Structural and functional diversity of blood group antigens

Biochemical and molecular genetic studies have revealed that blood group antigens are present on cell surface molecules of wide structural diversity, including carbohydrate epitopes on glycoproteins and/or glycolipids, and peptide antigens on proteins inserted within the membrane via single or multi-pass transmembrane domains, or via glycosylphosphatidylinositol linkages. These studies have also shown that some blood group antigens are carried by complexes consisting of several membrane components which may be lacking or severely deficient in rare blood group 'null' phenotypes. In addition, although all blood group antigens are serologically detectable on red blood cells (RBCs), most of them are also expressed in non-erythroid tissues, raising further questions on their physiological function under normal and pathological conditions. In addition to their structural diversity, blood group antigens also possess wide functional diversity, and can be schematically subdivided into five classes: i) transporters and channels; ii) receptors for ligands, viruses, bacteria and parasites; iii) adhesion molecules; iv) enzymes; and v) structural proteins. The purpose of this review is to summarize recent findings on these molecules, and in particular to illustrate the existing structure-function relationships.

Uncoupling of inflammatory and destructive mechanisms in arthritis

OBJECTIVE

To update clinicians on recent advances in the differentiation of the mechanisms of inflammation and cartilage destruction in the pathogenesis of rheumatoid arthritis (RA).

METHODS

We present analysis of recent published literature and abstracts that elucidates the independent actions of pivotal proinflammatory cytokines. These experimental data provide the framework for understanding the uncoupling of destructive and inflammatory mechanisms in arthritis.

RESULTS

Tumor necrosis factor-alpha (TNF-alpha) is an important mediator in the inflammation that occurs in RA. Interleukin-1 (IL-1) has a dominant effect on cartilage destruction that occurs later in the disease process. TNF-independent IL-1 production occurs in many RA model situations. Cytokine balance determines the erosive nature of the disease.

CONCLUSION

IL-1 is at least as important as TNF-alpha in promoting the disease process. The pathways by which the inflammatory and destructive changes occur suggest that targeted anticytokine intervention will arrest the cartilage damage that occurs in patients with RA.

Revisiting the enzymes stored in the laticifers of Carica papaya in the context of their possible participation in the plant defence mechanism

In the tropical species Carica papaya, the articulated and anastomosing laticifers form a dense network of vessels displayed in all aerial parts of the plant. Damaging the papaya tree inevitably severs its laticifers, eliciting an abrupt release of latex. Besides the well-known cysteine proteinases, papain, chymopapain, caricain and glycyl endopeptidase, papaya latex is also a rich source of other enzymes. Together, these enzymes could provide an important contribution to plant defence mechanisms by sanitising and sealing the wounded areas on the tree.

Biosynthesis of vitamin b2 (riboflavin)

The biosynthesis of one riboflavin molecule requires one molecule of GTP and two molecules of ribulose 5-phosphate as substrates. The imidazole ring of GTP is hydrolytically opened, yielding a 4, 5-diaminopyrimidine which is converted to 5-amino-6-ribitylamino-2, 4(1H,3H)-pyrimidinedione by a sequence of deamination, side chain reduction and dephosphorylation. Condensation of 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione with 3, 4-dihydroxy-2-butanone 4-phosphate obtained from ribulose 5-phosphate affords 6,7-dimethyl-8-ribityllumazine. Dismutation of the lumazine derivative yields riboflavin and 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione, which is recycled in the biosynthetic pathway. The structure of the biosynthetic enzyme, 6,7-dimethyl-8-ribityllumazine synthase, has been studied in considerable detail.

Development of applied microbiology to modern biotechnology in Japan

Development of modern biotechnology in Japan is characterized by unique contributions from applied microbiology and bioindustry. This review tries to summarize these original contributions with special emphasis on industrial production of useful substances by microorganisms. In the first part, development of applied microbiology and bioindustry in the last half of the twentieth century is summarized with a brief overview of the traditional background. In the second part, recent progress is reviewed with citation of typical achievements in biotechnology, applied enzymology, secondary metabolites, genetic engineering, and screening of microbial diversity, respectively.

Physiological and nutritional regulation of enzymes of triacylglycerol synthesis

Although triacylglycerol stores play the critical role in an organism's ability to withstand fuel deprivation and are strongly associated with such disorders as diabetes, obesity, and atherosclerotic heart disease, information concerning the enzymes of triacylglycerol synthesis, their regulation by hormones, nutrients, and physiological conditions, their mechanisms of action, and the roles of specific isoforms has been limited by a lack of cloned cDNAs and purified proteins. Fortunately, molecular tools for several key enzymes in the synthetic pathway are becoming available. This review summarizes recent studies of these enzymes, their regulation under varying physiological conditions, their purported roles in synthesis of triacylglycerol and related glycerolipids, the possible functions of different isoenzymes, and the evidence for specialized cellular pools of triacylglycerol and glycerolipid intermediates.

Enabling the chemistry of life

Enzymes are the subset of proteins that catalyse the chemistry of life, transforming both macromolecular substrates and small molecules. The precise three-dimensional architecture of enzymes permits almost unerring selectivity in physical and chemical steps to impose remarkable rate accelerations and specificity in product-determining reactions. Many enzymes are members of families that carry out related chemical transformations and offer opportunities for directed in vitro evolution, to tailor catalytic properties to particular functions.

Signal transduction from bradykinin, angiotensin, adrenergic and muscarinic receptors to effector enzymes, including ADP-ribosyl cyclase

Muscarinic acetylcholine receptors in NG108-15 neuroblastoma x glioma cells, and beta-adrenergic or angiotensin II receptors in cortical astrocytes and/or ventricular myocytes, utilize the direct signaling pathway to ADP-ribosyl cyclase within cell membranes to produce cyclic ADP-ribose (cADPR) from beta-NAD+. This signal cascade is analogous to the previously established transduction pathways from bradykinin receptors to phospholipase Cbeta and beta-adrenoceptors to adenylyl cyclase via G proteins. Upon receptor stimulation, the newly-formed cADPR may coordinately function to upregulate the release of Ca2+ from the type II ryanodine receptors as well as to facilitate Ca2+ influx through voltage-dependent Ca2+ channels. cADPR interacts with FK506, an immunosuppressant, at FKBP12.6, FK506-binding-protein, and calcineurin, or ryanodine receptors. cADPR also functions through activating calcineurin released from A-kinase anchoring protein (AKAP79). Thus, some G(q/11)-coupled receptors can control cADPR-dependent modulation in Ca2+ signaling.

Biological indicators of genotoxic risk and metabolic polymorphisms

International scientific publications on the influence of metabolic genotypes on biological indicators of genotoxic risk in environmental or occupational exposure are reviewed. Biomarkers of exposure (substance or its metabolites in biological fluids, urinary mutagenicity, protein and DNA adducts) and of effects (chromosome aberrations (CAs), sister chromatid exchanges (SCEs), micronuclei (Mn), COMET assay, HPRT mutants) have been evaluated according to different genotypes (or phenotypes) of several activating/detoxifying metabolic activities. In less than half the studies (43 out of 95), the influence of genotype on the examined biological indicator was found, of which four report poorly reliable results (i.e., with scarce biological plausibility, because of the inconsistency of modulated effect with the type of enzymatic activity expressed). As regards urinary metabolites, the excretion of mercapturic acids (MA) is greater in subjects with high GST activity, that of 1-pyrenol and other PAH metabolites turns out to be significantly influenced by genotypes CYP1A1 or GSTM1 null, and that of exposure indicators to aromatic amines (AA) (acetylated and non-acetylated metabolites) is modulated by NAT2. In benzene exposure, preliminary results suggest an increase in urinary t, t-muconic acid (t,t-MA) in subjects with some genotypes. On urinary mutagenicity of PAH-exposed subjects, the effects of genotype GSTM1 null, alone or combined with NAT2 slow are reported. When DNA adduct levels are clearly increased in PAH-exposed group (18 out of 22), 7 out of 18 studies report the influence of GSTM1 null on this biomarker, and of the five studies which also examined genotype CYP1A1, four report the influence of genotype CYP1A1, alone or in combination with GSTM1 null. A total of 25 out of 41 publications (61%) evaluating the influence of metabolic polymorphisms on biomarkers of effect (cytogenetic markers, COMET assay, HPRT mutants) do not record any increase in the indicator due to exposure to the genotoxic agents studied, confirming the scarce sensitivity of these indicators (mainly HPRT mutants, Mn, COMET assay) for assessing environmental or occupational exposure to genotoxic substances. Concluding, in determining urinary metabolites for monitoring exposure to genotoxic substances, there is sufficient evidence that genetically-based metabolic polymorphisms must be taken into account in the future. The unfavourable association for the activating/detoxifying metabolism of PAH is also confirmed as a risk factor due to the formation of PAH-DNA adducts. The clearly protective role played by GSTT1 on DEB (and/or related compound)-induced sister chromatid exchanges (SCEs) should be noted. The modulating effects of genotypes on protein adduct levels in environmental and occupational exposure have not yet been documented, and most studies on the influence of genotype on biological indicators of early genotoxic effects report negative results.

Protective function of proteins and lipids in human milk

Human milk provides the infant with protection against infectious diseases. This protection is conferred through several mechanisms: specific antibody targeted protection against pathogens in the infant's environment (through milk IgA, IgG, and IgM) and broad-spectrum, nonspecific protection provided through several distinct mechanisms. These are: bactericidal effects (lactoferrin), bacteriostatic action (lactoferrin, lysozyme), lysis of microorganisms (lysozyme), antiviral effects (lactoferrin, products of milk fat digestion), antiprotozoan activity (free fatty acids produced during gastric and intestinal digestion of milk fat), and ligand action (inhibition of Helicobacter pylori adhesion to gastric mucosa by kappa-casein). In addition to these protective functions of the proteins and lipids of human milk, several enzymes present in human milk might provide protection by generating components that are bactericidal (bile salt dependent lipase, peroxidase), prevent inflammatory reactions (platelet-activating factor acetylhydrolase), or protect the integrity of milk proteins (antiproteases).

From external to internal measurement: a form theory approach to evolution

The point of view of external observers has led to an explanation of life based on digitally encoded information. In contrast, the existence of natural internal observers, or agents that belong to the same scale of the observed objects, explains the appearance of form centered approaches. The main controversies in thermodynamics and evolution are due to the changes of perspective, so as to speak, if measurement is considered to be external or internal. Equilibrium theories developed for closed systems under ideal conditions are analogous to external measurements. On the other hand, morphogenetic perspectives as far from equilibrium thermodynamics applicable to open systems allow to imagine self-organizing agents that perform local measurements. Chaitin's algorithmic approach would help to elucidate the relation between digitally encoded information and active forms, because forms and shapes are responsible for specific pattern recognition and play a major role in the process of finding the proper measuring standard. The predominance of form over digital records is illustrated by studying the mapping between genetic descriptions and functional shapes, originally suggested for RNA, by Schuster. Therefore, interactions between living entities are seen as reciprocal measurement processes that bring about couplings (shortened descriptions and local decreases of entropy) that are paid by partial record erasure (increase of entropy). To conclude, this approach centered on the inner dynamics or form is appropriate for understanding how Lamarckism and the modern neutral theory of evolution can be integrated for expanding the neoDarwinian perspective.

Modulation of calcium-evoked [3H]noradrenaline release from permeabilized cerebrocortical synaptosomes by the MARCKS protein, calmodulin and the actin cytoskeleton

In order to examine intracellular modulation of CNS catecholamine release, cerebrocortical synaptosomes were prelabeled with [3H]noradrenaline and permeabilized with streptolysin-O in the absence or presence of Ca(2+). Plasma membrane permeabilization allowed efflux of cytosol and left a compartmentalized pool of [3H]noradrenaline intact, approximately 10% of which was released by addition of 10(-5) M Ca(2+). Addition of activators or inhibitors of protein kinase C, as well as inhibitors of Ca(2+)-calmodulin kinase II or calcineurin, failed to change Ca(2+)-induced noradrenaline release. Evoked release from permeabilized synaptosomes deficient in the vesicle-associated phosphoprotein synapsin I was also unchanged. In contrast, addition of a synthetic 'active domain' peptide from the myristoylated, alanine-rich C-kinase substrate (MARCKS) protein increased, while addition of calmodulin decreased Ca(2+)-induced release from the permeabilized synaptosomes, the latter effect being reversed by a peptide inhibitor of calcineurin. Moreover, addition of the actin-destabilizing agent DNase I, as well as antibodies to MARCKS, appeared to increase spontaneous, Ca(2+)-independent release from noradrenergic vesicles. These results indicate that the MARCKS protein may modulate release from permeabilized noradrenergic synaptosomes, possibly by modulating calmodulin levels and/or the actin cytoskeleton.

Function and mechanism of zinc metalloenzymes

Zinc is required for the activity of > 300 enzymes, covering all six classes of enzymes. Zinc binding sites in proteins are often distorted tetrahedral or trigonal bipyramidal geometry, made up of the sulfur of cysteine, the nitrogen of histidine or the oxygen of aspartate and glutamate, or a combination. Zinc in proteins can either participate directly in chemical catalysis or be important for maintaining protein structure and stability. In all catalytic sites, the zinc ion functions as a Lewis acid. Researchers in our laboratory are dissecting the determinants of molecular recognition and catalysis in the zinc-binding site of carbonic anhydrase. These studies demonstrate that the chemical nature of the direct ligands and the structure of the surrounding hydrogen bond network are crucial for both the activity of carbonic anhydrase and the metal ion affinity of the zinc-binding site. An understanding of naturally occurring zinc-binding sites will aid in creating de novo zinc-binding proteins and in designing new metal sites in existing proteins for novel purposes such as to serve as metal ion biosensors.

Etomoxir-induced PPARalpha-modulated enzymes protect during acute renal failure

Regulation of fatty acid beta-oxidation (FAO) represents an important mechanism for a sustained balance of energy production/utilization in kidney tissue. To examine the role of stimulated FAO during ischemia, Etomoxir (Eto), clofibrate, and WY-14,643 compounds were given 5 days prior to the induction of ischemia/reperfusion (I/R) injury. Compared with rats administered vehicle, Eto-, clofibrate-, and WY-treated rats had lower blood urea nitrogen and serum creatinines following I/R injury. Histological analysis confirmed a significant amelioration of acute tubular necrosis. I/R injury led to a threefold reduction of mRNA and protein levels of acyl CoA oxidase (AOX) and cytochrome P4A1, as well as twofold inhibition of their enzymatic activities. Eto treatment prevented the reduction of mRNA and protein levels and the inhibition of the enzymatic activities of these two peroxisome proliferator-activated receptor-alpha (PPARalpha) target genes during I/R injury. PPARalpha null mice subjected to I/R injury demonstrated significantly enhanced cortical necrosis and worse kidney function compared with wild-type controls. These results suggest that upregulation of PPARalpha-modulated FAO genes has an important role in the observed cytoprotection during I/R injury.

Why zinc in zinc enzymes? From biological roles to DNA base-selective recognition

Intrinsic chemical properties of the zinc(II) ion in zinc enzymes have been investigated by the model of 1:1 Zn2+-macrocyclic polyamine complexes, including Zn2+-1,5,9-triazacyclododecane ([12]aneN3) and 1,4,7,10-tetraazacyclododecane (cyclen). The physiologically most suitable pKa values for the Zn2+-bound H2O in enzymes were illustrated by the first model Zn2+-[12]aneN3 complex, which mimics the essential kinetic and thermodynamic roles of Zn2+ in carbonic anhydrase. The activation of proximate serine residues (in alkaline phosphatase) and activation of alcohols for hydride transfer to NAD+ (in alcohol dehydrogenase) were also mimicked by Zn2+ -[12]aneN3 complexes. The functions of two zincs in dinuclear metallophosphatases were explained by a new dinuclear Zn2+-cryptate. For an aldolase type II model, a Zn2+-cyclen derivative showed facile enolate formation from a proximate carbonyl pendant under physiological conditions. The strong anion affinities, which Zn2+ intrinsically possesses, were exploited into novel selective nucleobase thymine (or uracil) recognition of Zn2+-cyclen complexes by the strong Zn2+ -imido anion bond formation. The Zn2+-aromatic-pendant cyclen complexes selectively bind to T (or U) in single- and double-stranded DNA (or RNA). Thus, Zn2+ complexes act like molecular zippers to break A-T pairs in DNA, which was proven by various physicochemical measurements and DNA footprinting assays. These Zn2+ complexes showed some relevant biochemical and biological properties such as inhibition of transcriptional factor, TATA binding protein, or strong antimicrobial activities to gram-positive bacterial strains.

Enzymes are open systems

The exchange of mass, energy, and information with the environment typical of open systems can also be found in enzymes. An enzyme is able to receive information on substrate concentration in an arbitrary concentration range. This actually follows from the elementary solution of Michaelis-Menten kinetics. The Michaelis constant can be seen as a relation between the decreasing parameter of a zero-order reaction and the increasing parameter of a first-order reaction over a certain time interval. This excludes the state of zero-order kinetics and consequently the state of zero content of concentration information.

Enzymes that catalyse the restructuring of proteins

The large enzyme families of protein disulfide isomerases and peptidyl prolyl cis/trans isomerases have been shown to assist polypeptide restructuring. Various folding states of polypeptides may serve as substrates of the catalysed reaction. Our understanding of the cellular function of these enzymes is increasing as a result of the availability of more specific inhibitors, the discovery of natural substrates and the use of genetically modified organisms. Further highlights of these studies include insights into the three-dimensional structures of enzyme-ligand complexes, as well as into the mechanism of slow folding phases on the atomic level.

Development and application of cell-based biosensors

Biosensors incorporate a biological sensing element that converts a change in an immediate environment to signals conducive for processing. Biosensors have been implemented for a number of applications ranging from environmental pollutant detection to defense monitoring. Biosensors have two intriguing characteristics: (1) they have a naturally evolved selectivity to biological or biologically active analytes; and (2) biosensors have the capacity to respond to analytes in a physiologically relevant manner. In this paper, molecular biosensors, based on antibodies, enzymes, ion channels, or nucleic acids, are briefly reviewed. Moreover, cell-based biosensors are reviewed and discussed. Cell-based biosensors have been implemented using microorganisms, particularly for environmental monitoring of pollutants. Biosensors incorporating mammalian cells have a distinct advantage of responding in a manner that can offer insight into the physiological effect of an analyte. Several approaches for transduction of cellular signals are discussed: these approaches include measures of cell metabolism, impedance, intracellular potentials, and extracellular potentials. Among these approaches, networks of excitable cells cultured on microelectrode arrays are uniquely poised to provide rapid, functional classification of an analyte and ultimately constitute a potentially effective cell-based biosensor technology. Three challenges that constitute barriers to increased cell-based biosensor applications are presented: analytical methods, reproducibility, and cell sources. Possible future solutions to these challenges are discussed.

Predictive factors in prostate cancer: current concepts from the 1999 College of American Pathologists Conference on Solid Tumor Prognostic Factors and the 1999 World Health Organization Second International Consultation on Prostate Cancer

Many clinically important predictive factors in prostate cancer are derived from light microscopic examination of tissue specimens by the pathologist. Two separate international consensus conferences held in 1999 addressed the contemporary status of such prognostic factors, sponsored by the College of American Pathologists (CAP) and the World Health Organization (WHO). Both conferences concluded that the following factors are recommended for routine use based on evidence from multiple published trials: TNM stage, histological grade using the Gleason system, surgical margin status, and serum prostate-specific antigen concentration. The WHO conference additionally recommended use of WHO nuclear grade, location of cancer within the prostate, and pathological effects of treatment. Other factors were categorized as promising or of unproven utility, including a wide variety of histopathologic and genetic markers. Standards are needed for analysis and quantitation of methods of tissue analysis, particularly for immunohistochemical studies and genotypic studies. This report describes the recommendations and conclusions of these two conferences.