Kinetic studies on endo-beta-galactosidase by a novel colorimetric assay and synthesis of N-acetyllactosamine-repeating oligosaccharide beta-glycosides using its transglycosylation activity.

Novel chromogenic substrates for endo-beta-galactosidase were designed on the basis of the structural features of keratan sulfate. Galbeta1-4GlcNAcbeta1-3Galbeta1-4GlcNAcbeta-pNP (2), which consists of two repeating units of N-acetyllactosamine, was synthesized enzymatically by consecutive additions of GlcNAc and Gal residues to p-nitrophenyl beta-N-acetyllactosaminide. In a similar manner, GlcNAcbeta1-3Galbeta1-4GlcNAcbeta-pNP (1), GlcNAcbeta1-3Galbeta1-4Glcbeta-pNP (3), Galbeta1-4GlcNAcbeta1-3Galbeta1-4Glcbeta-pNP (4), Galbeta1-3GlcNAcbeta1-3Galbeta1-4Glcbeta-pNP (5), and Galbeta1-6GlcNAcbeta1-3Galbeta1-4Glcbeta-pNP (6) were synthesized as analogues of 2. Endo-beta-galactosidases released GlcNAcbeta-pNP or Glcbeta-pNP in an endo-manner from each substrate. A colorimetric assay for endo-beta-galactosidase was developed using the synthetic substrates on the basis of the determination of p-nitrophenol liberated from GlcNAcbeta-pNP or Glcbeta-pNP formed by the enzyme through a coupled reaction involving beta-N-acetylhexosaminidase (beta-NAHase) or beta-d-glucosidase. Kinetic analysis by this method showed that the value of Vmax/Km of 2 for Escherichia freundii endo-beta-galactosidase was 1.7-times higher than that for keratan sulfate, indicating that 2 is very suitable as a sensitive substrate for analytical use in an endo-beta-galactosidase assay. Compound 1 still acts as a fairly good substrate despite the absence of a Gal group in the terminal position. In addition, the hydrolytic action of the enzyme toward 2 was shown to be remarkably promoted compared to that of 4 by the presence of a 2-acetamide group adjacent to the p-nitrophenyl group. This was the same in the case of a comparison of 1 and 3. Furthermore, the enzyme also catalysed a transglycosylation on 1 and converted it into GlcNAcbeta1-3Galbeta1-4GlcNAcbeta1-3Galbeta1-4GlcNAcbeta-pNP (9) and GlcNAcbeta1-3Galbeta1-4GlcNAcbeta1-3Galbeta1-4GlcNAcbeta1-3Galbeta1-4GlcNAcbeta-pNP (10) as the major products, which have N-acetyllactosamine repeating units.     

Identification of recombinant AtPYL2, an abscisic acid receptor,in E. coli using a substrate-derived bioactive small molecule,a biotin linker with alkyne and amino groups,and a protein cross-linker

Target protein identification of bioactive small molecules is one of the most important research in forward chemical genetics. The affinity chromatography technique to use a resin bound with a small molecule is often used for identification of a target protein of a bioactive small molecule. Here we report a new method to isolate a protein targeted with a bioactive small molecule using a biotin linker with alkyne and amino groups, protein cross-linker containing disulfide bond, and a bioactive small molecule with an azido group (azido probe). After an azido probe is associated with a target protein, the complex of a target protein and azido probe is covalently bound through the biotin linker by azide-alkyne Huisgen cycloaddition and protein cross-linker containing disulfide bond. This ternary complex is immobilized on an affinity matrix with streptavidin, and then the target protein is selectively eluted with a buffer containing a reducing agent for cleavage of disulfide bonds. This method uses a probe having an azido group, which a small functional group, and has the possibility to be a solution strategy to overcome the hindrance of a functional group introduced into the probe that reduces association a target protein. The effectiveness of the method in this study was shown using linker 1, 3′-azidoabscisic acid 3, and protein cross-linker containing a disulfide bond (DTSSP 5).     

Altitudinal variation of the gut microbiota in wild house mice

The maintenance of oxygen homeostasis in the gut is critical for the maintenance of a healthy gut microbiota. However, few studies have explored how the concentration of atmospheric oxygen affects the gut microbiota in natural populations. High‐altitude environments provide an opportunity to study the potential effects of atmospheric oxygen on the composition and function of the gut microbiota. Here, we characterized the caecal microbial communities of wild house mice (Mus musculus domesticus) in two independent altitudinal transects, one in Ecuador and one in Bolivia, from sea level to nearly 4,000 m. First, we found that differences in altitude were associated with differences in the gut microbial community after controlling for the effects of body mass, diet, reproductive status and population of origin. Second, obligate anaerobes tended to show a positive correlation with altitude, while all other microbes tended to show a negative correlation with altitude. These patterns were seen independently in both transects, consistent with the expected effects of atmospheric oxygen on gut microbes. Prevotella was the most‐enriched genus at high elevations in both transects, consistent with observations in high‐altitude populations of pikas, ruminants and humans, and also consistent with observations of laboratory mice exposed to hypoxic conditions. Lastly, the renin–angiotensin system, a recently proposed microbiota‐mediated pathway of blood pressure regulation, was the top predicted metagenomic pathway enriched in high altitudes in both transects. These results suggest that high‐altitude environments affect the composition and function of the gut microbiota in wild mammals.     

Stabilization of hyperactive dihydrofolate reductase by cyanocysteine-mediated backbone cyclization

Stabilization of an enzyme while maintaining its activity has been a major challenge in protein chemistry. Although it is difficult to simultaneously improve stability and activity of a protein by amino acid substitutions due to the activity-stability trade-off, backbone cyclization by connecting the N and C termini with a linker is promising as a general method of stabilizing a protein without affecting its activity. Recently, we created a hyperactive, methionine- and cysteine-free mutant of dihydrofolate reductase from Escherichia coli, called ANLYF, by introducing seven amino acid substitutions, which, however, destabilized the protein. Here we show that ANLYF is stabilized without a loss of its high activity by a novel backbone cyclization method for unprotected proteins. The method is based on the in vitro cyanocysteine-mediated intramolecular ligation reaction, which can be conducted with relatively high efficiency by a simple procedure and under mild conditions. We also show that the reversibility of thermal denaturation is highly improved by the cyclization. Thus, activity and stability of the protein can be separately improved by amino acid substitutions and backbone cyclization, respectively. We suggest that the cyanocysteine-mediated cyclization method is complementary to the intein-mediated cyclization method in stabilizing a protein without affecting its activity.     

Core protein machinery for mammalian phosphatidylinositol 3,5-bisphosphate synthesis and turnover that regulates the progression of endosomal transport. Novel Sac phosphatase joins the ArPIKfyve-PIKfyve complex

Perturbations in phosphatidylinositol 3,5-bisphosphate (PtdIns(3,5)P2)-synthesizing enzymes result in enlarged endocytic organelles from yeast to humans, indicating evolutionarily conserved function of PtdIns(3,5)P2 in endosome-related events. This is reinforced by the structural and functional homology of yeast Vac14 and human Vac14 (ArPIKfyve), which activate yeast and mammalian PtdIns(3,5)P2-producing enzymes, Fab1 and PIKfyve, respectively. In yeast, PtdIns(3,5)P2-specific phosphatase, Fig4, in association with Vac14, turns over PtdIns(3,5)P2, but whether such a mechanism operates in mammalian cells and what the identity of mammalian Fig4 may be are unknown. Here we have identified and characterized Sac3, a Sac domain phosphatase, as the Fig4 mammalian counterpart. Endogenous Sac3, a widespread 97-kDa protein, formed a stable ternary complex with ArPIKfyve and PIKfyve. Concordantly, Sac3 cofractionated and colocalized with ArPIKfyve and PIKfyve. The intrinsic Sac3(WT) phosphatase activity preferably hydrolyzed PtdIns(3,5)P2 in vitro, although the other D5-phosphorylated polyphosphoinositides were also substrates. Ablation of endogenous Sac3 by short interfering RNAs elevated PtdIns(3,5)P2 in (32)P-labeled HEK293 cells. Ectopically expressed Sac3(WT) in COS cells colocalized with and dilated EEA1-positive endosomes, consistent with the PtdIns(3,5)P2 requirement in early endosome dynamics. In vitro reconstitution of carrier vesicle formation from donor early endosomes revealed a gain of function upon Sac3 loss, whereas PIKfyve or ArPIKfyve protein depletion produced a loss of function. These data demonstrate a coupling between the machinery for PtdIns(3,5)P2 synthesis and turnover achieved through a physical assembly of PIKfyve, ArPIKfyve, and Sac3. We suggest that the tight regulation in PtdIns(3,5)P2 homeostasis is mechanistically linked to early endosome dynamics in the course of cargo transport.     

A stable cellular marker for the analysis of mouse chimeras: the bacterial chloramphenicol acetyltransferase gene driven by the human elongation factor la promoter

We have developed a method of marking of mouse cells by means of transfection of a foreign gene. The transgene chosen here was the plasmid pEF321CAT which contains the bacterial chloramphenicol acetyl transferase (CAT) gene linked to the promoter region of the human polypeptide chain elongation factor 1 alpha (hEF1 alpha) gene. Evaluation of the plasmid pEF321CAT as a cellular marker for mouse cells involved intensive examination of a transgenic mouse carrying pEF321CAT. The CAT gene was expressed in all tissues examined, demonstrating that the hEF1 alpha promoter was active in a wide range of mouse cells. The plasmid itself did not exert any harmful effect on the normal development of mice, and the CAT activity was immunohistologically detectable on sectioned tissues by the use of anti-CAT serum. When the plasmid was transferred into embryonal carcinoma (EC) cells and embryonic stem (ES) cells, the CAT gene was also found to be expressed constantly irrespective of their differentiation. These results demonstrated that the plasmid pEF321CAT can be used as a reliable and feasible cellular marker that would distinguish unequivocally the cells of each of genotype in chimeric tissues.     

Membrane microdomains from early gastrula embryos of medaka, <Emphasis Type="Italic">Oryzias latipes</Emphasis>, are a platform of E-cadherin- and carbohydrate-mediated cell–cell interactions during epiboly

Formation of membrane microdomain is critical for cell migration (epiboly) during gastrulation of medaka fish [Adachi et al. (Biochem. Biophys. Res. Commun. 358:848–853, 2007)]. In this study, we characterized membrane microdomain from gastrula embryos to understand its roles in epiboly. A cell adhesion molecule (E-cadherin), its associated protein (β-catenin), transducer proteins (PLCγ, cSrc), and a cytoskeleton protein (β-actin) were enriched in the membrane microdomain. Le^X-containing glycolipids and glycoproteins (Le^X-gp) were exclusively enriched in the membrane microdomain. Interestingly, the isolated membrane microdomain had the ability to bind to each other in the presence of Ca²⁺. This membrane microdomain binding was achieved through the E-cadherin homophilic and the Le^X-glycan-mediated interactions. E-cadherin and Le^X-gp were co-localized on the same membrane microdomain, suggesting that these two interactions are operative at the same time. Thus, the membrane microdomain functions as a platform of the E-cadherin- and Le^X-glycan-mediated cell adhesion and signal transduction.

Distribution and morphological characteristics of the interstitial cells of Cajal in the ileocaecal junction of the guinea-pig

The guinea-pig ileocaecal junction including the valve was studied by immunohistochemistry to clarify the organization of the muscle bundles, the enteric nerves and the interstitial cells of Cajal (ICC). This region clearly exhibited characteristic features in the distribution patterns of ICC in a proximal to distal direction: (1) the thickened portion of the terminal ileum immediately adjacent to the ileocecal junction contained many ICC throughout the circular (ICC-CM) and longitudinal (ICC-LM) muscle layers, but ICC were few or absent in the rest of the ileum; (2) the ileal side of the valve contained ICC associated with the deep muscular plexus (ICC-DMP) as in the small intestine, whereas ICC-DMP were absent in the caecal side as in the caecum; (3) the valve contained many ICC-CM and ICC-LM in both the ileal and caecal sides; (4) many ICC associated with the myenteric plexus were observed in both the ileal and caecal sides of the valve, whereas they were only sparsely found in the caecum; (5) ICC were also observed around the submucosal plexus in a confined area of the terminal ileum and the ileocaecal valve. These observations provide morphological evidence that the terminal ileum and ileocaecal valve are specially equipped for their active involvement in the movement of the junctional area.     

Boron deficiency: How does the defect in cell wall damage the cells?

Boron (B) is an essential micronutrient for vascular plants. Boron plays a structural role in cell walls through binding to pectic polysaccharides. It still remains unclear how B deficiency, and hence probably alterations in cell wall structure, leads to various metabolic disorders and cell death. To understand the process, we analyzed the physiological changes in suspension- cultured tobacco (Nicotiana tabacum) BY-2 cells under B deficiency. The results indicated that the cells deprived of B did not undergo a typical programmed cell death process. Oxidative damage was proven to be the direct and major cause of cell death. We discuss possible mechanisms for the generation and accumulation of reactive oxygen species under B deprivation.Key words: boron deficiency, cell death, cell wall, oxidative damage, pectic polysaccharides, rhamnogalacturonan II, tobaccoBoron (B) deficiency is the most widespread micronutrient deficiency around the world and causes large losses in crop production both quantitatively and qualitatively.¹ Boron deficiency affects vegetative and reproductive growth of plants resulting in inhibition of cell expansion, death of meristem and reduced fertility.²Plants contain B both in a water-soluble and insoluble form. In intact plants, the amount of water-soluble B fluctuates with the quantity of B supplied, while insoluble B does not.³ The appearance of B deficiency symptoms coincides with the decrease of water-insoluble B, from which it is concluded that the insoluble B is the functional form while the soluble B represents the surplus. We found at least 98% of the insoluble B in tobacco cells bound to the cell wall,⁴ and identified their molecular entity as the borate diester with rhamnogalacturonan II (RG-II) regions of pectic polysaccharides.⁵ The diester crosslinks pectic polysaccharides to form a network and thereby contributes to construction of a supramolecular cell wall structure.⁶ Mutant plants with altered RG-II structures are dwarf and sterile, indicating that the B-RG-II complex is essential for normal plant growth and development.⁷ Increasing evidence indicates that B is also essential for animals.⁸ The requirement for B in organisms lacking cell walls implies that B may also have additional roles in plants. To date, however, no molecule other than apiosyl residues in pectic polysaccharides has been demonstrated to form a borate ester which could be stable enough under physiological conditions. Thus it is reasonable to consider that B functions primarily, if not exclusively, as a structural component of the cell wall, and B deficiency symptoms arise from disturbance of the cell wall structure. How, then, does the disturbed cell wall structure lead to the damage and cell death that are observed under B deficiency? To understand the linkage, we have analyzed physiological changes of suspension-cultured tobacco (Nicotiana tabacum) BY-2 cells under B deficiency.When cells at the log phase of growth were transferred to B-free media, cell death was detectable as early as 12 h after the treatment. As cell walls play pivotal roles in plant development and growth, we assumed that the B deprivation, which probably causes aberrant cell wall structure, might induce programmed cell death (PCD) as an active response to eliminate damaged cells. Then we examined if the known biochemical hallmark of PCD could be observed in cells deprived of B (hereafter referred to as -B cells). However, internucleosomal DNA fragmentation, decrease in antioxidant content and antioxidant enzyme expression,⁹ or protection from death by cycloheximide, were not detected in these cells, suggesting that the cell death is necrosis. We found oxidative damage to be the direct and major cause of cell death, because -B cells contained more reactive oxygen species (ROS) than control cells, and because cell death was effectively suppressed by supplementing the media with lipophilic antioxidants. The deprivation treatment did not induce an oxidative burst, as the extracellular H₂O₂ concentration was not significantly different between -B and control cells at all time points examined. Resupply of B immediately suppressed cell death. Collectively, these results suggest that low but persistent ROS production occurred under the -B condition.In the study described above, we demonstrated that B deprivation, and hence probably a defective cell wall structure, leads to oxidative damage. How and why B deprivation induces ROS overproduction remains to be clarified. We hypothesize that ROS are originally produced as a signal for disturbance of the cell wall structure, and build up to a toxic level unless B is resupplied and the cell wall structure is restored. It has been reported that the mechanical strength of the squash root cell wall decreases within minutes after B deprivation.^10,11 The mechanical change could be brought about by insufficient crosslinking of pectic polysaccharides at RG-II regions, as the B-RG-II complex significantly contributes to the wall tensile strength.¹² If the cell wall becomes weaker and less resistant to turgor, then the plasma membrane would stretch. The change may lead to opening of mechanosensitive channels¹³ and generation of signals for the altered cell wall structure. To test this hypothesis, we are now analyzing the immediate and early responses of tobacco BY-2 cells to B deprivation, and preliminary results do indicate the involvement of Ca²⁺ influx in the responses. Identification of the mechanism by which cells sense the external B status will greatly contribute to our understanding of the cell wall-symplast interaction in plants.¹⁴