bluuebunny/crossref_metadata_2025 huggingface dataset:
Is MK2 (mitogen-activated protein kinase-activated protein kinase 2) the key for understanding post-transcriptional regulation of gene expression?
Authors: Kotlyarov A. , Gaestel M.
Published: June 2004

The phenotype of mitogen-activated protein kinase-activated protein kinase-2 (MK2) knockout mice revealed the essential role of this enzyme in post-transcriptional regulation of lipopolysaccharide-induced expression of cytokines such as tumour necrosis factor (TNF)-α, interleukin-6 and interferon-γ, at the level of mRNA stability and translation. In the case of TNF-α, this regulation depends on the AU-rich element in TNF-α mRNA. In addition to cytokine expression, MK2 is also essential for cell migration in vitro. Although the role of MK2 in cytokine expression depends mainly on catalytic activity, its role in cell migration is also dependent on a proline-rich N-terminal motif. However, the molecular mechanisms involved and the relevant protein targets for MK2 are not completely defined. Here we discuss the possible mechanisms by which two potential target proteins of MK2, small heat-shock protein 25/27 (Hsp25/27) and tristetraprolin, could contribute to our understanding of the above regulation.
Stress granules: sites of mRNA triage that regulate mRNA stability and translatability
Authors: Kedersha N. , Anderson P.
Published: June 2004

Mammalian stress granules (SGs) are cytoplasmic domains into which mRNAs are sorted dynamically in response to phosphorylation of eukaryotic initiation factor (eIF) 2α, a key regulatory step in translational initiation. The activation of one or more of the eIF2α kinases leads to SG assembly by decreasing the levels of eIF2-GTP-tRNAMet, the ternary complex that is normally required for loading the initiator methionine onto the 48 S preinitiation complex to begin translation. This stress-induced scarcity of eIF2-GTP-tRNAMet allows the RNA-binding proteins TIA-1 (T-cell internal antigen-1) and TIAR (TIA-1-related protein) to bind the 48 S complex in lieu of the ternary complex, thereby promoting polysome disassembly and the concurrent routing of the mRNA into a SG. The actual formation of SGs occurs upon auto-aggregation of the prion-like C-termini of TIA-1 proteins; this aggregation is reversed in vivo by overexpression of the heat-shock protein (HSP) chaperone HSP70. Remarkably, HSP70 mRNA is excluded from SGs and is preferentially translated during stress, indicating that the RNA composition of the SG is selective. Moreover, the effects of HSP70 on TIA aggregation suggest a feedback loop whereby HSP70 synthesis is auto-regulated. Proteins that promote mRNA stability [e.g. HuR (Hu protein R)] and destabilize mRNA [i.e. tristetraprolin (TTP)] are also recruited to SGs, suggesting that SGs effect a process of mRNA triage, by promoting polysome disassembly and routing mRNAs to cytoplasmic domains enriched for HuR and TTP. This model reveals connections between the eIF2α kinase system, mRNA stability and cellular chaperone levels.
Factor H family proteins: on complement, microbes and human diseases
Authors: Zipfel P. F. , Skerka C. , Hellwage J. , Jokiranta S. T. , Meri S. , Brade V. , Kraiczy P. , Noris M. , Remuzzi G.
Published: June 2004

At present, the human Factor H protein family represents seven multidomain, multifunctional serum proteins. This group includes the complement and immune regulators Factor H, the Factor H-like protein 1 (FHL-1) and five Factor H-related proteins proteins (FHR-1, -2, -3, -4 and -5). Each is exclusively composed of individually folded protein domains, termed short consensus repeats (SCRs) or complement control modules. Structure-function analyses allowed the localization of the complement regulatory domain of Factor H and FHL-1 in the N-terminal region within SCRs 1–4. In addition, multiple binding sites for C3b, heparin and microbial surface proteins were localized in the N-terminus, within the middle region and also in the C-terminus of Factor H and FHL-1. Recent results show a central role for the C-terminus of Factor H, i.e. SCRs 19–20. These particular domains are conserved in all FHRs identified so far, include contact points for C3b, heparin and microbial surface proteins and represent a ‘hot-spot’ for gene mutations in patients that suffer from the Factor H-associated form of haemolytic uraemic syndrome.
Structure of complement receptor (CR) 2 and CR2-C3d complexes
Authors: Hannan J. , Young K. , Szakonyi G. , Overduin M. J. , Perkins S. J. , Chen X. , Holers V. M.
Published: June 2004

Using X-ray crystallography, we have determined the structure of the first two short consensus repeats (SCRs) of human complement receptor (CR) 2 in complex with C3d. These studies revealed: (i) a primary site of interaction for C3d within SCR2 of CR2, (ii) a hydrophobic patch holding SCR1 to SCR2 in a rigid V-shape, (iii) a dimer formed by interactions between SCR1 of each molecule, (iv) several non-linear sequences on C3d that interact with CR2 and (v) mutations of C3d amino acids within the co-crystal interface that resulted in decreased binding. In addition, a polymorphism that results in decreased C3d binding and introduces a new glycosylation site predicted to disrupt the dimer interface was found in the New Zealand White autoimmune mouse strain. Although the co-crystal complex results are in agreement with a subset of prior studies, our additional findings, which demonstrate an extended SCR1-SCR2 structure in solution and differences in the kinetics of ligand-receptor interactions with longer forms of CR2, have suggested a more complex receptor-ligand interaction. To characterize this interaction further, several approaches directed at the determination of solution phase interactions as well as the analysis of the three-dimensional structure of CR2 alone and key CR2 mutants will be necessary.
Structure and function of complement C5 convertase enzymes
Authors: Pangburn M. K. , Rawal N.
Published: June 2004

The multisubunit enzymes of the complement system that cleave C5 have many unusual properties, the most striking of which is that they acquire their specificity for C5 following cleavage of another substrate C3. C5 convertases are assemblies of two proteins C4b and C2a (classical or lectin pathways) or C3b and Bb (alternative pathway) and additional C3b molecules. The catalytic complexes (C4b, C2a or C3b, Bb) are intrinsically unstable (t1,2 = 1–3 min) and the enzymes are controlled by numerous regulatory proteins that accelerate this natural decay rate. Immediately after assembly, the bi-molecular enzymes preferentially cleave the protein C3 and exhibit poor activity toward C5 (a Km of approx. 25 μM and a C5 cleavage rate of 0.3-1 C5/min at Vmax). Efficient C3 activation results in the covalent attachment of C3b to the cell surface and to the enzyme itself, resulting in formation of C3b-C3b and C4b-C3b complexes. Our studies have shown that deposition of C3b alters the specificity of the enzymes of both pathways by changing the Km for C5 more than 1000-fold from far above the physiological C5 concentration to far below it. Thus, after processing sufficient C3 at the surface of a microorganism, the enzymes switch to processing C5, which initiates the formation of the cytolytic membrane attack complex of complement.
Structure-function studies of the receptors for complement C1q
Authors: McGreal E. , Gasque P.
Published: June 2004

C1q is an essential component of the phylo-genetically ancient innate complement (C) system and is crucial to our natural ability to ward off infection and clear toxic cell debris (e.g. amyloid fibrils, apoptotic cells). Several candidate C1q receptors [C1q receptor for phagocytosis enhancement (C1qRp), complement receptor (CR) 1, calreticulin (CRT), binding protein for the globular head of C1q (gC1qbp)] have been described, and the aim of this review is to shed light on their structure-function relationships. One cell-surface molecule, C1qRp, has emerged as a defence collagen receptor for C1q, as well as mannose-binding lectin (MBL) and surfactant protein A. C1qRp (also known as the AA4 antigen in rodents) is the antigen recognized by a pro-adhesive monoclonal antibody called mNI-11 and antibodies against CD93, but recent results failed to confirm C1q binding activity. CR1 (CD35), a multifunctional receptor both in its ligand specificity and in its C regulation activities, is found on circulating monocytes and neutrophils, but the major site of expression is B-lymphocytes. As a receptor, CR1 binds to C1q, other C opsonins (C4b, C3b, iC3b) and MBL, and as such, has been involved in promoting phagocytosis. Several studies support a role for the cell surface receptor for the collagenous domains of C1q (cC1qR; also known as CRT). CRT belongs to the family of heat-shock proteins, the most abundant and ubiquitous soluble intracellular proteins. Though CRT does not have a transmembrane domain, it seems to mediate phagocytosis of the apoptotic cells through association with CD91. A 33 kDa protein interacts with the globular head of C1q and, logically, has been termed gC1qbp. This protein is located in mitochondria, suggesting that gC1 qbp is not a cell-surface receptor itself.
Interactions of CD55 with non-complement ligands
Authors: Lea S.
Published: June 2004

Decay Accelerating Factor (or CD55) is a major regulator of the alternative and classical pathways of complement activation and is expressed on all serum-exposed cells. It is commonly hijacked by invading pathogens, including many enteroviruses and uropathogenic Escherichia coli, to promote cellular attachment prior to infection. This review will attempt to summarize our knowledge about these interactions between CD55 and various pathogens and also what is known about the non-complement interaction between CD55 and CD97.
Tailoring anti-complement therapeutics
Authors: Harris C. L. , Fraser D. A. , Morgan B. P.
Published: June 2004

Complement is a core component of the immune system, which performs vital roles in immune surveillance. However, the active products that enable complement to perform its physiological roles can inappropriately target self tissues and cause pathology. Complement-mediated inflammation and tissue destruction is an important drive to pathology in diseases as diverse as rheumatoid arthritis and dementia. Two decades ago there were no agents that could be used therapeutically to inhibit the activation of complement, but increased understanding of the natural control of complement in vivo has markedly changed this situation. The realization that drugs mimicking the action of the complement regulatory proteins present on self cells, and in plasma, could effectively control pathological activation of complement has opened the door to the use of anti-complement therapy in disease. Here we will review the development of anticomplement therapeutics from the first generation agents, which are unmodified recombinant forms of natural regulators, to recent strategies for making better drugs. We will describe strategies for targeting the anticomplement activity to the site of disease, and for extending the plasma half-life of the agent. Finally, we will illustrate a novel approach to the delivery of anticomplement agents, making prodrugs that are activated only at disease sites thus minimizing the deleterious effects of systemic complement inhibition.
Structural aspects and design of low-molecular-mass complement inhibitors
Authors: Morikis D. , Lambris J. D.
Published: June 2004

We present a mini-review on the structure-based design of three promising complement inhibitors. Firstly, we review compstatin, a 13-residue cyclic peptide that binds to C3 and inhibits the cleavage of C3 to C3a and C3b. Secondly, we review a six-residue cyclic peptide that binds to C5aR and antagonizes the binding of C5a to its receptor C5aR. Finally, we review three small molecules that bind to Factor D and inhibit the enzymic action of Factor D, during which Factor D proteolytically cleaves Factor B in complex with C3 or C3b.
Transcription factors acting on the promoter of the rat fatty acid synthase gene
Authors: Schweizer M. , Roder K. , Zhang L. , Wolf S. S.
Published: June 2004

Fatty acid synthase (FAS), one of the main lipogenic enzymes, converts dietary calories into a storage form of energy. The transcription factors, stimulatory proteins 1 and 3 (Sp1 and Sp3), nuclear factor Y (NF-Y), upstream stimulatory factor (USF) and sterol regulatory element binding protein-1 (SREBP-1) have cognate binding sites on the promoter of the FAS gene. It was shown that Sp1 and NF-Y interact co-operatively at the diet-induced DNase I-hypersensitive site at position —500. Adjacent binding sites for NF-Y and Sp1 have also been found between —71 and —52, and —91 and —83. cAMP regulation is mediated via the inverted CAAT element (ICE) at —99 to —92, which binds NF-Y. The FAS insulin-responsive element 3 (FIRE3)-binding site at —71 to —52 is capable of binding NF-Y, USF and SREBP-1, and is required for the sterol response in conjunction with the co-activator NF-Y around —100. Surprisingly, both FIRE3 and ICE are also necessary for the response to retinoic acid that plays a role in development and is an essential component of the diet.
Yeast desaturases
Authors: Martin C. E. , Oh C.-S. , Kandasamy P. , Chellapa R. , Vemula M.
Published: June 2004

The Saccharomyces OLE1 gene encodes the intrinsic membrane-bound Δ-9 fatty acid desaturase. OLE1 expression is regulated at the levels of transcription and mRNA stability by nutrient fatty acids and molecular oxygen. Its transcription is controlled through two distinct promoter elements, the fatty acid response element (FAR) region, and a downstream low-oxygen response element (LORE) that dramatically amplifies FAR-activated expression under hypoxic or cobalt-stimulated growth conditions. Transcription activation through both elements is repressed by unsaturated fatty acids. The half-life of the OLE1 mRNA is also dramatically reduced upon exposure to unsaturated fatty acids. OLE1 expression is governed by two homologous membrane-bound proteins, Spt23p and Mga2p, which activate OLE1 expression through N-terminal polypeptides that are released from the membrane through a ubiquitin-mediated mechanism that involves processing by the 23 S proteosome. Although proteolytic processing of Spt23p can be repressed by polyunsaturated fatty acids, Mga2p processing in normoxic cells appears to be regulated by a different mechanism. Mga2p is essential, however, for the induction of the high levels of expression that are triggered by hypoxia through the LORE promoter element. Surprisingly, Mga2p also plays a critical role in controlling OLE1 mRNA stability, suggesting that there may be a functional linkage between OLE1 transcription and the regulation of OLE1 mRNA stability.
The role of desaturases in cold-induced lipid restructuring
Authors: Cossins A. R. , Murray P. A. , Gracey A. Y. , Logue J. , Polley S. , Caddick M. , Brooks S. , Postle T. , Maclean N.
Published: June 2004

All organisms respond to environmental challenge by adaptive responses, although, in many cases, the underlying molecular mechanisms are not understood. In the case of membranes, the physical structure of membrane phospholipids is conserved in the face of cold, rigidifying conditions by the elevated proportions of unsaturated fatty acids. We have observed a clear positional specificity in this substitution and head group preferences in carp liver membranes. We have also demonstrated changes in the activity of lipid desaturases that mediate the unsaturation response, caused by both transcriptional and post-translational mechanisms. Another hepatic isoform has recently been discovered with sensitivity, not to cooling, but to dietary variations. Finally, we are testing the importance of desaturase inductions in the inducible cold tolerance of the whole animal.
Sterol regulatory element-binding proteins: transcriptional activators of lipid synthesis
Authors: Horton J. D.
Published: June 2004

Sterol regulatory element-binding proteins (SREBPs) are a family of transcription factors that regulate lipid homoeostasis. Three SREBP iso-forms control the expression of more than 30 genes required for the biosynthesis of cholesterol, fatty acids, triacylglycerols and phospholipids. The unique regulation and activation properties of each SREBP isoform facilitates the co-ordinate regulation of all essential lipid building blocks required for cell membranes as well as for very-low-density lipoprotein formation in hepatocytes.
Manipulating desaturase activities in transgenic crop plants
Authors: Kinney A. J. , Cahoon E. B. , Hitz W. D.
Published: June 2004

The properties of edible vegetable oils are determined to a large extent by the relative content of the triacylglycerol fatty acids. The degree of saturation of these fatty acids can determine the functional, sensory and nutritional value of the oil. One method of altering the unsaturated fatty acid content of oilseeds is by manipulating the expression of desaturase genes of these plants. Manipulating the expression of desaturase genes in transgenic crops such as soybean, maize and canola (oilseed rape) has led to oils with improved functionality and nutrition. We have also been successful in manipulating the fatty acid content of domesticated oilseed plants by expressing heterologous desaturase and desaturase-related genes from exotic plants that produce unusual fatty acids. We have discovered that metabolic regulation, the number of genetic alleles that encode fatty acid biosynthetic enzymes, and the movement of fatty acids between complex lipids in the cell, all have a role in determining the effect of a transgene on the phenotype of the crop plant and the fatty acid composition of its seed oil.
The hammerhead ribozyme
Authors: Blount K. F. , Uhlenbeck O. C.
Published: June 2004

The hammerhead ribozyme is a small RNA motif consisting of three helices that intersect at a conserved core. When correctly folded, the hammerhead ribozyme stimulates nearly complete cleavage of the phosphodiester chain at a defined internal site to give 2′,3′-cyclic and 5′-hydroxy termini. The cleavage rate is approx. 1 min-1 at 25 °C, pH 7.5, and increases proportionally with hydroxide ion concentration between pH 5 and pH 9. As the rate of non-catalysed cleavage of RNA to form the same products is approx. 10-6 min-1 under similar conditions, an important goal is to understand how the folded structure of this small ribozyme increases the rate of alkaline cleavage 106-fold at this specific site.
The Neurospora Varkud satellite ribozyme
Authors: Collins R. A.
Published: June 2004

Presented is a review of the discovery and characterization of the Neurospora Varkud satellite ribozyme. It outlines the approaches and observations that have led to our current level of understanding of the structure and function of this ribozyme, and highlights its distinctive features compared with other naturally occurring small ribozymes.
Biochemical identification of A-minor motifs within RNA tertiary structure by interference analysis
Authors: Strobel S. A.
Published: June 2004

A-minor motifs are the most common tertiary structural elements in RNA helix packing. Biochemical identification of these interactions is now feasible using interference mapping analysis with the adenosine analogues 2′-deoxyadenosine and 3-deaza-adenosine. This approach was used to demonstrate that A-minor motifs mediate helix packing interactions that are important for 5′-splice site selection in the group I intron. By analysing the interference pattern of several analogues it is possible to identify and distinguish the four variants of the A-minor motif.
Molecular aspects of the ribosomal peptidyl transferase
Authors: Dorner S. , Polacek N. , Schulmeister U. , Panuschka C. , Barta A.
Published: June 2004

The proteins in a living cell are synthesized on a large bipartite ribonucleoprotein complex termed the ribosome. The peptidyl transferase, which polymerizes amino acids to yield peptides, is localized on the large subunit. Biochemical investigations over the past 35 years have led to the hypothesis that rRNA has a major role in all ribosomal functions. The recent high resolution X-ray structures of the ribosomal subunits clearly demonstrated that peptidyl transfer is an RNA-mediated process. As all ribosomal activities are dependent on bivalent metal ions, as is the case for most ribozymes, we investigated metal-ion-binding sites in rRNA by metal-ion-cleavage reactions. Some cleavage sites are near active sites and are evolutionarily highly conserved. The structure of the active site is flexible and undergoes changes during translocation and activation of the ribosome. Using modified P-site substrates, we showed that the 2′-OH group of the terminal adenosine is important for peptidyl transfer. These substrates were also used to investigate the metal ion dependency of the peptidyl transferase reaction.
Ribozyme-catalysed carbon-carbon bond formation
Authors: Jäschke A. , Stuhlmann F. , Bebenroth D. , Keiper S. , Wombacher R.
Published: June 2004

Numerous RNA molecules with new catalytic properties have been isolated from synthetic combinatorial libraries. A broad range of chemical reactions is catalysed, and nucleic acids can accelerate bond formation between small organic substrates. This review focuses on carbon-carbon bond formation accelerated by in vitro selected ribozymes. Mechanistic investigations and structure-function relationships are discussed.
Intracellular ribozyme applications
Authors: Castanotto D. , Li J. R. , Michienzi A. , Langlois M.-A. , Lee N. S. , Puymirat J. , Rossi J. J.
Published: June 2004

The exquisite target selectivity of trans-acting ribozymes has fostered their use as potential therapeutic agents and tools for down-regulating cellular transcripts. In living cells, free diffusion of RNAs is extremely limited, if it exists at all. Thus, getting ribozymes to base-pair with their cognate targets requires co-localizing the ribozyme transcript with the target RNA. In addition, not all sites along a given target RNA are equally accessible to ribozyme base pairing. Cellular proteins greatly influence the trafficking and structure of RNA, and therefore making ribozymes work effectively in cells a significant challenge. This article addresses the problems of getting engineered ribozymes to effectively pair with and cleave targets in cells. The work described here illuminates methods for target-site selection on native mRNAs, methods for ribozyme expression, and strategies for obtaining a discrete intracellular localization of ribozymes.
Mechanism of action of hammerhead ribozymes and their applications in vivo: rapid identification of functional genes in the post-genome era by novel hybrid ribozyme libraries
Authors: Takagi Y. , Suyama E. , Kawasaki H. , Miyagishi M. , Taira K.
Published: June 2004

A hammerhead ribozyme was demonstrated to be a metalloenzyme. By controlling the metal-binding ability of the hammerhead ribozyme in the presence or absence of a specific sequence of interest, we engineered an allosterically controllable ribozyme, designated the maxizyme. Hybrid ribozymes were then constructed by coupling the site-specific cleavage activity of a hammerhead ribozyme with the unwinding activity of an endogenous RNA helicase. This leads to extremely efficient cleavage of target mRNA, not only in vitro, but also in vivo, and eliminates one of the major problems arising in the application of ribozymes for cleavage of mRNA in vivo: that many target sites on the RNA were previously inaccessible to cleavage owing to secondary and/or tertiary structure formation. Since hybrid ribozymes can efficiently attack target sites within mRNA, libraries were made of hybrid ribozymes with randomized binding arms, which were then introduced into cells. This procedure made it possible to readily identify the relevant genes associated with a specific phenotype, such as in apoptosis and cancer metastasis pathways. This application of a randomized library of hybrid ribozymes represents a simple, yet powerful, method for the identification of genes associated with specific phenotypes in the post-genome era. Moreover, vector-based siRNA (short-interfering RNA for RNA interference, RNAi) can also be used for the creation of the libraries and for the subsequent confirmation of the identified genes, relevant in the examined phenotype.
Group I introns and RNA folding
Authors: Westhof E.
Published: June 2004

Before the discovery of catalytic RNA, tRNA molecules were the most studied RNA molecules for understanding RNA folding. Afterwards, group I introns, because of their stability and the fact that structural folding could be monitored by following their catalytic activity, became the molecule of choice for studying RNA architecture and folding. A major advantage of group I introns for studying the catalytic activity of RNA molecules is that catalytic activity is triggered by the addition of external guanosine co-factors. The self-splicing activity can therefore be precisely controlled. Using group I introns, several RNA motifs central to RNA-RNA self-assembly and folding were discovered. The analysis of the recent X-ray structures of the rRNA subunits indicates that several motifs present in the ribosome occur also in various group I introns.
Ribozymes, the first 20 years
Authors: Cech T. R.
Published: June 2004

In 1982 we reported the first catalytic RNA or ribozyme: the self-splicing intron of the Tetrahymena pre-rRNA. Additional examples of natural ribozymes were soon found, and research in the field focused on their enzymic mechanism and secondary and tertiary structure. Ribozymes identified through in vitro selection extended the repertoire of RNA catalysis. Two directions of current and future interest are the determination of atomic-resolution structures of large ribozymes by X-ray crystallography and the structural and mechanistic analysis of complexes of ribozymes with protein facilitators of their activity.
Folding mechanisms of group I ribozymes: role of stability and contact order
Authors: Woodson S. A.
Published: June 2004

The mechanism by which RNA molecules assemble into unique three-dimensional conformations is important for understanding their function, regulation and interactions with substrates. The Tetrahymena group I ribozyme is an excellent model system for understanding RNA folding mechanisms, because the catalytic activity of the native RNA is easily measured. Folding of the Tetrahymena ribozyme is dominated by intermediates in which the stable P4-P6 domain is correctly formed, but the P3-P9 domain is partially misfolded. The propensity of the RNA to misfold depends on the relative stability of native and non-native interactions. Circular permutation of the Tetrahymena ribozyme shows that the distance in the primary sequence between native interactions also influences the folding pathway.
The structure and active site of the Varkud satellite ribozyme
Authors: Lafontaine D. A. , Norman D. G. , Lilley D. M. J.
Published: June 2004

The Varkud satellite ribozyme is the largest of the small nucleolytic ribozymes, and the only one for which there is no crystal structure. It can be divided into a trans-acting ribozyme, consisting of five helices organized by two three-way helical junctions, and a stem-loop substrate with which it interacts, primarily by tertiary interactions. We have determined the global fold of the ribozyme, and the manner by which it interacts with the substrate. The substrate interacts with a cleft formed between helices II and VI (organized by the lower helical junction), where it contacts the A730 loop, the probable active site of the ribozyme. Within this loop, there is a critical adenine base (A756) that is a candidate for direct nucleo-base participation in the cleavage reaction.
How to (or not to) communicate science
Authors: Rose S.P.R.
Published: June 2004

Protagonists for ‘the public understanding of science’ still sometimes fail to recognize that there is also a need for ‘the scientists’ understanding of the public’ and that for most of science most of the time we are all public. ‘Science’ is communicated to ‘the public’ through popular books, museums, TV, the Internet, but far too often the present state of scientific belief is presented uncritically as the onward march of truth as discovered by Euro-American males. This has contributed to a widespread public concern, if not mistrust, in many areas of science, not least genetics and neuroscience. Although researchers often criticize the media for misrepresenting their work, the hype and simplifications often begin with the press releases put out by the researchers, their institutions and the scientific journals themselves. I conclude by looking more optimistically at the ways in which, by bringing natural science into theatre, novels and other art forms, the fragmentation of our culture may be diminished.
Sulphated endothelial ligands for L-selectin in lymphocyte homing and inflammation
Authors: van Zante A. , Rosen S.D.
Published: June 2004

Lymphocytes from the blood home to secondary lymphoid tissues through a process of tethering, rolling, firm adhesion and transmigration. Tethering and rolling of lymphocytes is mediated by the interaction of L-selectin on lymphocytes with sulphated ligands expressed by the specialized endothelial cells of high endothelial venules (HEVs). The sulphate-dependent monoclonal antibody MECA79 stains HEVs in peripheral lymph nodes and recognizes the complex of HEV ligands for L-selectin termed peripheral node addressin. High endothelial cell GlcNAc-6-sulphotransferase/L-selectin ligand sulphotransferase is a HEV-expressed sulphotransferase that contributes to the formation of the MECA79 epitope and L-selectin ligands on lymph node HEVs. MECA79-reactive vessels are also common at sites of chronic inflammation, suggesting mechanistic parallels between lymphocyte homing and inflammatory trafficking.
Sulphotransferases acting on mucin-type oligosaccharides
Authors: Brockhausen I.
Published: June 2004

This review summarizes the occurrence, properties and role in mucin O-glycosylation pathways of the various members of glycoprotein sulphotransferase families. Although a number of sulphotransferases have been cloned that act on mucin-type substrates in vitro, it is still difficult to determine exactly which enzymes are responsible for mucin sulphation in vivo. Sulphotransferases play a critical role in determining the chemical, physical and biological properties of mucins. Several of these enzymes have been shown to differ in expression and activity in cancer and inflammation.
Heparan sulphate N-sulphotransferase activity: reaction mechanism and substrate recognition
Authors: Kakuta Y. , Li L. , Pedersen L.C. , Pedersen L.G. , Negishi M.
Published: June 2004

Human heparan sulphate N-deacetylase/N-sulphotransferase 1 sulphates the NH3+ group of the glucosamine moiety of the heparan chain in heparan sulphate/heparin biosynthesis. An open cleft that runs perpendicular to the sulphate donor 3´-phosphoadenosine 5´-phosphosulphate may constitute the acceptor substrate-binding site of the sulphotransferase domain (hNST1) [Kakuta, Sueyoshi, Negishi and Pedersen (1999) J. Biol. Chem. 274, 10673–10676]. When a hexasaccharide model chain is docked into the active site, only a trisaccharide (-IdoA-GlcN-IdoA-) portion interacts directly with the cleft residues: Trp-713, His-716 and His-720 from α helix 6, and Phe-640, Glu-641, Glu-642, Gln-644 and Asn-647 from random coil (residues 640–647). Mutation of these residues either abolishes or greatly reduces hNST1 activity. Glu-642 may play the critical role of catalytic base in the sulphuryl group transfer reaction, as indicated by its hydrogen-bonding distance to the NH3+ group of the glucosamine moiety in the model and by mutational data.
Chondroitin sulphate proteoglycans in the central nervous system: changes and synthesis after injury
Authors: Properzi F. , Asher R.A. , Fawcett J.W.
Published: June 2004

Chondroitin sulphate proteoglycans (CSPGs) are up-regulated in the central nervous system after injury, specifically around the lesion site where the glial scar forms. This structure contains astrocytes, oligodendrocyte precursor cells, microglia and meningeal cells, and forms an inhibitory substrate for axon re-growth. CSPGs have been shown to be closely involved in this neuronal growth inhibition, specifically through their sugar chains. These chains are composed of repeats of the same disaccharide unit carrying sulphate groups in different positions. The sulphation pattern directly influences the CSPG binding properties and function; the specific sulphation pattern required for the inhibitory activity of these molecules on axon growth is unknown at present. The expression of the chondroitin sulphotransferases, which sulphate the disaccharide residues of CSPGs and thus are responsible for the structural diversity of the chondroitin sulphate sugar chains, is regulated differently in central nervous system during development and after injury, suggesting the implication of a specific sulphation pattern in the inhibitory activity of CSPGs.
Glucosaminyl N-deacetylase/N-sulphotransferases in heparan sulphate biosynthesis and biology
Authors: Kjellén L.
Published: June 2004

During the biosynthesis of heparan sulphate (HS) in the Golgi compartment, the first modification enzyme, glucosaminyl N-deacetylase/N-sulphotransferase (NDST), starts to work on the growing HS polysaccharide chain. This enzyme defines the overall design of the sulphation pattern, which will determine the ability of the HS chain to interact with target molecules. NDST removes acetyl groups from glucosamine residues and replaces them with sulphate groups. These N-sulphate groups are essential for further modification during biosynthesis; without N-sulphation, no O-sulphation or conversion of glucuronic acid into iduronic acid will occur. Four NDST isoforms, transcribed from four genes, have been identified. Much of our work is concentrated on how the enzymes are organized within the Golgi compartment and the identification of interacting partners. In addition, we study mice in which the gene encoding NDST-1 or NDST-2 has been knocked out. NDST-1 knockout mice with altered HS structure die at birth due to lung failure, whereas lack of NDST-2 results in abnormal mast cells. Since NDSTs have a key role in HS design (see above), these mice can be used to study HS function. Areas of interest are cell differentiation, growth, inflammation, cancer, lipid metabolism and microbial infection.
A gravimetric analysis of protein–oligosaccharide interactions
Authors: Rudd T. , Gallagher J.T. , Ron D. , Nichols R.J. , Fernig D.G.
Published: June 2004

Interactions between an immobilized, heparin-derived octasaccharide and growth factors have been observed using a quartz crystal microbalance-dissipation (QCM-D). This device can measure the amount of growth factors binding to the octasaccharide surface and also the change of dissipation of the surface. Dissipation is a measure of how the adhered material ‘damps’ the surface vibrations. The octasaccharides were anchored through their reducing ends by the intermediary of the alkanethiol molecule, which covalently binds to the crystal surface through the thiol group. As expected, heparin sulphate binding growth factors bound to the octasaccharide, but the change in mass of growth factor bound per unit change in dissipation is different for the different growth factors. Suggesting that the structures of the various growth factor–octasaccharide complexes are different, therefore, indicates that the change in dissipation can give insights into the structure, orientation and packing of the oligosaccharide-growth factor complexes.
Polyamine dependence of normal cell-cycle progression
Authors: Oredsson S.M.
Published: June 2004

The driving force of the cell cycle is the activities of cyclin-dependent kinases (CDKs). Key steps in the regulation of the cell cycle therefore must impinge upon the activities of the CDKs. CDKs exert their functions when bound to cyclins that are expressed cyclically during the cell cycle. Polyamine biosynthesis varies bicyclically during the cell cycle with peaks in enzyme activities at the G1/S and S/G2 transitions. The enzyme activities are regulated at transcriptional, translational and post-translational levels. When cells are seeded in the presence of drugs that interfere with polyamine biosynthesis, cell cycle progression is affected within one cell cycle after seeding. The cell cycle phase that is most sensitive to polyamine biosynthesis inhibition is the S phase, while effects on the G1 and G2/M phases occur at later time points. The elongation step of DNA replication is negatively affected when polyamine pools are not allowed to increase normally during cell proliferation. Cyclin A is expressed during the S phase and cyclin A/CDK2 is important for a normal rate of DNA elongation. Cyclin A expression is lowered in cells treated with polyamine biosynthesis inhibitors. Thus, polyamines may affect S phase progression by participating in the regulation of cyclin A expression.
Polyamines and prostatic cancer
Authors: Schipper R.G. , Romijn J.C. , Cuijpers V.M.J.I. , Verhofstad A.A.J.
Published: June 2004

The importance of polyamines in prostatic growth and differentiation has prompted studies to evaluate the clinical relevance of the ornithine decarboxylase/polyamine system in prostatic cancer. These studies show that differences in biological behaviour of prostatic (cancer) cells are associated with changes in polyamine levels and/or the activity of their metabolic enzymes. Faulty antizyme regulation of polyamine homoeostasis may play an important role in the growth and progression of prostatic carcinoma. Treatment of human prostate carcinoma cells with inhibitors of polyamine metabolic enzymes or polyamine analogues induces cell growth arrest or (apoptotic) cell death. Our recent in vitro studies using conformationally restricted polyamine analogues show that these compounds inhibit cell growth, probably by inducing antizyme-mediated degradation of ornithine decarboxylase. Sensitivity of human prostate cancer cells for these compounds was increased in the absence of androgens. These results suggest that these analogues might have chemotherapeutic potential in case prostatic cancer has become androgen-independent. Pilot data in an in vivo model show that these analogues have effects on tumour cell proliferation, vascularity, blood perfusion and tissue hypoxia. Overall, these studies show that polyamines may serve as important biomarkers of prostatic malignancy and provide a promising target for chemotherapy of prostatic cancer.
Polyamine-reduced diet in metastatic hormone-refractory prostate cancer (HRPC) patients
Authors: Cipolla B. , Guillé F. , Moulinoux J.-P.
Published: June 2004

Polyamine (PA) deprivation is effective in prostate carcinoma models. We have assessed the observance by patients, tolerance and side effects of a PA-reduced diet (PRD) and intestinal decontamination (ID), in order to reduce PA dietary and intestinal bacterial pools, in metastatic, hormone-refractory prostate cancer (HRPC) patients. A total of 13 volunteers (mean age, 67±10 years) with metastatic HRPC were proposed for PRD and ID (0.75 g/day of oral neomycin every other week). The mean time from HRPC diagnosis to the start of the diet was 12±8 months. Of the total 13, seven patients had received prior chemotherapy or Estramustine phosphate. PRD was obtained after HPLC assessment of PA contents in current foods and given 5 days a week. Toxicity, performance and pain status were assessed according to the World Health Organisation and EORTC scales. Prostatic specific antigen (PSA), blood counts, ionograms, transaminases and erythrocyte PA spermidine (Spd) and spermine (Spm; assessed by HPLC) were evaluated regularly. Mean observance was 8±7 months (range, 2–26 months). One case of grade II toxicity to neomycin was observed. Cancer-specific survival (after the diet) was 14±7 months, and two patients are still alive. All the other patients have died of their cancer at 12±6 months (range, 4–20 months). Cancer-specific survival after hormonal escape was 27±11 months (range, 9–45 months). Performance status was improved during the regimen and deteriorated 3 months after stopping. Pain score was improved (1.3 versus 0.6; P=0.04) during the diet and increased (2.1 versus 0.3) 3 months after stopping. Erythrocyte Spd (11.6±7 versus 7.7±2 nmol/8×109 erythrocytes; P=0.036) and Spm (7±6 versus 3.9±1.6 nmol/8×109 erythrocytes; P=0.036) levels were significantly reduced at 3 months. One patient had a >50% reduction in PSA, three patients had PSA stabilization for 6 months. PSA progression was observed in all other patients. No significant modification of other studied biological parameters was noted. Reducing PA dietary intake and ID is a well-observed and tolerated regimen and seems to be beneficial for patient quality of life and pain control. Patients with low initial PSA can experience durable stabilization. These encouraging results in such an aggressive disease certainly warrant further investigation.
Polyamines as modifiers of genetic risk factors in human intestinal cancers
Authors: Babbar N. , Gerner E.W.
Published: June 2004

Polyamines are downstream mediators of genetic risk factors in human intestinal cancers. The adenomatous polyposis coli (APC) tumour-suppressor gene, which is mutated in essentially all human colon cancers, regulates the expression of several e-box transcription factors. These factors, in turn, regulate the transcription of ornithine decarboxylase (ODC), the first enzyme in polyamine synthesis. The Kirsten ras (K-ras) oncogene regulates the expression of several genes, including suppressing the expression of peroxisomal proliferator-activated receptor γ (PPARγ). This PPAR, in turn, activates the expression of the spermidine/spermine-N1-acetyltransferase (SSAT), the first enzyme in polyamine catabolism. The non-steroidal anti-inflammatory drug (NSAID) sulindac induces the transcription of SSAT via activation of PPARγ. Inactivation of the APC tumour-suppressor gene, and the activation of K-ras, have a combined effect on increasing tissue polyamine contents due to increased synthesis and decreased catabolism of the polyamines. Pharmacological strategies for suppressing ODC (e.g. the enzyme-activated inhibitor α-difluoromethylornithine) and activating SSAT (e.g. NSAIDs) are potent inhibitors of intestinal carcinogenesis in rodent models. Clinical trials combining these classes of agent in humans with risk factors for colon cancer are in progress.
Polyamines and novel polyamine conjugates interact with DNA in ways that can be exploited in non-viral gene therapy
Authors: Blagbrough I.S. , Geall A.J. , Neal A.P.
Published: June 2004

As a part of our continuing studies on ‘Polyamines and their role in human disease’ we are investigating how polyamines, and especially how novel polyamine conjugates, interact with DNA. We are studying how these conjugates interact with circular plasmids in order to produce nanometre-sized particles suitable for transfecting cells. Our considerations of structure--activity relationships (SAR) within naturally occurring and synthetic polyamines have shown the significance of the inter-atomic distances between the basic nitrogen atoms. As these atoms are typically fully protonated under physiological conditions, they exist in equilibrium as polyammonium ions. The covalent addition of a lipid moiety, typically one or two alkyl or alkenyl chains, or a steroid, allows much greater efficiency in DNA condensation and in the cellular transfection achieved. Thus efficient DNA condensation and subsequently drug delivery (i.e. with DNA as the drug) can be brought about using novel polyamine conjugates. Taking further advantage of the functionalization of specific steroids (e.g. cholesterol and certain bile acids), we have designed and prepared novel fluorescent molecular probes as tools to throw light on the problematic steps in non-viral gene delivery which still impede efficient gene therapy. Thus, the current aims of our research are to understand, design and prepare small-molecule lipopolyamines for non-viral gene therapy (NVGT). The rational design and practical preparation of non-symmetrical polyamine carbamates and amides, based on steroid templates of cholesterol and the bile acid lithocholic acid as the lipid moiety, provides fluorescent molecular probes that condense DNA. These novel lipopolyamine conjugates mimic the positive charge distribution found in the triamine spermidine and the tetra-amine spermine alkaloids. After optimizing their SAR, these fluorescent probes will be useful in monitoring gene delivery in NVGT.
Turnover of trypanosomal ornithine decarboxylases
Authors: Persson L. , Jeppsson A. , Nasizadeh S.
Published: June 2004

Interestingly, there is a major difference in turnover rate between ornithine decarboxylases (ODCs) from various trypanosomatids. ODCs from Trypanosoma brucei and Leishmania donovani are both stable proteins, whereas ODC from Crithidia fasciculata is a metabolically unstable protein in the parasite. C. fasciculata ODC is also rapidly degraded in mammalian systems, whereas the closely related L. donovani ODC is not. The degradation of C. fasciculata ODC in the mammalian systems is shown to be dependent on a functional 26 S proteasome. However, in contrast to the degradation of mammalian ODC, the degradation of C. fasciculata ODC does not involve antizyme. Instead, it appears the degradation of C. fasciculata ODC may be associated with poly-ubiquitination of the enzyme.
Polyamine metabolism in the Microsporidia
Authors: Bacchi C.J. , Yarlett N. , Weiss L.M.
Published: June 2004

Members of the phylum Microspora are all obligate intracellular parasites. Little is known concerning metabolic pathways in these parasites, some of which pose serious problems in immunocompromised patients. We investigated polyamine metabolism in the systemic pathogen Enterocytozoon cuniculi using intact pre-emergent spores, and cell-free preparations. We found both polyamine synthetic and interconversion pathways to be operative, as evidenced by conversion of ornithine into polyamines, and production of spermidine from spermine by pre-emergent spores. Recent developments in the antitumour field have highlighted the ability of bis-ethylated polyamine analogues to reduce polyamine levels and block growth of tumour cells. In light of enhanced polyamine uptake in Enc. cuniculi, we have begun to study bis-aryl 3-7-3 and bis-ethyl oligoamine analogues as leads for chemotherapy of microsporidia.
Translational regulation of the plant S-adenosylmethionine decarboxylase
Authors: Hanfrey C. , Franceschetti M. , Mayer M.J. , Illingworth C. , Elliott K. , Collier M. , Thompson B. , Perry B. , Michael A.J.
Published: June 2004

It is becoming apparent that control of protein synthesis by metabolites is more common than previously thought. Much of that control is exerted at the level of initiation of mRNA translation, orchestrated by upstream open reading frames (uORFs) and RNA secondary structure. S-Adenosylmethionine decarboxylase (AdoMetDC) is a key enzyme in polyamine biosynthesis and both mammalian and plant AdoMetDCs are translationally regulated by uORFs in response to polyamine levels by distinct mechanisms.
Modern approaches to drug discovery and design: setting the scene
Authors: Kelly D.E. , Clark A.
Published: June 2004

The raison d'ítre for the drug discovery and development process is to provide safe and effective treatments for diseases. Bringing a new drug to market, however, is a time-consuming and expensive process and it remains an imperative for drug companies that they identify ways in which they can accelerate the identification of potential targets and their screening and development in order to maintain a competitive edge. Successful drug discovery efforts include biochemical, biophysical, genetic and immunological approaches, targeting such processes as signal transduction, cell cycle control, apoptosis, gene regulation and metastasis. As the number of these biological targets increases, reliance on bioinformatics and chemoinformatics to improve decision making, by identifying characteristics of successful drugs and sharing knowledge gained within the scientific community, has become a burgeoning area in the post-genomic era of drug discovery.