GPI-anchor synthesis

The glycosyl phosphatidylinositol (GPI) anchor of membrane proteins is widely distributed in eukaryotes and parasitic protozoa. The structure and biosynthetic pathway of its core have been elucidated and appear to be conserved in various species. Some of the genes involved in mammalian GPI-anchor biosynthesis have recently been isolated using GPI-anchor-deficient mutant cell lines and expression cloning methods. One of these genes proved to be responsible for a GPI-anchor deficiency known as paroxysmal nocturnal hemoglobinuria. Since the core of the GPI anchor is variously modified in different species and since there may be other differences between its biosynthetic pathway in parasites and their hosts, this pathway could be a target for chemotherapy. In this review, Taroh Kinoshita and Junji Takeda focus on the GPI-anchor biosynthetic pathway and the genes involved in it.     

Enhanced sterol synthesis in concanavalin A-stimulated lymphocytes: correlation with phospholipid synthesis and DNA synthesis.

Incorporation of (14C)choline and (3H)myo-inositol into the total lipid fraction, incorporation of (14C)acetate into the sterol fraction and incorporation of (3H)thymidine into DNA were studied in human lymphocyte cultures. Concanavalin A induced an increase in the incorporation of these labels with the following features: (a) Phospholipid synthesis was increased promptly. The lag time for the increase in sterol synthesis and DNA synthesis were 5 hours and 27 hours respectively; (b) The increase in phospholipid synthesis and sterol synthesis was proportional to ConA concentration initially. Cells treated with a high concentration of ConA showed very low levels of DNA synthesis; (c) The increase in phospholipid synthesis could be abolished immediately by alpha-Methyl-Mannoside. alpha-Methyl-Mannoside blunted but did not abolish the increase in sterol synthesis. alpha-Methyl-Mannoside enhanced DNA synthesis of those cells which had been treated by a high concentration of ConA; and (d) Selective inhibition of sterol synthesis with 25-hydroxycholesterol did not prevent the increase in phospholipid synthesis, but it blocked the increase in DNA synthesis. Supplement of LDL, HDL or total lipoproteins to lymphocyte cultures was effective in preventing the inhibition of DNA synthesis by 25-hydroxy-cholesterol. These results suggest that in lymphocyte activation by ConA phospholipid synthesis, sterol synthesis and DNA synthesis were sequentially increased. The rate of cellular commitment to mitogenesis was proportional to ConA concentrations. High concentrations of ConA arrested the cell growth at a postcommitment point in the G1 phase. Enhanced phospholipid synthesis was a precommitment event. Enhanced sterol synthesis was a postcommitment event and reflected the requirement of an increased cholesterol supply for the passage of cell growth through G1.     

Lag-phase and rate of synthesis in light-mediated anthocyanin synthesis

Mustard (Sinapis alba L.) seedlings were irradiated with continuous far-red light either with or without a pretreatment with 3 or 6 h of the same far-red light, separated by a 15 h dark period. The pretreatment increases the initial rate of anthocyanin accumulation — as caused by the 2nd light treatment — at least 6-fold but leads to an earlier cessation of anthocyanin accumulation. Moreover, the pretreatment seems to shorten the apparent lag-phase of anthocyanin accumulation considerably but it does not eliminate the lag. If the pretreatment with far-red light is terminated before the seedling reaches competence (with regard to phytochrome and anthocyanin synthesis) the pretreatment has no effect on the apparent lag-phase even though the future capacity of anthocyanin biogenesis is considerably stimulated by the pretreatment. The time course of induction of anthocyanin and that of phenylalanine ammonia-lyase (PAL) (Acton et al. 1980, Fig. 1) is in line with the concept that induction of PAL by light is a prerequisite for the onset of light-mediated anthocyanin synthesis.Abbreviation PAL phenylalanine ammonia-lyase     

Anatomy--analysis and synthesis

Scientific knowledge is a continuum, and anatomy is a part of this subject to the same methods, principles, and the need of synthesis, both within anatomy and with other syntheses. Western science is the spearhead of human progress in understanding the universe around us and the world of Earth, from which we cannot escape. Science may also, in its power of synthesis, bringing together not only those who practise it but also uniting the nations. Excellent as are the applications of science in technology, knowledge has its own value in producing a synthesis of human awareness,--and also it may prevent us from ruining the Earth, which is our only possible home.     

Light-driven chemical synthesis

Depletion of the fossil fuel reserves of the Earth has prompted research into sources of renewable and sustainable energy, and feedstock for the chemical and pharmaceutical industries to support the transition towards a bio-based society. Photosynthesis efficiently captures solar energy, but its subsequent conversion into chemical energy in the form of biomass is limited to a final output in the 1-4% range. Re-routing of photosynthetic electron transport and reducing power directly into desired biosynthetic pathways offers a new avenue for sustainable production of high-value products.     

Non-Bayesian contour synthesis

Recent research has witnessed an explosive increase in models that treat percepts as optimal probabilistic inference. The ubiquity of partial camouflage and occlusion in natural scenes, and the demonstrated capacity of the visual system to synthesize coherent contours and surfaces from fragmented image data, has inspired numerous attempts to model visual interpolation processes as rational inference. Here, we report striking new forms of visual interpolation that generate highly improbable percepts. We present motion displays depicting simple occlusion sequences that elicit vivid percepts of illusory contours (ICs) in displays for which they play no necessary explanatory role. These ICs define a second, redundant occluding surface, even though all of the image data can be fully explained by an occluding surface that is clearly visible. The formation of ICs in these images therefore entails an extraordinarily improbable co-occurrence of two occluding surfaces that arise from the same local occlusion events. The perceived strength of the ICs depends on simple low-level image properties, which suggests that they emerge as the outputs of mechanisms that automatically synthesize contours from the pattern of occlusion and disocclusion of local contour segments. These percepts challenge attempts to model visual interpolation as a form of rational inference and suggest the need to consider a broader space of computational problems and/or implementation level constraints to understand their genesis.     

Organic synthesis

Some comments on the problems that are encountered by organic chemists who attempt the total synthesis of a molecule having several asymmetric centers. These difficulties explain the relatively slow progress of that branch of chemistry, although some of its successes merit being considered works of art.     

An amalgamation of solid phase peptide synthesis and ribosomal peptide synthesis

Expressed protein ligation (EPL) is a protein semisynthesis technique that allows the site-specific introduction of unnatural amino acids and biophysical probes into proteins. In the present study, we illustrate the utility of the approach through the generation of two semisynthetic proteins bearing spectroscopic probes. Dihydrofolate reductase containing a single (13)C probe in an active site loop was generated through the ligation of a synthetic peptide-alpha-thioester to a recombinantly generated fragment containing an N-terminal Cys. Similarly, c-Crk-II was assembled by the sequential ligation of three recombinant polypeptide building blocks, allowing the incorporation of (15)N isotopes in the central domain of the protein. These examples showcase the scope of the protein ligation strategy for selective introduction of isotopic labels into proteins, and the protocols described will be of value to those interested in using EPL on other systems.     

Glycoconjugate synthesis during early pregnancy: hyaluronate synthesis and function

The synthesis of various glycoconjugate classes by mouse uteri during the pre- and peri-implantation period has been examined using [3H]glucosamine as a metabolic precursor. A unique and dramatic (five- to sixfold) increase was observed in the synthesis of hyaluronate on the day upon which embryo implantation normally occurs. Mated, but nonpregnant mice did not display increased hyaluronate biosynthesis. In contrast to hyaluronate, the synthesis of most other types of glycoconjugates remained fairly constant during the first 5 days of pregnancy. Low (1500-5000)-molecular-weight N-linked oligosaccharides constituted the major class of oligosaccharides synthesized under all conditions. High (greater than 10,000)-molecular-weight glycoconjugates constituted the second most abundant class of glycoconjugates synthesized (20-30%). Most (85%) of the newly synthesized hyaluronate was associated with the nonepithelial cell types of the uterus. Experiments using ovariectomized mice receiving steroid hormones demonstrated that uterine hyaluronate synthesis was induced preferentially by an artificial decidual stimulus and implicated stromal cells as the site of hyaluronate synthesis. In addition, it was demonstrated that tissue culture plates coated with hyaluronate, but not other polysaccharides, support attachment and spreading of a large fraction (60 to 70%) of embryos cultured in serum-free medium. Collectively, these studies indicate that increased hyaluronate biosynthesis accompanies decidual responses in the endometrium and may promote embryo implantation following initial penetration of the uterine epithelium.     

Multiple peptide synthesis

The synthesis of large numbers of peptides can be very labor intensive and, if a conventional peptide synthesizer is used, only small numbers of peptides can be produced within a reasonable time. The techniques described below can make large numbers of different peptides simultaneously with varying degrees of mechanization, ranging from the wholly manual methods, to those involving complete mechanization of the whole synthesis process. Most of the multiple synthesis methods are primarily intended for small scale production ranging from microgram amounts up to a few tens of milligrams. All of the systems are economical in use of solvents and reagents, enabling cost-effective synthesis. The techniques described can also be used to prepare peptide libraries, containing several millions of peptide sequences, to enable the rapid screening of all possible permutations of amino acids within short peptides. However, it is considered that multiple synthesis methods are not particularly suited where extreme high purity or very long peptides are required.     

Inhibition of protein synthesis also inhibits synthesis of lipid-linked oligosaccharides.

Studies were initiated to determine whether the formation of lipid-linked oligosaccharides was coupled to the synthesis of protein. Canine kidney cells were grown with [2-3H]mannose or [3H]leucine in the presence of cycloheximide or puromycin and the effect of these inhibitors on the synthesis of proteins and lipid-linked oligosaccharides was measured. In all cases, the inhibition of protein synthesis resulted in a substantial inhibition in the incorporation of mannose into the lipid-linked oligosaccharides, although the synthesis of mannosyl-phosphoryl-dolichol was only slightly inhibited. Cycloheximide had no effect on the in vitro incorporation of mannose into lipid-linked oligosaccharides when GDP-[14C]mannose was incubated with aorta microsomal preparations. The inhibition of lipid-linked oligosaccharides was apparently not due to a decrease in the amount of glycosyltransferases as a result of protein degradation in the absence of protein synthesis, nor was it the result of a more rapid degradation of lipid-linked oligosaccharides. The inhibition also did not appear to be due to limitations in the available dolichyl-phosphate. The results suggest that the formation of lipid-linked oligosaccharides may be regulated by end product inhibition.     

Biocatalytic combinatorial synthesis

Combinatorial biocatalysis, based on a principle of the combinatorial use of biosynthetic steps rather than the combinatorial use of reagents, offers a complementary approach to combinatorial chemistry, which, used individually or in connection with synthetic organic transformations, provides access to analogues not readily accessible by chemical synthetic means alone. The issues and strategies particular to this approach are discussed. Examples are given demonstrating these principles as well as the unique advantages of achieving chemo-, regio- and stereoselectivity under mild reaction conditions that biocatalytic methods offer.     

Chemical protein synthesis

Since the mid-1990s, chemical synthesis has emerged as a powerful technique for the study of structure/function relationships in proteins. During the review period, the applicability of chemical protein synthesis techniques has been significantly broadened by increases in the size of synthetically accessible proteins through two new techniques: solid-phase protein synthesis and expressed protein ligation. Also in the period under review, synthetic access to novel classes of proteins has been established, including metalloproteins with tuned properties and integral membrane proteins.     

Norepinephrine-stimulated vascular prostacyclin synthesis. Receptor-dependent calcium channels control prostaglandin synthesis

Norepinephrine-stimulated prostacyclin synthesis was studied in rat aortic rings by measuring 6-keto-prostaglandin F1 alpha (6-keto-PGF1 alpha) by radioimmunoassay. Norepinephrine (10(-6) M) results in a 10- to 20-fold increase in 6-keto-PGF1 alpha synthesis by rat aortic rings (54 +/- 11 to 437 +/- 260 pg X mg wet weight-1 X 20 min-1). The maximal stimulation of 6-keto-PGF1 alpha synthesis was observed with a norepinephrine concentration of 10(-5) M at a mean effective concentration (EC50) of 9.5 +/- 3.2 X 10(-7) M which is similar to the contractile response (Emax = 10(-5) M, EC50 = 6.5 +/- 1.8 X 10(-7) M). Potassium chloride (30 mM), although causing a similar maximal contractile response as 10(-6) M norepinephrine, did not increase 6-keto-PGF1 alpha synthesis. Norepinephrine-stimulated 6-keto-PGF1 alpha synthesis was dependent upon extracellular calcium. Norepinephrine stimulation in Ca2+-free medium did not lead to a significant increase in 6-keto-PGF1 alpha synthesis. However, on the introduction of Ca2+, 6-keto-PGF1 alpha synthesis was restored to its initial level. Phentolamine (10(-6) M) (an alpha-adrenergic antagonist) and trifluroperazine (2.5 X 10(-4) M) (a calmodulin inhibitor) completely inhibited norepinephrine-stimulated 6-keto-PGF1 alpha synthesis, whereas verapamil 3 X 10(-6) M (a calcium channel blocking drug) only partially inhibited synthesis (control, 74 +/- 12; norepinephrine, 437 +/- 260; norepinephrine + verapamil, 123 +/- 8 pg X mg wet weight-1 X 20 min-1).(ABSTRACT TRUNCATED AT 250 WORDS)     

Pepsin-catalyzed peptide synthesis

The use of pepsin as a catalyst for the synthesis of peptide bonds was investigated. It is shown that the enzyme enables the preparation of several protected dipeptides and tripeptides containing two adjacent aromatic residues of the type P-Al-Phe-Y, P-PHe-Ar-Y, or P-AR-Phe-Y where P and Y are amino and carboxyl protecting groups, AL is an aliphatic amino acid residue, and Ar is an aromatic, amino acid residue. They yields are in the rang 25–97%. The high yields, combined with the enzyme's stereospecificity, permit the isolation of optically pure enantiomers from racemic mixtures. For example, when Z-DL -Ph-OH is allowed to react with an excess of H-L -Phe-NH₂, the stereoisomer Z-L -Phe-L -Phe-NH₂ is obtained in practically quantitative yield. At the same time, the unreacted, optically pure Z-D -Phe-OH can be recovered (Z = carbobenzyloxy, Phe = phenylalanine). The advantages and disadvantages of the enzymatic coupling procedure as a possible routine method for peptide synthesis are discussed.     

Yeast cell-wall synthesis

1. A study of wall synthesis has been made by following the incorporation of radioactive glucose and threonine into the cytoplasm and wall of yeast. 2. Both glucose and threonine are incorporated into a mannan glycopeptide. The glucose is also synthesized into a structural glucan of the wall. 3. The mannan glycopeptide contains high-molecular-weight mannan and low-molecular-weight mannose and oligosaccharide units composed of mannose. Both types of carbohydrate are attached to the peptide. The extent of radioactive incorporation into these different carbohydrate constituents of the glycopeptide remained constant during a pulse-chase experiment. No evidence of a sequential synthesis of oligosaccharides and high-molecular-weight mannan was obtained. 4. Cycloheximide inhibits the incorporation of threonine into the wall but only partially inhibits the incorporation of glucose. Thus not all the polysaccharide deposited into the wall is dependent on a simultaneous peptide synthesis and incorporation. 5. Protoplasts grown in an iso-osmotic medium secreted a mannan polymer that was probably a glycopeptide.     

Lipase-catalyzed polyester synthesis

Summary The effects of residual enzyme activity, stepwise addition of lipase at different reaction times, and enzyme quantity in direct polyesterification of sebacic acid and 1,4-butanediol catalyzed by a lipase from Rhizomucor miehei were investigated. Although the lipase activity dropped sharply in the beginning period of the reaction, the molar mass of the polyester increased rapidly, up to 39,000 g mol^–1 in 72 h. The residual lipase activity (hydrolytic) was only 14 %. Stepwise addition of lipase did not improve polyester synthesis. Highest mass average molar mass of 56,000 g mol^–1 was obtained with 0.125 g of lipase (28.5%, w/w) in 5 days.     

Transformation of type polysaccharide antigen synthesis and hemolysin synthesis in streptococci

Transformation of the ability to synthesize type polysaccharide antigen and beta-hemolysin has been obtained in group F streptococci. Colonies possessing cells transformed to antigen synthesis were detected on the agar surface with fluorescein-labeled anti-type serum. This selection method, in contrast to those with antibiotics, allowed both transformed and nontransformed cells to grow, resulting in sectored colonies. These colonies could be subcultured to further establish the synthesis of antigen. Group F, group A, and group-like z deoxyribonucleic acid (DNA) labeled with type II antigen and hemolysin, and streptomycin resistance transferred each marker to a group F strain lacking a type antigen. DNA from group F and z3 strains labeled with type III antigen, and streptomycin resistance transferred both markers to group F and z3 strains lacking type antigen. A second F strain without type antigen was not transformed with any of these markers. A group H strain was transformed to streptomycin resistance only by the same types of DNA. Transformation to type II antigen synthesis always resulted in the formation of beta-hemolysin. All strains isolated from natural sources contained both markers. A mutant, obtained by nitrosoguanidine treatment of an FII(sr) strain, did not synthesize either the hemolysin or the antigen. This mutant still possessed the group antigen and streptomycin resistance. A close linkage of type II antigen and beta-hemolysin is indicated. The fluorescent-antibody staining of cells containing both group and type antigens showed a more intense ultraviolet adsorption for type than group antigen. A surface location (microcapsular) for the type antigen appeared likely. These results are of interest for studies on antigen biosynthesis, genetics, and classification of the streptococci.     

Recent patents on oligonucleotide synthesis and gene synthesis

Gene synthesis is an emerging field which has widespread implications in synthetic biology and molecular biology. The field is constantly evolving which has led to key advances in oligonucleotide synthesis and gene synthesis technologies, with simplicity, cost effectiveness and high throughput. The miniaturization, multiplexing, microfluidic processing and the integrated microchip engineering will drive down cost and increase productivity without compromising DNA synthesis fidelity, whereas the gigantic amount of genome information provides infinite source of DNA elements and genes as raw material for synthetic biology. This article describes some of the recent patents on oligonucleotide synthesis and gene synthesis.