based on the information available from the complete sequence of its genome.
Chromium(VI)-induced damage to the cytoskeleton and cell death in isolated hepatocytes
Authors: Gunaratnam M. , Grant M. H.
Published: June 2004

Cr(VI) is a known human carcinogen. Although it has been investigated widely, the mechanism(s) of its action is/are not fully understood. The aim of this study was to evaluate Cr(VI)-induced damage to the cell cytoskeleton and the mode of cell death in primary cultures of hepatocytes. Exposure of the cultured cells (105/cm2) to 1 and 5 μM Cr(VI) for 24 h resulted in loss of the cell cytoskeleton, and this was accompanied by membrane blebbing and shrinking of the cell. Staining of the cells with annexin V and propidium iodide showed that Cr(VI) induces apoptosis at low concentrations (5 μM), whereas at higher concentrations (25 μ) it induces necrosis. This study shows that Cr(VI) causes damage to the cell cytoskeleton, and induces apoptosis at low concentrations. However, the importance of necrosis and apoptosis in vivo, and the effects of longer exposure times, which simulate environmental and occupational exposure to Cr(VI), remain to be investigated.
The role of oxidative stress in the toxicity of pyridoxal isonicotinoyl hydrazone (PIH) analogues
Authors: Buss J. L. , Neuzil J. , Ponka P.
Published: June 2004

Pyridoxal isonicotinoyl hydrazone (PIH) analogues are effective iron chelators in vivo and in vitro, and may be of value for the treatment of secondary iron overload. The sensitivity of Jurkat cells to Fe-chelator complexes was enhanced several-fold by the depletion of the antioxidant glutathione, indicating the role of oxidative stress in their toxicity. K562 cells loaded with eicosapentaenoic acid, a fatty acid particularly susceptible to oxidation, were also more sensitive to the toxic effects of the Fe complexes, and toxicity was proportional to lipid peroxidation. Thus Fechelator complexes cause oxidative stress, which may be a major component of their toxicity. As was the case for their Fe complexes, the toxicity of PIH analogues was enhanced by glutathione depletion of Jurkat cells and eicosapentaenoic acidloading of K562 cells. Thus the toxicity of the chelators themselves is also enhanced by compromised cellular redox status. In addition, the toxicity of the chelators was diminished by culturing Jurkat cells under hypoxic conditions, which may limit the production of the reactive oxygen species that initiate oxidative stress. A significant part of the toxicity of the chelators may be due to intracellular formation of Fe-chelator complexes, which oxidatively destroy the cell.
The influence of iron homoeostasis on macrophage function
Authors: Ward R. J. , Wilmet S. , Legssyer R. , Crichton R. R.
Published: June 2004

Iron loading of alveolar macrophages in vivo significantly altered their ability to respond to various inflammatory stimuli. This was exemplified by reduced synthesis of inducible nitric oxide synthase after stimulus with lipopolysaccharide and interferonγ, and an enhanced activation of nuclear factor kB in the absence of tumour necrosis factor α stimulation, and enhanced production of reactive oxygen species after activation with activated zymosan and PMA. Such results may indicate an imbalance in the production of reactive oxygen and reactive nitrogen species generated by
Responses of plants to iron, zinc and copper deficiencies
Authors: Wintz H. , Fox T. , Vulpe C.
Published: June 2004

Iron, copper and zinc are essential metals for cell metabolism. Plants have evolved different schemes to efficiently mobilize low-solubility nutrients such as metals from their environment and to transport them between organs. In this review we highlight the divergences and convergences of the iron, copper and zinc uptake, transport and homoeostatic pathways.
Repression of ferritin expression modulates cell responsiveness to H-ras-induced growth
Authors: Kakhlon O. , Gruenbaum Y. , Cabantchik Z. I.
Published: June 2004

We assessed the role of the cell labile iron pool in mediating oncogene-induced cell proliferation via repression of ferritin expression. When HEK-293 cells, engineered to inducibly express either active (+) or dominant-negative (-) forms of the H-ras oncogene, were treated with antisense nucleotides to ferritin subunits they displayed (a) decreased ferritin levels, (b) increased labile iron pool and either (c) faster growth in cells induced to express H-Ras (+) or (d) recovery from growth retardation in dominant-negative H-Ras-induced cells. Our studies support the view that the role of down-modulation of ferritin expression by some oncogene-evoked proliferation proceeds via expansion of the cellular labile iron pool.
Identification of members of the Aspergillus nidulans SREA regulon: genes involved in siderophore biosynthesis and utilization
Authors: Oberegger H. , Zadra I. , Schoeser M. , Abt B. , Parson W. , Haas H.
Published: June 2004

Iron is an essential trace element for almost all organisms. However, an excess of this metal within cells can be deleterious on account of catalysis of cell-damaging hydroxyl radicals. Therefore, the concentration of iron within cells is tightly regulated and the primary control occurs by regulating its uptake. Under conditions of low iron availability, most fungi mobilize extracellular iron by excretion of low-molecular-mass ferric iron chelators, termed siderophores. Due to the potential impact of iron metabolism on fungal pathogenicity, a better insight into siderophore-mediated iron uptake is needed. In Aspergillus nidulans, siderophore biosynthesis and uptake are negatively regulated by the GATA-type transcription factor SREA. Hence, genes involved in siderophore biosynthesis and uptake are characterized by transcriptional induction under iron limitation in wild-type strain and de-repression in an sreA-deletion strain under conditions of sufficient iron supply. Such genes have been searched for using different strategies, e.g. differential mRNA display and expression analysis of candidate genes from various A. nidulans sequence databases. The identified genes presumably encode enzymes needed for siderophore biosynthesis, and transporters involved in siderophore uptake and/or excretion. The functional characterization of these genes will help to unravel the pathways involved in siderophore biosynthesis and uptake.
Virtual screening: a real screening complement to high-throughput screening
Authors: Mestres J.
Published: June 2004

Virtual screening is being routinely used as an integral part of today's hit-identification strategies for, on one hand, prioritizing large corporate screening collections and, on the other hand, to extend the scope of screening to external databases. A brief description of the essential elements required for virtual screening and an application example to the identification of agonist hits for the oestrogen receptor subtype ERα are presented.
CD19-CD21 complex regulates an intrinsic Src family kinase amplification loop that links innate immunity with B-lymphocyte intracellular calcium responses
Authors: Tedder T. F. , Haas K. M. , Poe J. C.
Published: June 2004

CD19 is a B-lymphocyte cell surface molecule that functions as a general response regulator or rheostat, which defines intrinsic and B-cell antigen receptor-induced signalling thresholds that are critical for humoral immunity and expansion of the peripheral B-cell pool. In addition, B-cell responses are influenced by signals transduced through a CD19-CD21 cell surface receptor complex, where the binding of complement C3d to CD21 links humoral immune responses with the innate immune system. This review outlines recent biochemical and genetic studies that characterize the signal transduction pathways utilized by this receptor complex to regulate B-cell intracellular calcium responses.
Clinical importance of the intervertebral disc, or back pain for biochemists
Authors: Fairbank J.
Published: June 2004

The object of this paper is to give biochemists some insight into current thinking on back pain. I shall discuss the important, but limited, relationship of back pain to the principal pathological changes in the lumbar intervertebral discs. I shall point out some of the areas where scientists may be able to help clinicians understand and treat this common, but complex, condition. The literature on back pain is enormous, so I have made no attempt to select even a small part of it for this article.
Collagen polymorphisms of the intervertebral disc
Authors: Eyre D. R. , Matsui Y. , Wu J.-J.
Published: June 2004

The mechanical function and the collagen pheno-type of the disc are complex, each a hybrid of elements of ligament and cartilage. In detail, the collagen properties are unique. Collagens I and II provide the bulk of the tissue fabric interwoven in opposing radial concentration gradients. From analysis of isolated cross-linked peptides, some degree of commingling of these major fibrillar collagens occurs down to the molecular level. Collagens V, VI, IX, XI, XII and XIV all contribute to the matrix. Collagen IX is the short molecular form that lacks a non-collagenous (NC)4 domain, not the long form found in most hyaline cartilages. Protein sequence and reverse transcriptase-PCR analysis confirmed this was the result of expression from the alternative transcription start site, not proteolysis of the long form. In view of recent reports that common single nucleotide polymorphisms in COL9A2 and COL9A3 are linked to chronic sciatica associated with disc pathology, the specific interactions and role of collagen IX in disc tissue are important to define.
Compartmentalization of the matrix formed by nucleus pulposus and annulus fibrosus cells in alginate gel
Authors: Thonar E. , An H. , Masuda K.
Published: June 2004

Intervertebral disc cells cultured in alginate gel are capable of reforming in alginate, a matrix that consists of two compartments: a rim of metabolically active cell-associated matrix and a more abundant, but metabolically less active, further removed matrix. At any one age and in most species, the cell-associated matrix formed by a nucleus pulposus or annulus fibrosus cell cultured in this way is less abundant than that formed by an articular chondrocyte. In both the cell-associated matrix and further removed matrix, the ratio of aggrecan to collagen is significantly higher in the case of nucleus pulposus than of annulus fibrosus, a feature that also distinguishes the matrices of the nucleus pulposus and annulus fibrosus in vivo. Nucleus pulposus and annulus fibrosus cells from older donors show a decreased ability to reform a cell-associated matrix rich in aggrecan. There is, however, some evidence that gene therapy and/or exposure of the cells to defined stimulatory factors can help overcome some of these age-related limitations. This contention is supported by recent evidence that nucleus pulposus and annulus fibrosus cells from adult donors can be manipulated to form, using the recently developed alginate-recovered chondrocyte system, a resilient tissue that bears many of the characteristics of the tissue in which these cells reside in vivo.
Clinical aspects of food allergy
Authors: Papageorgiou P. S.
Published: June 2004

Food allergy affects 2.5% of adults and 6–8% of children, and is a leading cause of life-threatening anaphylactic episodes. Food allergy is defined as an adverse reaction to foods that is mediated immunologically and involves specific IgE or non-IgE mechanisms. In this review only IgE-related food allergy will be considered. Many food allergens are glycoproteins, but they do not share any striking biochemical similarities. The definition of many food proteins at the molecular level has tremendously facilitated our understanding of clinical syndromes and seemingly bizarre observations. Clinical manifestations of food allergy include symptoms of the gastrointestinal, cutaneous and respiratory systems, as well as systemic anaphylaxis. The diagnosis of food allergy involves a stepwise approach, including medical history taking, demonstration of specific IgE and confirmation by oral food challenge. The management of the food-allergic patient at present consists of avoidance of the culprit food and education, while future advances may include specific immunotherapy with modified allergens or DNA vaccination.
Plant protein families and their relationships to food allergy
Authors: Shewry P. R. , Beaudoin F. , Jenkins J. , Griffiths-Jones S. , Mills E. N. C.
Published: June 2004

The analysis of plant proteins has a long and distinguished history, with work dating back over 250 years. Much of the work has focused on seed proteins, which are important in animal nutrition and food processing. Early studies classified plant proteins into groups based on solubility (‘Osborne fractions’) or protein function. More recently, families have been defined based on stuctural and evolutionary relationships. One of the most widespread groups of plant proteins is the prolaminin superfamily, which comprises cereal seed storage proteins, a range of low-molecular-mass sulphur-rich proteins (many of which are located in seeds) and some cell wall glycoproteins. This superfamily includes several major types of plant allergen: non-specific lipid transfer proteins, cereal seed inhibitors of α-amylase and/or trypsin, and 2 S albumin storage proteins of dicotyledonous seeds.
Allergens of the cupin superfamily
Authors: Mills E. N. C. , Jenkins J. , Marigheto N. , Belton P. S. , Gunning A. P. , Morris V. J.
Published: June 2004

The cupin family comprises a family of proteins possessing a common β-barrel structure that is thought to have originated in a prokaryotic ancestor. This structural motif is found as a single domain in fungal spherulins, fern sporulins and the germins/oxalate oxidase proteins of plants, while the globular storage proteins of plants, called legumins (11 S) and euvicilins (7 S), are two-domain cupins. The 11 S globulins are hexameric heteroligomeric proteins of Mr ~ 360000, with each subunit comprising an acidic 30000–40000-Mr polypeptide that is disulphide-linked to a 20000-Mr basic polypeptide. A number of cupins have been identified as major plant food allergens, including the 7 S globulins of soybean (β-conglycinin), peanut (conarachin; Ara h 1), walnut (Jug r 2) and lentil, and the 11 S globulins of peanut (arachin; Ara h 3), soybean (glycinin) and possibly also coconut and walnut. Other members of the cupin superfamily have not been identified as allergens, with the exception of one germin (germination-specific protein) from pepper. Cupins are generally very stable proteins. A summary of our current knowledge of allergenic seed storage globulins will be presented, together with an overview of cupin structure and stability properties, as illustrated by the allergenic soya globulins, glycinin and β-conglycinin.
Tristetraprolin and other CCCH tandem zinc-finger proteins in the regulation of mRNA turnover
Authors: Blackshear P. J.
Published: June 2004

The tristetraprolin (TTP) family of CCCH tandem zinc-finger proteins is composed of three known members in mammals, with a fourth member recently identified in frogs and fish. Although TTP was first cloned more than 10 years ago as a growth factor-induced gene, a physiological function for the protein has been discovered only within the last few years. TTP is now known to bind to so-called class II AU-rich elements within the mRNAs that encode tumour necrosis factor-α and granulocyte/macrophage colony-stimulating factor. In both cases, this binding results in destabilization of the mRNA and decreased secretion of the protein. Recent evidence suggests that TTP can accomplish this accelerated mRNA degradation by first promoting removal of the polyadenylated tail from the mRNA (deadenylation). In functional assays in cells, the other family members have similar activities, but are expressed differently in tissues and in response to stimuli, suggesting that they may control the stability of mRNAs under different circumstances from those in which TTP affects mRNA. All of these proteins are phosphoproteins and nucleo-cytoplasmic shuttling proteins, suggesting that their activities can be regulated in ways other than regulating gene transcription. Together, the TTP family members should be capable of complex regulation of short-lived mRNAs containing this type of AU-rich instability motif.
AU-rich element-mediated translational control: complexity and multiple activities of trans-activating factors
Authors: Zhang T. , Kruys V. , Huez G. , Gueydan C.
Published: June 2004

Tumour necrosis factor (TNF)-α mRNA contains an AU-rich element (ARE) in its 3′ untranslated region (3′UTR), which determines its half-life and translational efficiency. In unstimulated macrophages, TNF-α mRNA is repressed translationally, and becomes efficiently translated upon cell activation. Gel retardation experiments and screening of a macrophage cDNA expression library with the TNF-α ARE allowed the identification of TIA-1-related protein (TIAR), T-cell intracellular antigen-1 (TIA-1) and tristetraprolin (TTP) as TNF-α ARE-binding proteins. Whereas TIAR and TIA-1 bind the TNF-α ARE independently of the activation state of macrophages, the TTP-ARE complex is detectable upon stimulation with lipopolysaccharide (LPS). Moreover, treatment of LPS-induced macrophage extracts with phosphatase significantly abrogates TTP binding to the TNF-α ARE, indicating that TTP phosphorylation is required for ARE binding. Carballo, Lai and Blackshear [(1998) Science 281, 1001–1005] showed that TTP was a TNF-α mRNA destabilizer. In contrast, TIA-1, and most probably TIAR, acts as a TNF-α mRNA translational silencer. A two-hybrid screening with TIAR and TIA-1 revealed the capacity of these proteins to interact with other RNA-binding proteins. Interestingly, TIAR and TIA-1 are not engaged in the same interaction, indicating for the first time that TIAR and TIA-1 can be functionally distinct. These findings also suggest that ARE-binding proteins interact with RNA as multimeric complexes, which might define their function and their sequence specificity.
Three-dimensional structure and flexibility of proteins of the RCA family — a progress report
Authors: Herbert A. , O'Leary J. , Krych-Goldberg M. , Atkinson J. P. , Barlow P. N.
Published: June 2004

Members of the regulator of complement activation (RCA) protein family perform a vital role in health and disease. In this report we describe our efforts to solve the structures of human membrane cofactor protein (CD46), the vaccinia virus complement control protein, which mimics mammalian RCA proteins, and human complement receptor type 1 (CD35). These examples illustrate that, despite good progress over the last decade, the regulators of complement, as extracellular multiple domain glycoproteins, still pose formidable problems to structural biologists. Many important questions remain unanswered, in particular with regard to the flexibility of these proteins and the extent to which they undergo conformational rearrangements on engaging their binding partners
Solution structures of complement components by X-ray and neutron scattering and analytical ultracentrifugation
Authors: Perkins S. J. , Gilbert H. E. , Aslam M. , Hannan J. , Holers V. M. , Goodship T. H. J.
Published: June 2004

The short consensus/complement repeat (SCR) domain (also known as the complement control protein domain) is the most abundant domain type in the complement system. Crystal and NMR structures for proteins that contain single and multiple SCR domains have now been published. These contain inter-SCR linkers of between three and eight residues, and the structures show much variability in inter-SCR orientations. X-ray and neutron scattering, combined with analytical ultracentrifugation and constrained modelling based on known subunit structures will yield a medium-resolution structure for the protein of interest. The fewer parameters that are associated with the structure of interest, the more defined the structure of interest becomes. These solution studies have been applied to several SCR-containing proteins in the complement system, most notably Factor H with 20 SCR domains, a complement receptor type 2 fragment with two SCR domains, and rat complement receptor-related protein (Crry) which contains five SCR domains. The results show great conformational variability in the inter-SCR orientation, and these will be reviewed. Even though the rotational orientation cannot be modelled, it is nonetheless possible to measure the degree of extension of the multi-SCR proteins and, from this, to obtain functionally useful results.
Structural biology of Cl
Authors: Arlaud G. J. , Gaboriaud C. , Thielens N. M. , Rossi V.
Published: June 2004

The classical complement pathway is a major element of innate immunity against infection, and is also involved in immune tolerance, graft rejection and various pathologies. This pathway is triggered by C1, a multimolecular protease formed from the association of a recognition protein, C1q, and a catalytic subunit, the calcium-dependent tetramer C1s-C1r-C1r-C1s, which comprises two copies of each of the modular proteases C1r and C1s. All activators of the pathway are recognized by the C1q moiety of C1, a process that generates a conformational signal that triggers self-activation of C1r, which in turn activates C1s, the enzyme that mediates specific cleavage of C4 and C2, the C1 substrates. Early work based on biochemical and electron microscopy studies has allowed characterization of the domain structure of the C1 subcomponents and led to a low-resolution model of the complex in which the elongated C1s-C1r-C1r-C1s tetramer folds into a compact, figure-of-8-shaped conformation upon interaction with C1q. The strategy used over the past decade was based on a dissection of the C1 proteins into modular segments to characterize their function and solve their three-dimensional structure by X-ray crystallography or NMR spectroscopy. This approach allows deep insights into the structure-function relationships of C1, particularly with respect to the assembly of the C1 complex and the mechanisms underlying its activation and proteolytic activity.
Targeting anticomplement agents
Authors: Smith R. A. G.
Published: June 2004

Biological targeting is normally thought of as a process of specific direction of one molecule (the agent) to another (the target) in vivo. However, an addressive approach in which the agent is concentrated, first within the vasculature and then at a disease site containing one or more targets, may be more suitable for delivering therapeutic quantities of certain drugs. This approach has been applied to complement regulatory molecules expressed in recombinant soluble forms and attached post-translationally to highly soluble synthetic peptide derivatives comprising two addressin units, one with affinity for the membrane bilayer interior and the other for phospholipid headgroups. This combination conferred affinity for outer cell membranes in general, and areas of translocated acidic phospholipid in particular. Large increases in potency in cell-based antihaemolytic assays accompanied modification and were shown to be associated with membrane binding. Modified agents co-localized with glycosylphosphatidyl-inositol-anchored proteins in lipid rafts on cell membranes. One agent, a modified fragment of human complement receptor-1 (APT070), has been prepared on a large scale and has been shown to be an active anti-inflammatory agent when administered locally and systemically in animal models of vascular shock, rheumatoid arthritis and transplantation reperfusion injury. APT070 has been shown to be well tolerated in human subjects when given intravenously and is currently under study in rheumatoid arthritis patients to explore the therapeutic potential of localized complement inhibition in the synovial space.
Regulation of lipid accumulation in oleaginous micro-organisms
Authors: Ratledge C.
Published: June 2004

A small number of eukaryotic micro-organisms, the oleaginous species, can accumulate triacylglycerols as cellular storage lipids, sometimes up to 70% of the biomass. Some of these lipids, particularly those containing high proportions of polyunsaturated fatty acids of nutritional and dietary importance, are now in commercial production; these are known as single-cell oils. The biochemistry of lipid accumulation has been investigated in yeasts and filamentous fungi and can now be described in some detail: lipid accumulation is triggered by cells exhausting nitrogen from the culture medium, but glucose continues to be assimilated. Activity of isocitrate dehydrogenase within the mitochondrion, however, now slows or even stops due to the diminution of AMP within the cells. This leads to the accumulation of citrate, which is transported into the cytosol and cleaved to acetyl-CoA by ATP:citrate lyase, an enzyme that does not occur in non-oleaginous species. This enzyme is therefore essential for lipid accumulation. The presence of this enzyme does not, however, explain why different species of oleaginous micro-organisms have different capacities for lipid accumulation. The extent of lipid accumulation is considered to be controlled by the activity of malic enzyme (ME), which acts as the sole source of NADPH for fatty acid synthase (FAS). If ME is inhibited, or genetically disabled, then lipid accumulation is very low. There is no general pool of NADPH which can otherwise be used by FAS. The stability of ME is therefore crucial and it is proposed that ME is physically attached to FAS as part of the lipogenic metabolon. ME activity correlates closely with lipid accumulation in two filamentous fungi, Mucor circinelloides and Mortierella alpina. When ME ceases to be active, lipid accumulation also stops. No other enzyme activity shows such a correlation.
Mechanistic diversity and regulation of Type II fatty acid synthesis
Authors: Marrakchi H. , Zhang Y.-M. , Rock C. O.
Published: June 2004

Fatty acid biosynthesis is catalysed in most bacteria by a group of highly conserved proteins known as the Type II fatty acid synthase (FAS) system. The Type II system organization is distinct from its mammalian counterpart and offers several unique sites for selective inhibition by antibacterial agents. There has been remarkable progress in the understanding of the genetics, biochemistry and regulation of Type II FASs. One important advance is the discovery of the interaction between the fatty acid degradation regulator, FadR, and the fatty acid biosynthesis regulator, FabR, in the transcriptional control of unsaturated fatty acid synthesis in Escherichia coli. The availability of genomic sequences and high-resolution protein crystal structures has expanded our understanding of Type II FASs beyond the E. coli model system to a number of pathogens. The molecular diversity among the pathway enzymes is illustrated by the discovery of a new type of enoyl-reductase in Streptococcus pneumoniae [enoyl-acyl carrier protein (ACP) reductase II, FabK], the presence of two enoyl-reductases in Bacillus subtilis (enoyl-ACP reductases I and III, FabI and FabL), and the use of a new mechanism for unsaturated fatty acid formation in S. pneumoniae (trans-2-cis-3-enoyl-ACP isomerase, FabM). The solution structure of ACP from Mycobacterium tuberculosis revealed features common to all ACPs, but its extended C-terminal domain may reflect a specific interaction with very-long-chain intermediates.
Regulation of fatty acid synthesis and oxidation by the AMP-activated protein kinase
Authors: Hardie D. G. , Pan D. A.
Published: June 2004

The AMP-activated protein kinase (AMPK) is a sensor of cellular energy charge and a ‘metabolic master switch’. When activated by ATP depletion, it switches off ATP-consuming processes, while switching on catabolic pathways that generate ATP. AMPK exists as heterotrimeric complexes comprising catalytic α subunits and regulatory β and γ subunits, each of which occurs as multiple isoforms. Rising AMP and falling ATP, brought about by various types of cellular stress (including exercise in skeletal muscle), stimulate the system in an ultrasensitive manner. Acetyl-CoA carboxylase (ACC) exists in mammals as two isoforms, termed ACC-1 and ACC-2 (also known as ACC-α and ACC-β). AMPK phosphorylates and inactivates both isoforms at the equivalent site. Knockout mice, and other approaches, suggest that the malonyl-CoA produced by ACC-2 is exclusively involved in regulation of fatty acid oxidation, whereas that produced by ACC-1 is utilized in fatty acid synthesis. Activation of AMPK by cellular stress or exercise therefore switches on fatty acid oxidation (via phosphorylation of ACC-2) while switching off fatty acid synthesis (via phosphorylation of ACC-1). The Drosophila melanogaster genome contains single genes encoding homologues of the α, β and γ subunits of AMPK (DmAMPK) and of ACC (DmACC). Studies in a Drosophila embryonal cell line show that DmAMPK is activated by stresses that cause ATP depletion (oligomycin, hypoxia or glucose deprivation) and that this is associated with phosphorylation of the site on DmACC equivalent to the AMPK sites on mammalian ACC-1 and ACC-2. This is abolished when expression of DmAMPK is ablated using an RNA interference approach, proving that DmAMPK is necessary for phosphorylation of DmACC in response to ATP depletion.
Isolation and characterization of a cDNA encoding a Δ8 sphingolipid desaturase from Aquilegia vulgaris
Authors: Michaelson L. V. , Longman A. J. , Sayanova O. , Stobart A. K. , Napier J. A.
Published: June 2004

We have isolated a cDNA encoding the Δ8 sphingolipid desaturase from the plant Aquilegia vulgaris L. via a PCR-based strategy using primers designed to target the conserved histidine box regions of microsomal desaturases. The function of the cDNA was confirmed by expression in the yeast, Saccharomyces cerevisiae. Analysis of the long-chain sphingoid bases as their dinitrophenyl derivatives by reverse-phase HPLC demonstrated the accumulation of cis- and trans-desaturated sphingoid bases which were not present in the wild-type yeast cells. The Δ8 desaturated products co-eluted with known Δ8-desaturated phytosphingenine and the molecular mass of these products was confirmed by liquid chromatography-MS. The Δ8 long-chain base desaturase was also able to desaturate dihydrosphingosine substrates. This is the first report of the functional characterization of an A. vulgaris gene product.
Gene regulation of mammalian desaturases
Authors: Nakamura M. T. , Nara T. Y.
Published: June 2004

Stearoyl-CoA desaturase (SCD) catalyses the synthesis of oleic acid (18:1, n - 9), which is mostly esterified into triacylglycerols (TAGs) as an energy reserve. Δ-6 Desaturase (D6D) and Δ-5 desaturase (D5D) are the key enzymes for the synthesis of highly unsaturated fatty acids (HUFAs), such as arachidonic acid (20:4, n - 6) and docosahexaenoic acid (22:6, n - 3), that are incorporated in phospholipids (PLs) and perform essential physiological functions. Despite these different physiological roles of SCD and D6D/D5D, these desaturases share common regulatory features, including dependence of expression on insulin, suppression by HUFAs, and induction by peroxisome proliferators (PPs). A key regulator of desaturase gene expression is sterol-regulatory element binding protein-1c (SREBP-1c), which mediates transcriptional activation of the SCD and D6D genes by insulin and inhibition by HUFAs. Because HUFAs are poorly incorporated into TAGs, the primary role of SREBP-1c in liver may be monitoring and regulating fatty acid composition in PLs rather than the regulation of TAG synthesis. The induction of desaturases by PPs is enigmatic because the major effect of PPs is induction of fatty acid oxidation enzymes by activating PP-activated receptor-α (PPARa). To our knowledge, no other gene that is induced by both SREBP-1 and PP has been identified. It is yet to be determined whether PPARa mediates the process directly. Available data suggest that the induction of desaturases by PPs may be a compensatory response to an increased demand for unsaturated fatty acids because PPs increase fatty acid degradation and induce proliferation of peroxisomes.
Peroxisome proliferator-activated receptors and the regulation of mammalian lipid metabolism
Authors: Smith S. A.
Published: June 2004

Peroxisome proliferator-activated receptors (PPARs) are members of the superfamily of ligand-activated nuclear transcription factors. Three PPAR subtypes, PPARα, PPARδ (PPARβ) and PPARγ, have been described in mammals. The tissue distribution of PPARs is heterogeneous: PPARα is highly expressed in liver and skeletal muscle, PPARγ is preferentially expressed in adipose tissues, and PPARδ is expressed in most cell types with relative abundance. Unlike most receptors, PPARs show low ligand specificity, being activated by many long-chain saturated and unsaturated fatty acids, or by eicosanoids. PPARs are transcriptionally active as heterodimeric complexes with the retinoid X receptor and bind to specific recognition sequences in the regulatory region of target genes. Many PPAR-regulated genes encode proteins that regulate fatty acid oxidation and storage. Elucidation of the biological functions of PPARs has been aided by the development of PPAR-null mice and the identification of humans bearing PPAR mutations, together with the discovery of synthetic small-molecule ligands that selectively activate individual PPAR subtypes. Using these genetic and pharmacological approaches, it has been shown that PPARα predominantly regulates pathways of fatty acid oxidation, whereas PPARγ modifies fatty acid synthesis and storage in adipose tissues. By reducing systemic fatty acid availability, thiazolidinedione PPARγ activators regulate glucose metabolism and are now used clinically in the treatment of Type II diabetes. In summary, PPARs play a central role in the mechanisms that balance fatty acid oxidation and storage in the face of fluctuations of dietary fat intake and energy expenditure.
The catalytic mechanism of the hairpin ribozyme
Authors: Fedor M. J.
Published: June 2004

Evidence that hairpin ribozymes function in the absence of bivalent cation cofactors suggests that active site nucleobases might participate directly in catalytic chemistry. We have adopted an abasic ribozyme rescue strategy to begin to dissect the roles of specific nucleobases in hairpin ribozyme activity. Loss of one active site nucleobase, G8, could be compensated by providing certain nucleobases and nucleobase analogues in solution. Comparison of the biochemical and structural features that are shared among small molecules that mediate rescue provides a new perspective on potential mechanisms of hairpin ribozyme catalysis.
Structure of the 70 S ribosome: implications for movement
Authors: Noller H. F. , Baucom A.
Published: June 2004

The ribosome is a complex molecular machine, with moving parts, many of which are structural elements of rRNA. We compared the X-ray crystal structures of three different functional states of the 30 S ribosomal subunit - two from crystal structures of the isolated 30 S subunit from the Ramakrishnan group and one from a complex of the 70 S ribosome. Even though all three structures are in what could be called the ‘ground state’ of the subunit, many conformational differences are found, distributed over the whole structure. A striking example is the undulating movement of the penultimate stem of 16S rRNA, which forms several intersubunit bridges with the 50 S subunit.
Folding of the td pre-RNA with the help of the RNA chaperone StpA
Authors: Mayer O. , Waldsich C. , Grossberger R. , Schroeder R.
Published: June 2004

The td group I intron is inserted in the reading frame of the thymidylate synthase gene, which is mainly devoid of structural elements. In vivo, translation of the pre-mRNA is required for efficient folding of the intron into its splicing-competent structure. The ribosome probably resolves exon-intron interactions that interfere with splicing. Uncoupling splicing from translation, by introducing a non-sense codon into the upstream exon, reduces the splicing efficiency of the mutant pre-mRNA. Alternatively to the ribosome, co-expression of genes that encode proteins with RNA chaperone activity promote folding of the td pre-mRNA in vivo. These proteins also efficiently accelerate folding of the td pre-mRNA in vitro. In order to understand the mechanism of action of RNA chaperones, we probed the impact of the RNA chaperone StpA on the structure of the td intron in vivo and compared it with that of the well characterized Cyt-18 protein, which is a group-I-intron-specific splicing factor. We found that the two proteins have opposite effects on the structure of the td intron. While StpA loosens the three-dimensional structure, Cyt-18 tightens it up. Furthermore, mutations that destabilize the intron structure render the mutants sensitive to StpA, whereas splicing of these mutants is rescued by Cyt-18. Our results provide direct evidence for protein-induced conformational changes within a catalytic RNA in vivo. Whereas StpA resolves tertiary contacts enabling the RNA to refold, Cyt-18 contributes to the stabilization of the native three-dimensional structure.
Genes in food – why the furore?
Authors: Dixon B.
Published: June 2004

Although unprecedented and perhaps unique in its irrationality, the recent furore over genetically modified (GM) food holds extremely important lessons for scientists. Some sections of the media undoubtedly bear a heavy responsibility for giving the expression ‘GM’ threatening connotations that are quite unwarranted. However, influential contributions to the hysteria have come from a surprising range of other sources, including some scientists. The research community has failed in its responsibility to society in three ways. Firstly, plant scientists did not appreciate that certain techniques (such as the use of antibiotic resistance genes as markers during plant transformation) would inevitably provoke public consternation. As a result, they took no steps to address such concerns. Secondly, researchers overlooked, minimized or in some cases simply dismissed the significance of public fears that they were ‘interfering with Nature’ or ‘playing God’. Thirdly, plant breeders apparently saw no need to take pro-active measures with regard to the media and public in placing potential environmental and nutritional benefits of GM crops on the agenda in a positive fashion. Partly because of this failure, GM food is now firmly established in the public mind as wholly objectionable. One measure of how far we have travelled down that road is that it hardly matters any more whether objections are based on alleged environmental risks of cultivating GM crops or alleged toxicological hazards of eating them. ‘Genetically modified organism’, like ‘radioactivity’, has become an odious, generic shibboleth. Given that millions of people throughout the world are already benefiting from pharmaceuticals made by GM organisms, this is bizarre.
Interaction between glial-cell-line-derived neurotrophic factor (GDNF) and 2-O-sulphated heparin-related glycosaminoglycans
Authors: Rider C.C.
Published: June 2004

Glial cell line-derived growth factor (GDNF) is a cytokine of the transforming growth factor (TGF)-β family with potent neuroprotective activity. Clinical trials of recombinant GDNF in advanced Parkinson's disease are currently under way. It is known that mice homozygous for disruption of the gene encoding heparan sulphate 2-O-sulphotransferase die perinatally, due to the complete absence of kidneys. Similar phenotypes arise from targeted disruption of the genes encoding either GDNF, or its receptors, GFRα1 and c-Ret. It may therefore be proposed that GDNF normally binds to 2-O-sulphate-rich heparan sulphate within kidney progenitor tissues, and that this interaction is essential for its activity in kidney development. In support of this hypothesis we have shown in ELISA studies that GNDF binds to heparin and heparan sulphate. This binding is unusually sensitive to the chemical 2-O-desulphation, and promotes the binding of GNDF to GFRα.
Hepatocyte growth factor/scatter factor and its interaction with heparan sulphate and dermatan sulphate
Authors: Catlow K. , Deakin J.A. , Delehedde M. , Fernig D.G. , Gallagher J.T. , Pavão M.S.G. , Lyon M.
Published: June 2004

Hepatocyte growth factor (HGF)/scatter factor (SF) is a unique growth factor, in that it binds both heparan sulphate (HS) and dermatan sulphate (DS). The sequences in HS and DS that specifically interact with and modulate HGF/SF activity have not yet been fully identified. Ascidian DS, which uniquely possesses O-sulphation at C-6 (and not C-4) of its N-acetylgalactosamine unit, was analysed for HGF/SF-binding activity in the biosensor. The kinetic analysis revealed a strong, biologically relevant interaction with an equilibrium dissociation constant (Kd) of approx. 1 nM. An Erk activation assay also demonstrated stimulation of the MAP kinase pathway downstream of the Met receptor following addition of both HGF/SF and ascidian DS to the glycosaminoglycan-deficient CHO-745 mutant cell line. Furthermore, the activation of Met and the MAP kinase pathway by HGF/SF and ascidian DS leads to a cellular response in the form of migration.
Polyamines and their role in human disease – an introduction
Authors: Wallace H.M.
Published: June 2004

The naturally occurring polyamines are found in all living cells, where they fulfil a number of critical functions in relation to cell growth. The quest to identify these functions has been the subject of five independent colloquia hosted by the Biochemical Society and today still occupies several hundred scientists across Europe, the U.S.A. and Japan.
The role of polyamine catabolism in anti-tumour drug response
Authors: Casero R.A. , Wang Y. , Stewart T.M. , Devereux W. , Hacker A. , Wang Y. , Smith R. , Woster P.M.
Published: June 2004

Interest in polyamine catabolism has increased since it has been directly associated with the cytotoxic response of multiple tumour types to exposure to specific anti-tumour polyamine analogues. Human polyamine catabolism was considered to be a two-step pathway regulated by the rate-limiting enzyme spermidine/spermine N1-acetyltransferase (SSAT) that provides substrate for an acetylpolyamine oxidase (APAO). Further, the super-induction of SSAT by several anti-tumour polyamine analogues has been implicated in the cytotoxic response of specific solid-tumour phenotypes to these agents. This high induction of SSAT has been correlated with cellular response to the anti-tumour polyamine analogues in several systems and considerable progress has been made in understanding the molecular mechanisms that regulate the analogue-induced expression of SSAT. A polyamine response element has been identified and the transacting transcription factors that bind and stimulate transcription of SSAT have been cloned and characterized. The link between SSAT activity and cellular toxicity is thought to be based on the production of H2O2 by the activity of the constitutive APAO that uses the SSAT-produced acetylated polyamines. The high induction of SSAT and the subsequent activity of APAO are linked to the cytotoxic response of some tumour cell types to specific polyamine analogues. However, we have recently cloned a variably spliced human polyamine oxidase (PAOh1) that is inducible by specific polyamine analogues, efficiently uses unacetylated spermine as a substrate, and also produces toxic H2O2 as a product. The results of studies with PAOh1 suggest that it is an additional enzyme in polyamine catabolism that has the potential to significantly contribute to polyamine homoeostasis and drug response. Most importantly, PAOh1 is induced by specific polyamine analogues in a tumour-phenotype-specific manner in cell lines representative of the major forms of solid tumours, including lung, breast, colon and prostate. The sensitivity to these anti-tumour polyamine analogues can be significantly reduced if the tumour cells are co-treated with 250 μM of the polyamine oxidase inhibitor N1, N4-bis(2,3-butadienyl)-1,4-butanediamine (MDL 72,527), suggesting that the H2O2 produced by PAOh1 does in fact play a direct role in the observed cytotoxicity. These results strongly implicate PAOh1 as a new target that, in combination with SSAT, may be exploited for therapeutic advantage. The current understanding of the role and regulation of these two important polyamine catabolic enzymes are discussed.
Polyamine analogues as anticancer drugs
Authors: Wallace H.M. , Fraser A.V.
Published: June 2004

Just over 30 years ago, the late Diane Russell published the first in a series of papers linking polyamines and cancer. These early studies led to a flurry of research activity in the polyamine field that continues to this day attempting to identify a role for the polyamines in cancer development, treatment and/or prevention. The recognition that polyamines are critical for the growth of cancer cells, and consequently the identification of their metabolic pathways as a target for therapeutic intervention, led to the development of a number of useful inhibitors of polyamine biosynthesis. Arguably the most significant addition to the polyamine field in the last 30 years was the synthesis of α-difluoromethylornithine (DFMO), which is being tested currently as a cancer chemopreventative agent in man and is used also as a highly effective trypanocidal agent. Although an extremely useful tool experimentally, DFMO has been disappointing in clinical trials with little therapeutic efficacy. Despite this setback, the polyamine pathway is still considered a viable target for chemotherapeutic intervention. This has led to the development of the polyamine analogues as multifunctional inhibitors that will produce inhibition of tumour cell growth, polyamine depletion and optimum therapeutic efficacy.