Attachment of an NMR-invisible solubility enhancement tag using a sortase-mediated protein ligation method

Sample solubility is essential for structural studies of proteins by solution NMR. Attachment of a solubility enhancement tag, such as GB1, MBP and thioredoxin, to a target protein has been used for this purpose. However, signal overlap of the tag with the target protein often made the spectral analysis difficult. Here we report a sortase-mediated protein ligation method to eliminate NMR signals arising from the tag by preparing the isotopically labeled target protein attached with the non-labeled GB1 tag at the C-terminus. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

CO2 reduction potentials by utilizing waste plastics in steel works

Background, aim, and scope  Feedstock recycling has received attention as an effective method to recycle waste plastics. However, estimating the reduction potential by life cycle assessment using coke oven and blast furnace in steel works has been a challenging task due to the complex structure of energy flow in steel works. Municipal waste plastics consist of several plastic resins. Previous studies have generally disregarded the composition of waste plastics, which varies significantly depending on the geographical area. If the reduction potentials by using each plastic resin in steel works can be quantified, the potential of municipal waste plastics (mixtures of plastic resins) can be estimated by summing up the potential of each resin multiplied by the composition of each resin in municipal waste plastics. Therefore, the goal of this study is to investigate the reduction potentials of CO₂ emissions by using individual plastic resins (polyethylene (PE), polypropylene (PP), polystyrene (PS), polyethylene terephthalate (PET)) and those for municipal waste plastics in the coke oven and blast furnace. Materials and methods  A model was developed to clarify the energy flow in steel works. In order to estimate the changes in energy and material balance in coke ovens when waste plastics are charged, the equations to calculate the coke product yield, gas product yield, and oil product yields of each plastic resin were derived from previous studies. The Rist model was adopted to quantify the changes in the inputs and outputs when plastics were fed into a blast furnace. Then, a matrix calculation method was used to calculate the change in energy balance before and after plastics are fed into a coke oven. Results  It was confirmed that product yields of municipal waste plastics (mixtures of plastic resins) could be estimated by summing up the product yield of each plastic resin multiplied by the composition of each resin in municipal waste plastics. In both cases of coke oven and blast furnace feedstock recycling, the reduction potential of CO₂ emissions varies significantly depending on the plastic resins. For example, in the case of coke oven chemical feedstock recycling, the reduction potential of PS and PP is larger than that of PE. On the other hand, in the case of blast furnace feedstock recycling, PE has the largest CO₂ emissions reduction potential, whereas the CO₂ emission reduction potential of PP is smaller than those of PE and PS. In both cases, PET has negative CO₂ emission reduction potentials, i.e., there is an increase of CO₂ emissions. In addition, the reduction potentials of CO₂ emissions are slightly different in each city. Discussions  The differences in the reduction potentials of CO₂ emissions by coke oven chemical feedstock recycling of each plastic resin is attributable to the differences in calorific values and coke product yields of each plastic resin. On the other hand, the difference in the CO₂ emission reduction potential for each plastic resin in blast furnace feedstock recycling is attributable to the difference in calorific values and the carbon and hydrogen content of each plastic resin, which leads to a difference in the coke substitution effect by each plastic resin. In both cases, the difference in those of municipal waste plastics is mostly attributable to the amount of impurities (e.g., ash, water) in the municipal waste plastics. Conclusions  It was found that the reduction potential of CO₂ emissions by coke oven and blast furnace feedstock recycling of municipal waste plastics (mixtures of plastic resins) could be estimated by summing up the potential of each resin multiplied by the composition of each resin in municipal waste plastics. It was also clarified that feedstock recycling of waste plastic in steel works is effective for avoiding the increase in CO₂ emissions by incinerating waste plastics, such as those from household mixtures of different resins. Recommendations and perspectives  With the results obtained in this study, reduction potentials of CO₂ emissions can be calculated for any waste plastics because differences in composition are taken into account.     

A locus conferring resistance to Colletotrichum higginsianum is shared by four geographically distinct Arabidopsis accessions

Colletotrichum higginsianum is a hemibiotrophic fungal pathogen that causes anthracnose disease on Arabidopsis and other crucifer hosts. By exploiting natural variation in Arabidopsis we identified a resistance locus that is shared by four geographically distinct accessions (Ws‐0, Kondara, Gifu‐2 and Can‐0). A combination of quantitative trait loci (QTL) and Mendelian mapping positioned this locus within the major recognition gene complex MRC‐J on chromosome 5 containing the Toll‐interleukin‐1 receptor/nucleotide‐binding site/leucine‐rich repeat (TIR‐NB‐LRR) genes RPS4 and RRS1 that confer dual resistance to C. higginsianum in Ws‐0 ( Narusaka et al., 2009 ). We find that the resistance shared by these diverse Arabidopsis accessions is expressed at an early stage of fungal invasion, at the level of appressorial penetration and establishment of intracellular biotrophic hyphae, and that this determines disease progression. Resistance is not associated with host hypersensitive cell death, an oxidative burst or callose deposition in epidermal cells but requires the defense regulator EDS1, highlighting new functions of TIR‐NB‐LRR genes and EDS1 in limiting early establishment of fungal biotrophy. While the Arabidopsis accession Ler‐0 is fully susceptible to C. higginsianum infection, Col‐0 displays intermediate resistance that also maps to MRC‐J. By analysis of null mutants of RPS4 and RRS1 in Col‐0 we show that these genes, individually, do not contribute strongly to C. higginsianum resistance but are both required for resistance to Pseudomonas syringae bacteria expressing the Type III effector, AvrRps4. We conclude that distinct allelic forms of RPS4 and RRS1 probably cooperate to confer resistance to different pathogens.     

Structural characterization of an O-linked tetrasaccharide from Pseudomonas syringae pv. tabaci flagellin

The flagellin of Pseudomonas syringae pv. tabaci is a glycoprotein that contains O-linked oligosaccharides composed of rhamnosyl and 4,6-dideoxy-4-(3-hydroxybutanamido)-2-O-methylglucosyl residues. These O-linked glycans are released by hydrazinolysis and then labeled at their reducing ends with 2-aminopyridine (PA). A PA-labeled trisaccharide and a PA-labeled tetrasaccharide are isolated by normal-phase high-performance liquid chromatography. These oligosaccharides are structurally characterized using mass spectrometry and NMR spectroscopy. Our data show that P. syringae pv. tabaci flagellin is glycosylated with a tetrasaccharide, 4,6-dideoxy-4-(3-hydroxybutanamido)-2-O-methyl-Glcp-(1→3)-α-l-Rhap-(1→2)-α-l-Rhap-(1→2)-α-l-Rha-(1→, as well a trisaccharide, 4,6-dideoxy-4-(3-hydroxybutanamido)-2-O-methyl-Glcp-(1→3)-α-l-Rhap-(1→2)-α-l-Rha-(1→, which was identified in a previous study.     

Role of CCN,a vertebrate specific gene family,in development

The CCN family of genes constitutes six members of small secreted cysteine rich proteins, which exists only in vertebrates. The major members of CCN are CCN1 (Cyr61), CCN2 (CTGF), and CCN3 (Nov). CCN4, CCN5, and CCN6 were formerly reported to be in the Wisp family, but they are now integrated into CCN due to the resemblance of their four principal modules: insulin like growth factor binding protein, von Willebrand factor type C, thrombospondin type 1, and carboxy‐terminal domain. CCNs show a wide and highly variable expression pattern in adult and in embryonic tissues, but most studies have focused on their principal role in osteo/chondrogenesis and vasculo/angiogenesis from the aspect of migration, growth, and differentiation of mesenchymal cells. CCN proteins simultaneously integrate and modulate the signals of integrins, bone morphogenetic protein, vascular endothelial growth factor, Wnt, and Notch by direct binding. However, the priority in the use of the signals is different depending on the cell status. Even the equivalent counterparts show a difference in signal usage among species. It may be that the evolution of the CCN family continues to keep pace with vertebrate evolution itself.     

Mesenchymal to embryonic incomplete transition of human cells by chimeric OCT4/3 (POU5F1) with physiological co-activator EWS

POU5F1 (more commonly known as OCT4/3) is one of the stem cell markers, and affects direction of differentiation in embryonic stem cells. To investigate whether cells of mesenchymal origin acquire embryonic phenotypes, we generated human cells of mesodermal origin with overexpression of the chimeric OCT4/3 gene with physiological co-activator EWS (product of the EWSR1 gene), which is driven by the potent EWS promoter by translocation. The cells expressed embryonic stem cell genes such as NANOG, lost mesenchymal phenotypes, and exhibited embryonal stem cell-like alveolar structures when implanted into the subcutaneous tissue of immunodeficient mice. Hierarchical analysis by microchip analysis and cell surface analysis revealed that the cells are subcategorized into the group of human embryonic stem cells and embryonal carcinoma cells. These results imply that cells of mesenchymal origin can be traced back to cells of embryonic phenotype by the OCT4/3 gene in collaboration with the potent cis-regulatory element and the fused co-activator. The cells generated in this study with overexpression of chimeric OCT4/3 provide us with insight into cell plasticity involving OCT4/3 that is essential for embryonic cell maintenance, and the complexity required for changing cellular identity.     

Photo-immobilization of biological components on gold-coated chips for measurements using surface plasmon resonance (SPR) and a quartz crystal microbalance (QCM)

The photo-immobilization technique is useful for immobilization of various biomolecules on assorted material surfaces, independent of the organic functional groups that may be present. Here, we report a convenient new photo-immobilization technique that was developed by combining a nonbiofouling polymer containing polyethylene glycol and a photoreactive crosslinker for surface plasmon resonance (SPR) and quartz crystal microbalance (QCM) measurements. By this method, nonspecific interactions were reduced and various types of molecules, bovine serum albumin, heparin, dsDNA, phosphatidylserine, Tobacco Mosaic Virus, and norfloxacine, were immobilized on an alkane thiol-modified gold surface by a single method. The interactions of photo-immobilized biomolecules and their corresponding antibodies were investigated by SPR and QCM. In addition, SPR imaging was possible using the present method.     

Involvement of Ca in globular adiponectin-induced reactive oxygen species

Globular adiponectin (gAd) induces the generation of reactive oxygen species (ROS) and nitric oxide (NO) in the murine macrophage cell line RAW 264. We investigated the role of Ca²⁺ in gAd-induced ROS and NO generation. Pretreatment with BAPTA-AM, a selective chelator of intracellular Ca²⁺ ([Ca²⁺]_i), partially reduced gAd-induced generation of ROS and NO in gAd-treated RAW 264 cells. The lowest [Ca²⁺]_i occurred 30 min after gAd treatment, after which [Ca²⁺]_i increased continually and exceeded the initial level. The mitochondrial Ca²⁺ ([Ca²⁺]_m) detected by Rhod-2 fluorescence started to increase at 6 h after gAd treatment. Pretreatment with a NAD(P)H oxidase inhibitor, diphenyleneiodonium, prevented the reduction of [Ca²⁺]_i in the early phase after gAd treatment. Calcium depletion by BAPTA-AM had no effect on the gAd-induced [Ca²⁺]_m oscillation. The administration of a specific calmodulin inhibitor, calmidazolium, significantly suppressed gAd-induced ROS and NO generation and NOS activity.     

Minocycline attenuates both OGD-induced HMGB1 release and HMGB1-induced cell death in ischemic neuronal injury in PC12 cells

High mobility group box-1 (HMGB1), a non-histone DNA-binding protein, is massively released into the extracellular space from neuronal cells after ischemic insult and exacerbates brain tissue damage in rats. Minocycline is a semisynthetic second-generation tetracycline antibiotic which has recently been shown to be a promising neuroprotective agent. In this study, we found that minocycline inhibited HMGB1 release in oxygen-glucose deprivation (OGD)-treated PC12 cells and triggered the activation of p38mitogen-activated protein kinase (MAPK) and extracellular signal-regulated kinases (ERK1/2). The ERK kinase (MEK)1/2 inhibitor U-0126 and p38MAPK inhibitor SB203580 blocked HMGB1 release in response to OGD. Furthermore, HMGB1 triggered cell death in a dose-dependent fashion. Minocycline significantly rescued HMGB1-induced cell death in a dose-dependent manner. In light of recent observations as well as the good safety profile of minocycline in humans, we propose that minocycline might play a potent neuroprotective role through the inhibition of HMGB1-induced neuronal cell death in cerebral infarction.     

Delayed liver regeneration after partial hepatectomy in adiponectin knockout mice

We previously demonstrated that adiponectin has anti-fibrogenic and anti-inflammatory effects in the liver of mouse models of various liver diseases. However, its role in liver regeneration remains unclear. The aim of this study was to determine the role of adiponectin in liver regeneration. We assessed liver regeneration after partial hepatectomy in wild-type (WT) and adiponectin knockout (KO) mice. We analyzed DNA replication and various signaling pathways involved in cell proliferation and metabolism. Adiponectin KO mice exhibited delayed DNA replication and increased lipid accumulation in the regenerating liver. The expression levels of peroxisome proliferator-activated receptor (PPAR) α and carnitine palmitoyltransferase-1 (CPT-1), a key enzyme in mitochondrial fatty acid oxidation, were decreased in adiponectin KO mice, suggesting possible contribution of altered fat metabolism to these phenomena. Collectively, the present results highlight a new role for adiponectin in the process of liver regeneration.