Retrotransposable elements in the Dictyostelium discoideum genome

Repetitive DNA is a major component of any living cell. In eukaryotes retrotransposable elements make up several percent of the genome size, and consequently, retroelements are often identified in experiments aimed at establishing physical maps and whole genome sequences. In this review, recent progress in the characterization of retrotransposable elements in the genome of the eukaryotic mi croorganism Dictyostelium discoideum is summarized with a focus on retroelements which integrate near transfer RNA genes with intriguing position specificity. Received 21 November 1997; received after revision 6 January 1998; accepted 6 January 1998     

A VEGF-A splice variant defective for heparan sulfate and neuropilin-1 binding shows attenuated signaling through VEGFR-2

The development of functional blood and lymphatic vessels requires spatio-temporal coordination of the production and release of growth factors such as vascular endothelial growth factors (VEGFs). VEGF family proteins are produced in multiple isoforms with distinct biological properties and bind to three types of VEGF receptors. A VEGF-A splice variant, VEGF-A₁₆₅b, has recently been isolated from kidney epithelial cells. This variant is identical to VEGF-A₁₆₅ except for the last six amino acids encoded by an alternative exon. VEGF-A₁₆₅b and VEGF-A₁₆₅ bind VEGF receptors 1 and 2 with similar affinity. VEGF-A₁₆₅b elicits drastically reduced activity in angiogenesis assays and even counteracts signaling by VEGF-A₁₆₅. VEGF-A₁₆₅b weakly binds to heparan sulfate and does not interact with neuropilin-1, a coreceptor for VEGF receptor 2. To determine the molecular basis for altered signaling by VEGF-A₁₆₅b we measured VEGF receptor 2 and ERK kinase activity in endothelial cells in culture. VEGF-A₁₆₅ induced strong and sustained activation of VEGF receptor 2 and ERK-1 and −2, while activation by VEGF-A₁₆₅b was only weak and transient. Taken together these data show that VEGF-A₁₆₅b has attenuated signaling potential through VEGF receptor 2 defining this new member of the VEGF family as a partial receptor agonist. Received 31 May 2006; received after revision 26 June 2006; accepted 14 July 2006     

The eosinophil ribonucleases

The eosinophil ribonucleases, eosinophil-derived neurotoxin (EDN/RNase 2) and eosinophil cationic protein (ECP/RNase 3) are two closely related proteins with intriguing functional and evolutionary properties. While both EDN and ECP maintain the structural and catalytic residues typical of the RNase A superfamily, the role of ribonuclease activity in the physiologic function of these proteins remains unclear. The biochemistry and physiology of EDN, ECP and the recently discovered ribonuclease k6 (RNase 6) will be reviewed in this chapter.     

The mechanism of glutamine-dependent amidotransferases

Glutamine-dependent amidotransferases have been known for more than 30 years. The mechanism by which these enzymes generate ammonia from the glutamine amide nitrogen and transfer it to seven different chemical classes of acceptors has been the subject of intense scrutiny for the last 5 years. The increasing number of biochemical and structural studies dealing with amidotransferases and with mechanistically related enzymes has disclosed the dichotomy of the mechanisms within these enzymes for achieving the glutamine amide bond cleavage. Some of them use a catalytic Cys/His/Glu triad similar to serine protease, whereas the aminoterminal cysteine of the others is believed to play the same function. The transfer of ammonia from the glutamine site to the acceptor site which must operate in a concerted manner has been demonstrated in two cases to involve channelling but is still matter of investigation.     

Cyclooxygenase,lipoxygenase and tumor angiogenesis

Arachidonic acid metabolism through cyclooxygenase (COX) and lipoxygenase (LOX) pathways generates various biologically active lipids that play important roles in inflammation, thrombosis and tumor progression. Angiogenesis, the formation of new capillary vessels from preexisting ones, underpins a number of physiological processes and participates in the development of several pathological conditions such as arthritis, cancer and various eye diseases. The formation of new capillary vessels is a multistep process that involves endothelial cell proliferation, migration and tube formation. In the present review, we survey the literature on the regulation of angiogenesis by arachidonate metabolites, especially those from the COX and 12-LOX pathways in the context of tumor growth, and put forward some unanswered but important questions for future studies.     

Differential display analysis of gene expression in invertebrates

Screening for differentially expressed genes is a straightforward approach to study the molecular basis for changes in gene expression. Differential display analysis has been used by investigators in diverse fields of research since it was developed. Differential display has also been the approach of choice to investigate changes in gene expression in response to various biological challenges in invertebrates. We review the application of differential display analysis of gene expression in invertebrates, and provide a specific example using this technique for novel gene discovery in the nematode Caenorhabditis elegans.     

On the existence of cytokines in invertebrates

Based on the assumption that invertebrates, like vertebrates, possess factors regulating responses to infection or wounding, studies dealing with the evolution of immunity have focussed on the isolation and characterisation of putative cytokine-related molecules from invertebrates. Until recently, most of our knowledge of cytokine- and cytokine receptor-like molecules in invertebrates relies on functional assays and similarities at the physicochemical level. As such, a phylogenetic relationship between invertebrate cytokine-like molecules and vertebrate counterparts could not be convincingly demonstrated. Recent genomic sequence analyses of interleukin-1-receptor-related molecules, that is Toll-like receptors, and members of the transforming growth factor-β superfamily suggest that the innate immune system of invertebrates and vertebrates evolved independently. In addition, data from protochordates and annelids suggest that invertebrate cytokine-like molecules and vertebrate factors do not have the same evolutionary origin. We propose instead that the convergence of function of invertebrate cytokine-like molecules and vertebrate counterparts involved in innate immune defences may be based on similar lectin-like activities. Received 27 November 2000; received after revision 11 December 2000; accepted 13 December 2000     

The ubiquitin-specific protease USP25 interacts with three sarcomeric proteins

The biological functions of the more than one hundred genes coding for deubiquitinating enzymes in the human genome remain mostly unknown. The USP25 gene, located at 21q11.2, encodes three protein isoforms produced by alternative splicing. While two of the isoforms are expressed nearly ubiquituously, the expression of the longer USP25 isoform (USP25m) is restricted to muscular tissues and is upregulated during myogenesis. USP25m interacts with three sarcomeric proteins: actin alpha-1 (ACTA1), filamin C (FLNC), and myosin binding protein C1 (MyBPC1), which are critically involved in muscle differentiation and maintenance, and have been implicated in the pathogenesis of severe myopathies. Biochemical analyses demonstrated that MyBPC1 is a short-lived proteasomal substrate, and its degradation is prevented by over-expression of USP25m but not by other USP25 isoforms. In contrast, ACTA1 and FLNC appear to be stable proteins, indicating that their interaction with USP25m is not related to their turnover rate. Received 7 November 2005; received after revision 7 January 2006; accepted 13 January 2006     

生物活性物质的电致化学发光检测

电致化学发光是通过电极上直接或间接发生的电化学反应而产生的一种化学发光,因此电致化学发光检测是在化学发光和电化学基础上发展起来的一种新的分析技术。电致化学发光检测技术不但保留了化学发光分析和电化学分析固有的优点,同时还具有其自身的优点,如所发生的化学发光反应易于控制;方法更灵敏,更具有选择性;可以获得更多的化学信息;扩大了化学发光方法可检测的范围;更易于与现代分离技术联用。生物体中很多生物活性物质具有电活性,因此用现代电化学技术研究其电化学行为具有重要的理论意义和实际应用价值。生物体中的生物活性物质通常浓度很低,并且成分复杂,因此分离检测生物体中生物活性物质非常困难。由于电致化学发光检测具有灵敏度高,选择性好的特点,无疑是检测生物体中生物活性物质的强有力工具,如果它能与HPLC、CE及FIA等现代分离技术相结合,将表现出更加强大的生命力。     

The prolyl oligopeptidase family

A group of serine peptidases, the prolyl oligopeptidase family, cannot hydrolyze peptides containing more than about 30 residues. This group is unrelated to the classical trypsin and subtilisin families, and includes dipeptidyl peptidase IV, acylaminoacyl peptidase and oligopeptidase B, in addition to the prototype prolyl oligopeptidase. The recent crystal structure determination of prolyl oligopeptidase (80 kDa) has shown that the enzyme contains a peptidase domain with an α/β hydrolase fold, and its catalytic triad is covered by the central tunnel of an unusual seven-bladed β-propeller. This domain operates as a gating filter, excluding large, structured peptides from the active site. The binding mode of substrates and the catalytic mechanism differ from that of the classical serine peptidases in several features. The members of the family are important targets of drug design. Prolyl oligopeptidase is involved in amnesia, depression and blood pressure control, dipeptidyl peptidase IV in type 2 diabetes and oligopeptidase B in trypanosomiasis. Received 8 August 2001; received after revision 19 September 2001; accepted 21 September 2001     

Carboxypeptidase E and thrombospondin-1 are differently expressed in subcutaneous and visceral fat of obese subjects

The aim of this study was to identify candidate genes for visceral obesity by screening for genes strongly differentially expressed between human subcutaneous and visceral adipose depots. A cDNA microarray with human adipose-derived cDNAs was used as an initial screening to identify genes that are potentially differentially expressed between human subcutaneous and visceral abdominal fat tissues. For the two best candidates, carboxypeptidase E (CPE) and thrombospondin-1 (THBS1) (EST N72406), real-time RT-PCR was performed to confirm their depot specific expression in extremely obese individuals. Both genes appeared to be strongly differentially expressed, having a higher expression in the visceral depot than in the subcutaneous one. For THBS1, the difference in expression between the depots was greater in women than in men. The involvement of CPE and THBS1 in obesity allows us to suggest that the physiological processes controlled by these genes contribute to depot and gender-related differences in the metabolic complications of obesity. Received 7 August 2002; received after revision 19 Septemer 2002; accepted 24 September 2002     

Genes in sweeping competition

Analysis of DNA variation is a powerful tool for detecting adaptation at the genomic level. The contribution of adaptive evolution is evident from examples of rapidly evolving genes, which represent the likely targets for strong selection. More subtle adaptation is also an integral component of routine maintenance of gene performance, continuously applied to every gene. Adaptive changes in the population are accomplished through selective sweeps, i.e. complete or partial fixation of beneficial alleles. The evidence is accumulating that selective sweeps are quite frequent events which, together with associated genetic hitchhiking, represent dominant forces that influence molecular evolution by shaping the variability pattern in the genome. Received 5 May 2000; revised 22 August 2000; accepted 24 August 2000     

Structure and evolution of the genetic code viewed from the perspective of the experimentally expanded amino acid repertoire in vivo

Much effort has been devoted recently to expanding the amino acid repertoire in protein biosynthesis in vivo. From such experimental work it has emerged that some of the non-canonical amino acids are accepted by the cellular translational machinery while others are not, i.e. we have learned that some determinants must exist and that they can even be anticipated. Here, we propose a conceptual framework by which it should be possible to assess deeper levels of the structure of the genetic code, and based on this experiment to understand its evolution and establishment. First, we propose a standardised repertoire of 20 amino acids as a basic set of conserved building blocks in protein biosynthesis in living cells to be the main criteria for genetic code structure and evolutionary considerations. Second, based on such argumentation, we postulate the structure and evolution of the genetic code in the form of three general statements: (i) the nature of the genetic code is deterministic; (ii) the genetic code is conserved and universal; (iii) the genetic code is the oldest known level of complexity in the evolution of living organisms that is accessible to our direct observation and experimental manipulations. Such statements are discussed as our working hypotheses that are experimentally tested by recent findings in the field of expanded amino acid repertoire in vivo. Received 30 June 1999; accepted 9 July 1999     

The cephalopod heart: The evolution of a high-performance invertebrate pump

Cephalopods typically have high metabolic rates. They have blood in which the oxygen carrier is haemocyanin, a pigment that is found only in solution and which never seems to be present in concentrations that will transport more than 4–5 vols % of oxygen. Their hearts must in consequence have very high cardiac outputs. In this account the performance of the heart ofNautilus, the only surviving ectocochleate, is contrasted with the performance of the hearts of coleoids,Octopus which has a relatively low metabolic rate (for a coleoid) and squids which have very high oxygen uptakes by any standards. In all these animals, heartbeat frequency is temperature-dependent and the additional oxygen demand in exercise is met very largely by a 2–3-fold increase in stroke volume. With the exception ofNautilus, cephalopods tend to utilise nearly all of the oxygen transported in the blood even at rest; they show very limited factorial scopes. Specific power output has, however, increased dramatically from 2.7 mWg^–1 in an activeNautilus to 5.5 mWg^–1 inOctopus and up to 20 or 30 mWg^–1 in species ofLoligo. The increase is almost entirely due to a 10-fold increase in heartbeat frequency. It is argued that frequency cannot be used as a means of responding to extra demand in an animal that must also carry automatic compensation for changes in metabolic rate dependent upon the ambient temperature, and that the use of frequency in some squid may be associated with a reduced temperature tolerance. Cephalopod systemic hearts do not scale directly with body mass, like the hearts of fish and the higher vertebrates. Smaller cephalopods have relatively larger hearts (as Mass^0.9). A typical 100-g coleoid would have a heart mass of 0.15 g. Oegopsid squids appear to be exceptional with hearts twice as large.     

Vision in the ultraviolet

Sensitivity to ultraviolet light (UV) is achieved by photoreceptors in the eye that contain a class of visual pigments maximally sensitive to light at wavelengths <400 nm. It is widespread in the animal kingdom where it is used for mate choice, communication and foraging for food. UV sensitivity is not, however, a constant feature of the visual system, and in many vertebrate species, the UV-sensitive (UVS) pigment is replaced by a violet-sensitive (VS) pigment with maximal sensitivity between 410 and 435 nm. The role of protonation of the Schiff base-chromophore linkage and the mechanism for tuning of pigments into the UV is discussed in detail. Amino acid sequence analysis of vertebrate VS/UVS pigments indicates that the ancestral pigment was UVS, with loss of UV sensitivity occurring separately in mammals, amphibia and birds, and subsequently regained by a single amino acid substitution in certain bird species. In contrast, no loss of UV sensitivity has occurred in the UVS pigments of insects.     

Bacterial nonspecific acid phosphohydrolases: physiology, evolution and use as tools in microbial biotechnology

Bacterial nonspecific acid phosphohydrolases (NSAPs) are secreted enzymes, produced as soluble periplasmic proteins or as membrane-bound lipoproteins, that are usually able to dephosphorylate a broad array of structurally unrelated substrates and exhibit optimal catalytic activity at acidic to neutral pH values. Bacterial NSAPs are monomeric or oligomeric proteins containing polypeptide components with an M _r of 25 – 30 kDa. On the basis of amino acid sequence relatedness, three different molecular families of NSAPs can be distinguished, indicated as molecular class A, B and C, respectively. Members of each class share some common biophysical and functional features, but may also exhibit functional differences. NSAPs have been detected in several microbial taxa, and enzymes of different classes can be produced by the same bacterial species. Structural and phyletic relationships exist among the various bacterial NSAPs and some other bacterial and eucaryotic phosphohydrolases. Current knowledge on bacterial NSAPs is reviewed, together with analytical tools that may be useful for their characterization. An overview is also presented concerning the use of bacterial NSAPs in biotechnology. Received 21 November 1997; received after revision 10 March 1998; accepted 10 March 1998     

Structure, function and evolution of antifreeze proteins

Antifreeze proteins bind to ice crystals and modify their growth. These proteins show great diversity in structure, and they have been found in a variety of organisms. The ice-binding mechanisms of antifreeze proteins are not completely understood. Recent findings on the evolution of antifreeze proteins and on their structures and mechanisms of action have provided new understanding of these proteins in different contexts. The purpose of this review is to present the developments in contrasting research areas and unite them in order to gain further insight into the structure and function of the antifreeze proteins. Received 2 September 1998; received after revision 21 October 1998; accepted 2 November 1998     

The possible role of isoforms of cytochrome c oxidase subunit VIa in mammalian thermogenesis

A single cDNA of cytochrome c oxidase subunit VIa was characterised from liver, heart and the thermogenic organ of the partially endotherm tuna fish. The amino acid sequence revealed high identity with subunit VIa from carp and trout, but low identity to subunits VIaL (liver type) and VIaH (heart type) of mammalian cytochrome c oxidase. In reconstituted cytochrome c oxidase from bovine heart, the H ⁺/e⁻ stoichiometry is decreased from 1.0 to 0.5 at high intraliposomal ATP/ADP ratios via exchange of bound ADP by ATP at the matrix domain of the transmembraneous subunit VIaH. Reconstituted cytochrome c oxidase from bovine liver and kidney, containing subunit VIaL, revealed H ⁺/e⁻ ratios below 0.5, independent of the ATP/ADP ratio. The results suggest the evolution of three types of subunit VIa. Subunits VIaH and VIaL are postulated to participate in mammalian thermogenesis. Received 3 May 1999; received after revision 10 June 1999; accepted 29 June 1999     

Visual pigment: G-protein-coupled receptor for light signals

The visual pigment present in photoreceptor cells is a prototypical G-protein-coupled receptor (GPCR) that receives a light signal from the outer environment using a light-absorbing chromophore, 11-cis-retinal. Through cis-trans isomerization of the chromophore, light energy is transduced into chemical free energy, which is in turn utilized for conformational changes in the protein to activate the retinal G-protein. In combination with site-directed mutagenesis, various spectroscopic and biochemical studies identified functional residues responsible for chromophore binding, color regulation, intramolecular signal transduction and G-protein coupling. Extensive studies reveal that these residues are localized into specific domains of visual pigments, suggesting a highly manipulated molecular architecture in visual pigments. In addition to the recent findings on dysfunctional mutations in patients with retinitis pigmentosa or congenital night blindness, the mechanism of intramolecular signal transduction in visual pigments and their evolutionary relationship are discussed. Received 20 July 1998; received after revision 9 September 1998; accepted 23 September 1998     

Dexamethasone enhances CTLA-4 expression during T cell activation

T cell activation is enhanced by the costimulatory interaction of B7 on antigen-presenting cells and CD28 on T cells, resulting in long-term T cell proliferation, differentiation and production of large amounts of cytokines, such as interleukin (IL)-2. CTLA-4 is a co-stimulation receptor that shares 31% homology with CD28 and binds B7 family members with higher affinity. CTLA-4 is transiently expressed intracellularly and on the cell surface following activation of T cells. We have studied the kinetics of CTLA-4 expression and the effects of dexamethasone on CTLA-4 expression during T cell activation in cultures of mouse spleen cells stimulated by a mixture of immobilized anti-CD3 and anti-CD28 monoclonal antibodies (anti-CD3/CD28 mAb) or concanavalin A (ConA). CTLA-4 expression peaked on day 2 and returned to background levels after 7 days. Dexamethasone was found to potentiate CTLA-4 expression in a dose-dependent manner with an EC₅₀ effective concentration 50%) of about 10⁻⁸ M. In contrast, other immunosuppressive agents, such as rapamycin or cyclosporin A had no or an inhibitory effect on CTLA-4 expression, respectively. Dexamethasone also stimulated CD28 expression, but inhibited IL-2R expression during anti-CD3/CD28 mAb-induced mouse splenic T cell activation. Western blot analyses of lysates of activated mouse T cells showed that dexamethasone increased CTLA-4 protein levels twofold during anti-CD3/CD28 mAb-induced activation. Dexamethasone also enhanced CTLA-4 messenger RNA twofold as quantified by ribonuclease protection assay. The effects of dexamethasone on CTLA-4 expression were glucocorticoid-specific and completely inhibited by the glucocorticoid receptor antagonist mifepristone (RU486), indicating that the effect of dexamethasone on CTLA-4 expression is mediated through the glucocorticoid receptor. In conclusion, the immunosuppressive agent dexamethasone actually stimulates CTLA-4 expression, which is involved in downregulation of T cell activation. Received 19 May 1999; received after revision 13 July 1999; accepted 13 July 1999