Novel dextranase catalyzing cycloisomaltooligosaccharide formation and identification of catalytic amino acids and their functions using chemical rescue approach

A novel endodextranase from Paenibacillus sp. (Paenibacillus sp. dextranase; PsDex) was found to mainly produce isomaltotetraose and small amounts of cycloisomaltooligosaccharides (CIs) with a degree of polymerization of 7–14 from dextran. The 1,696-amino acid sequence belonging to the glycosyl hydrolase family 66 (GH-66) has a long insertion (632 residues; Thr⁴⁵¹–Val¹⁰⁸²), a portion of which shares identity (35% at Ala³⁹–Ser¹³⁰⁴ of PsDex) with Pro³²–Ala⁷⁵⁵ of CI glucanotransferase (CITase), a GH-66 enzyme that catalyzes the formation of CIs from dextran. This homologous sequence (Val⁸³⁷–Met⁹³² for PsDex and Tyr⁴⁰⁴–Tyr⁴⁹² for CITase), similar to carbohydrate-binding module 35, was not found in other endodextranases (Dexs) devoid of CITase activity. These results support the classification of GH-66 enzymes into three types: (i) Dex showing only dextranolytic activity, (ii) Dex catalyzing hydrolysis with low cyclization activity, and (iii) CITase showing CI-forming activity with low dextranolytic activity. The fact that a C-terminal truncated enzyme (having Ala³⁹–Ser¹³⁰⁴) has 50% wild-type PsDex activity indicates that the C-terminal 392 residues are not involved in hydrolysis. GH-66 enzymes possess four conserved acidic residues (Asp¹⁸⁹, Asp³⁴⁰, Glu⁴¹², and Asp¹²⁵⁴ of PsDex) of catalytic candidates. Their amide mutants decreased activity (1/1, 500 to 1/40, 000 times), and D1254N had 36% activity. A chemical rescue approach was applied to D189A, D340G, and E412Q using α-isomaltotetraosyl fluoride with NaN₃. D340G or E412Q formed a β- or α-isomaltotetraosyl azide, respectively, strongly indicating Asp³⁴⁰ and Glu⁴¹² as a nucleophile and acid/base catalyst, respectively. Interestingly, D189A synthesized small sized dextran from α-isomaltotetraosyl fluoride in the presence of NaN₃.     

Novel Phorbol Ester-binding Motif Mediates Hormonal Activation of Na+/H+ Exchanger

Protein kinase C (PKC) is considered crucial for hormonal Na⁺/H⁺ exchanger (NHE1) activation because phorbol esters (PEs) strongly activate NHE1. However, here we report that rather than PKC, direct binding of PEs/diacylglycerol to the NHE1 lipid-interacting domain (LID) and the subsequent tighter association of LID with the plasma membrane mainly underlies NHE1 activation. We show that (i) PEs directly interact with the LID of NHE1 in vitro, (ii) like PKC, green fluorescent protein (GFP)-labeled LID translocates to the plasma membrane in response to PEs and receptor agonists, (iii) LID mutations markedly inhibit these interactions and PE/receptor agonist-induced NHE1 activation, and (iv) PKC inhibitors ineffectively block NHE1 activation, except staurosporin, which itself inhibits NHE1 via LID. Thus, we propose a PKC-independent mechanism of NHE1 regulation via a PE-binding motif previously unrecognized.     

Interactive effects of elevated CO2, phosphorus deficiency, and soil drought on nodulation and nitrogenase activity in Alnus hirsuta and Alnus maximowiczii

We examined the interactive effects of elevated CO₂, soil phosphorus (P) availability, and soil drought on nodulation, nitrogenase activity, and biomass allocation in Alnus hirsuta and Alnus maximowiczii. Potted seedlings were grown in either ambient or elevated CO₂ (36 Pa and 72 Pa CO₂), with different levels of P (7.7 and 0.77 mgP pot^?1 week^?1 for high-P and low-P, respectively) and water supply in a natural daylight phytotron. Measurements of nitrogenase activity by an acetylene reduction assay failed to reveal significant effects of the treatments in any species. In high-P, nodule biomass increased under elevated CO₂ and decreased under drought. In low-P, nodule biomass decreased substantially compared to high-P, but the effect of elevated CO₂ on nodule biomass was unclear. Soil drought increased the partitioning of biomass into nodules, especially in A. hirsuta. These results suggest that with high P availability, elevated CO₂ could promote N₂ fixation by increasing nodule biomass even under drought. On the other hand, if soil P is limiting, elevated CO₂ may not enhance N₂ fixation because of the suppression of growth.     

Haprin‐deficient spermatozoa are incapable of in vitro fertilization

Haprin (TRIM36) is a ubiquitin‐protein ligase that mediates ubiquitination and subsequent proteasomal degradation of target proteins. It is expressed in the testes in both mice and humans and is thought to be involved in spermiogenesis, the acrosome reaction, and fertilization. However, the functional role of Haprin is poorly understood. The aim of this study was to investigate the physiological role of Haprin in fertility. Homozygous haprin‐deficient mice were generated and these mice, and their spermatozoa, were analyzed to detect morphological and fertility‐related abnormalities. In these models, normal spermatogenesis was observed but sperm quality was reduced with haprin‐deficient mice having poorer sperm morphology and motility than wild‐type mice. Interestingly, haprin‐deficient mice showed normal in vivo fertility but could not fertilize oocytes under standard in vitro fertilization conditions. In conclusion, this study demonstrated that Haprin deficiency causes morphological abnormalities in spermatozoa, indicating that Haprin is involved in spermiogenesis.     

Constant ratio of Cc to Ci under various CO2 concentrations and light intensities,and during progressive drought,in seedlings of Japanese white birch

Photosynthesis Research - Constant mesophyll conductance (gm), and two-resistance gm model (involved in resistances of cell wall and chloroplast), where gm reaches maximum under higher CO2...     

Proteomic identification of differentially expressed genes during differentiation of cynomolgus monkey (Macaca fascicularis) embryonic stem cells to astrocyte progenitor cells in vitro

Understanding astrocytogenesis is valuable for the treatment of nervous system disorders, as astrocytes provide structural, metabolic and defense support to neurons, and regulate neurons actively. However, there is limited information about the molecular events associated with the differentiation from primate ES cells to astrocytes. We therefore investigated the differentially expressed proteins in early astrocytogenesis, from cynomolgus monkey ES cells (CMK6 cell line) into astrocyte progenitor (AstP) cells via the formation of primitive neural stem spheres (Day 4), mature neural stem spheres (NSS), and neural stem (NS) cells in vitro, using two-dimensional gel electrophoresis (2-DE) and liquid chromatography-tandem mass spectrometry (LC-MS-MS). We identified 66 differentially expressed proteins involved in these five differentiation stages. Together with the results of Western blotting, RT-PCR, and a search of metabolic pathways related to the identified proteins, these results indicated that collapsin response mediator protein 2 (CRMP2), its phosphorylated forms, and cellular retinoic acid binding protein 1 (CRABP1) were upregulated from ES cells to Day 4 and NSS cells, to which differentiation stages apoptosis-associated proteins such as caspases were possibly related; Phosphorylated CRMP2s were further upregulated but CRABP1 was downregulated from NSS cells to NS cells, during which differentiation stage considerable axon guidance proteins for development of growth cones, axon attraction, and repulsion were possibly readied; Nonphosphorylated CRMP2 was downregulated but CRABP1 was re-upregulated from NS cells to AstP cells, in which differentiation stage reorganization of actin cytoskeleton linked to focal adhesion was possibly accompanied. These results provide insight into the molecular basis of early astrocytogenesis in monkey.     

CyClus: A fast,comprehensive cylindrical interface approximation clustering/reranking method for rigid‐body protein–protein docking decoys

We propose a fast clustering and reranking method, CyClus, for protein–protein docking decoys. This method enables comprehensive clustering of whole decoys generated by rigid‐body docking using cylindrical approximation of the protein–proteininterface and hierarchical clustering procedures. We demonstrate the clustering and reranking of 54,000 decoy structures generated by ZDOCK for each complex within a few minutes. After parameter tuning for the test set in ZDOCK benchmark 2.0 with the ZDOCK and ZRANK scoring functions, blind tests for the incremental data in ZDOCK benchmark 3.0 and 4.0 were conducted. CyClus successfully generated smaller subsets of decoys containing near‐native decoys. For example, the number of decoys required to create subsets containing near‐native decoys with 80% probability was reduced from 22% to 50% of the number required in the original ZDOCK. Although specific ZDOCK and ZRANK results were demonstrated, the CyClus algorithm was designed to be more general and can be applied to a wide range of decoys and scoring functions by adjusting just two parameters, p and T. CyClus results were also compared to those from ClusPro. Proteins 2013; © 2012 Wiley Periodicals, Inc.     

Intermolecular Interaction of Fluoro Propanes

Abstract

Intermolecular interaction is investigated for an isomeric pair of fluoro propane, CH₃CF₂CF₃ (HFC–245cb, CB) and CH₂FCF₂CHF₂ (HFC–245ca, CA). CB has a larger dipole moment than CA. This may suggest that CB has a larger intermolecular attractive interaction than CA; the reverse is, however, found from the experimental data: normal boiling point, critical temperature, and heat of vaporization. Systematic ab initio calculations have been done for both CB dimer and CA dimer, and confirmed that the former has a smaller attractive interaction than the latter.

On the basis of these calculations, analytic functions have been constructed as the pair potential models for the two isomers. Each of these models has 11 Lennard-Jones and Coulomb interaction sites in the molecule. The present models can explain why CB dimer has a smaller attractive interaction than CA dimer, and they will easily be extended to a series of fluoro propanes, and make it possible to perform the systematic molecular simulation studies.     

Water-soluble Polysaccharides in Bamboo Shoot

The enzyme system from Streptomyces sp. W19–1 formed several kinds of transfer products (TPs) when incubated in the presence of both stevioside (ST) and curdlan. Three of the major TPs (A, B, and C) were separated and purified using HP-20 column chromatography, gel filtration on TOYOPEARL HW-40F, and preparative high-performance liquid chromatography.

The structures of the three were identified by chemical and enzymatic methods; A is 13-O-β-sophorosyl-19-O-β-laminaribiosyl steviol, B is 13-O-β-3²-β-glucosylsophorosyl-19-O-β-glucosyl steviol, and C is 13-O-β-sophorosyl-19-O-β-laminaritriosyl steviol. The three were obtained for the first time in a pure state.     

Alkaloid constituents from flower buds and leaves of sacred lotus (Nelumbo nucifera,Nymphaeaceae) with melanogenesis inhibitory activity in B16 melanoma cells

Methanolic extracts from the flower buds and leaves of sacred lotus (Nelumbo nucifera, Nymphaeaceae) were found to show inhibitory effects on melanogenesis in theophylline-stimulated murine B16 melanoma 4A5 cells. From the methanolic extracts, a new alkaloid, N-methylasimilobine N-oxide, was isolated together with eleven benzylisoquinoline alkaloids. The absolute stereostructure of the new alkaloid was determined from chemical and physicochemical evidence. Among the constituents isolated, nuciferine, N-methylasimilobine, (?)-lirinidine, and 2-hydroxy-1-methoxy-6a,7-dehydroaporphine showed potent inhibition of melanogenesis. Comparison of the inhibitory activities of synthetic related alkaloids facilitated characterization of the structure-activity relationships of aporphine- and benzylisoquinoline-type alkaloids. In addition, 3–30 μM nuciferine and N-methylasimilobine inhibited the expression of tyrosinase mRNA, 3–30 μM N-methylasimilobine inhibited the expression of TRP-1 mRNA, and 10–30 μM nuciferine inhibited the expression of TRP-2 mRNA.