A glycosynthase derived from an inverting chitinase with an extended binding cleft
We created a glycosynthase from a GH19 chitinase from rye seeds (RSC-c), that has a long-extended binding cleft consisting of eight subsites; -4, -3, -2, -1, +1, +2, +3 and +4. When wild-type RSC-c was incubated with α-(GlcNAc)3-F [α-(GlcNAc)3 fluoride], (GlcNAc)3 and hydrogen fluoride were produced through the Hehre resynthesis–hydrolysis mechanism. Glu89, which acts as a catalytic base, and Ser120, which fixes a nucleophilic water molecule, were mutated to produce two single mutants, E89G and S120A, and a double mutant, E89G/S120A. E89G only produced a small amount of (GlcNAc)7 from α-(GlcNAc)3-F ...
Source: Journal of Biochemistry - July 27, 2016 Category: Biochemistry Authors: Ohnuma, T., Dozen, S., Honda, Y., Kitaoka, M., Fukamizo, T. Tags: Regular Papers Source Type: research
Subgroup differences in 'brain-type transferrin and {alpha}-synuclein in Parkinsons disease and multiple system atrophy
Two transferrin (Tf) glycan-isoforms were previously found in cerebrospinal fluid (CSF); one appears to be derived from serum (Tf-2) and the other from choroid plexus, a CSF-producing tissue (Tf-1). To analyse metabolic differences associated with the two isoforms, their ratio (Tf-2/Tf-1) was defined as the Tf index. Here we report that Tf indices of patients with tauopathies including Alzheimer’s disease (2.29 + 0.64) were similar to those of neurological controls (2.07 + 0.87) (P = 0.147). In contrast, Tf indices with Parkinson’s disease (PD, 3.38 ± 1.87) and multiple system atrophy (MSA, 3.15 ±...
Source: Journal of Biochemistry - July 27, 2016 Category: Biochemistry Authors: Yoshihara, A., Fukatsu, M., Hoshi, K., Ito, H., Nollet, K., Yamaguchi, Y., Ishii, R., Tokuda, T., Miyajima, M., Arai, H., Kato, T., Furukawa, K., Arai, H., Kikuchi, A., Takeda, A., Ugawa, Y., Hashimoto, Y. Tags: Regular Papers Source Type: research
Retrograde transport of neurotrophic factor signaling: implications in neuronal development and pathogenesis
Neurotrophic factors and their receptors play a central role in neuronal survival. Since neurons have a highly polarized morphology, target-derived neurotrophic factor signaling is transported retrogradely along the axon to the cell body. A body of evidence suggests that retrograde transport of the neurotrophic factors and their receptors is required for signal propagation. Retrograde transport of neurotrophic factor signaling is crucial not only for neuronal development, but also for preventing neuronal degeneration. Thus, elucidating the mechanism of retrograde transport will lead to insights into the developmental mecha...
Source: Journal of Biochemistry - July 27, 2016 Category: Biochemistry Authors: Ito, K., Enomoto, H. Tags: JB Reviews Source Type: research
Importin {alpha}: a key molecule in nuclear transport and non-transport functions
Importin α performs the indispensable role of ferrying proteins from the cytoplasm into the nucleus with a transport carrier, importin β1. Mammalian cells from mouse or human contain either six or seven importin α subtypes, respectively, each with a tightly regulated expression. Therefore, the combination of subtype expression in a cell defines distinct signaling pathways to achieve progressive changes in gene expression essential for cellular events, such as differentiation. Recent studies reveal that, in addition to nucleocytoplasmic transport, importin αs also serve non-transport functions. In thi...
Source: Journal of Biochemistry - July 27, 2016 Category: Biochemistry Authors: Miyamoto, Y., Yamada, K., Yoneda, Y. Tags: JB Reviews Source Type: research
Expression and characterization of EF-hand I loop mutants of aequorin replaced with other loop sequences of Ca2+-binding proteins: an approach to studying the EF-hand motif of proteins
The binding properties of Ca2+ to EF-hand I of aequorin (AQ) were characterized by replacing the loop sequence of EF-hand I (AQ[I]) with other known loop sequences of Ca2+-binding proteins, including photoproteins (aequorin, clytin-I, clytin-II and mitrocomin), Renilla luciferin-binding protein (RLBP) and calmodulin (CaM). For evaluation of the binding affinity of Ca2+ to AQ[I] mutants, the half-decay time of the maximum intensity in the luminescence reaction triggered by Ca2+ was used as an indicator and 22 kinds of AQ[I] mutants were expressed in Escherichia coli cells. AQ[I] mutants replaced with the EF-hand I and EF-ha...
Source: Journal of Biochemistry - June 23, 2016 Category: Biochemistry Authors: Inouye, S., Sahara-Miura, Y. Tags: Regular Papers Source Type: research
Suppression of mitochondrial transcription initiation complexes changes the balance of replication intermediates of mitochondrial DNA and reduces 7S DNA in cultured human cells
Analysis of replicating mammalian mitochondrial DNA (mtDNA) suggested that initiation of the replication occurs not only at the specific position, Ori-H but also across a broad zone in mtDNA. We investigated relationship of mitochondrial transcription initiation which takes place upstream of Ori-H and mtDNA replication initiation through analysing the effect of knockdown of mitochondrial transcription factor B2, TFB2M and mitochondrial RNA polymerase, POLRMT, components of the transcription initiation complexes in cultured human cells. Under the conditions where suppression of the transcription initiation complexes was ach...
Source: Journal of Biochemistry - June 23, 2016 Category: Biochemistry Authors: Qu, J., Yasukawa, T., Kang, D. Tags: Regular Papers Source Type: research
The repair capacity of lung cancer cell lines A549 and H1299 depends on HMGB1 expression level and the p53 status
Elucidation of the cellular components responsive to chemotherapeutic agents as cisplatin rationalizes the strategy for anticancer chemotherapy. The removal of the cisplatin/DNA lesions gives the chance to the cancer cells to survive and compromises the chemotherapeutical treatment. Therefore, the cell repair efficiency is substantial for the clinical outcome. High mobility group box 1 (HMGB1) protein is considered to be involved in the removal of the lesions as it binds with high affinity to cisplatin/DNA adducts. We demonstrated that overexpression of HMGB1 protein inhibited cis-platinated DNA repair in vivo and the effe...
Source: Journal of Biochemistry - June 23, 2016 Category: Biochemistry Authors: Yusein-Myashkova, S., Stoykov, I., Gospodinov, A., Ugrinova, I., Pasheva, E. Tags: Regular Papers Source Type: research
Two carbohydrate recognizing domains from Cycas revoluta leaf lectin show the distinct sugar-binding specificity--A unique mannooligosaccharide recognition by N-terminal domain
Cycas revoluta leaf lectin (CRLL) of mannose-recognizing jacalin-related lectin (mJRL) has two tandem repeated carbohydrate recognition domains, and shows the characteristic sugar-binding specificity toward high mannose-glycans, compared with other mJRLs. We expressed the N-terminal domain and C-terminal domain (CRLL-N and CRLL-C) separately, to determine the fine sugar-binding specificity of each domain, using frontal affinity chromatography, glycan array and equilibrium dialysis. The specificity of CRLL toward high mannose was basically derived from CRLL-N, whereas CRLL-C had affinity for α1-6 extended mono-antenna...
Source: Journal of Biochemistry - June 23, 2016 Category: Biochemistry Authors: Shimokawa, M., Haraguchi, T., Minami, Y., Yagi, F., Hiemori, K., Tateno, H., Hirabayashi, J. Tags: Regular Papers Source Type: research
(p)ppGpp-dependent and -independent pathways for salt tolerance in Escherichia coli
Addition of some kinds of translation inhibitors targeting the ribosome such as kasugamycin to the culture medium as well as removal of a ribosome maturation factor or a ribosomal protein provides Escherichia coli cells with tolerance to high salt stress. Here, we found that another kind of translation inhibitor, serine hydroxamate (SHX), which induces amino acid starvation leading to (p)ppGpp production, also has a similar effect, but via a different pathway. Unlike kasugamycin, SHX was not effective in (p)ppGpp-null mutant cells. SHX and depletion of RsgA, a ribosome maturation factor, had an additive effect on salt tole...
Source: Journal of Biochemistry - June 23, 2016 Category: Biochemistry Authors: Tarusawa, T., Ito, S., Goto, S., Ushida, C., Muto, A., Himeno, H. Tags: Regular Papers Source Type: research
Analysis of novel Sir3 binding regions in Saccharomyces cerevisiae
In Saccharomyces cerevisiae, the HMR, HML, telomere and rDNA regions are silenced. Silencing at the rDNA region requires Sir2, and silencing at the HMR, HML and telomere regions requires binding of a protein complex, consisting of Sir2, Sir3 and Sir4, that mediates repression of gene expression. Here, several novel Sir3 binding domains, termed CN domains (Chromosomal Novel Sir3 binding region), were identified using chromatin immunoprecipitation (ChIP) on chip analysis of S. cerevisiae chromosomes. Furthermore, analysis of G1-arrested cells demonstrated that Sir3 binding was elevated in G1-arrested cells compared with loga...
Source: Journal of Biochemistry - June 23, 2016 Category: Biochemistry Authors: Mitsumori, R., Ohashi, T., Kugou, K., Ichino, A., Taniguchi, K., Ohta, K., Uchida, H., Oki, M. Tags: Regular Papers Source Type: research
The diet-microbiota-metabolite axis regulates the host physiology
The intestinal microbiota has been implicated in a wide range of diseases, including inflammatory bowel disease, obesity and cancer. Food ingredients are considered a major determinant of gut microbial composition, as exemplified by high-fat diet-induced dysbiosis that can affect host physiology. Accumulating studies show that microbial metabolites are key regulators of the intestinal epithelial barrier and gut immunity. In particular, short-chain fatty acids produced by bacterial fermentation of indigestible polysaccharides have profound impacts on host physiology beyond the gut. In this review, we describe the influences...
Source: Journal of Biochemistry - June 23, 2016 Category: Biochemistry Authors: Yamada, T., Takahashi, D., Hase, K. Tags: JB Review Source Type: research
Transforming growth factor-{beta}1 induces invasion ability of HSC-4 human oral squamous cell carcinoma cells through the Slug/Wnt-5b/MMP-10 signalling axis
Molecular mechanism underlying the invasion of oral cancer cells remains to be clarified. We previously demonstrated that transforming growth factor-β1 (TGF-β1) induces the expression of mesenchymal markers in human oral squamous cell carcinoma HSC-4 cells. Intriguingly, the expression of the epithelial–mesenchymal transition-related transcription factor Slug was also significantly upregulated upon TGF-β1 stimulation. However, the mechanism by which Slug transduces the TGF-β1-induced signal to enhance the invasiveness of HSC-4 cells is poorly understood. Proteomic analysis revealed that the expres...
Source: Journal of Biochemistry - May 30, 2016 Category: Biochemistry Authors: Hino, M., Kamo, M., Saito, D., Kyakumoto, S., Shibata, T., Mizuki, H., Ishisaki, A. Tags: Regular Papers Source Type: research
Physicochemical and biological characterizations of Pxt peptides from amphibian (Xenopus tropicalis) skin
Pxt peptides (Pxt-1 through Pxt-12) have been isolated from amphibian, Xenopus tropicalis. Pxt-related peptides (Pxt-2, Pxt-5, Pxt-12, reverse Pxt-2, reverse Pxt-5 and reverse Pxt-12) with significant foaming properties were further characterized. In the physicochemical experiments, all Pxt-related peptides formed significant amphiphilic α-helices in 50% 2,2,2-trifluoroethanol by circular dichroism measurements. Among Pxt-related peptides, both Pxt-5 and reverse Pxt-5 were the most effective in reducing their surface tensions. Moreover, Pxt-2, Pxt-5 and reverse Pxt-5 produced constant surface tensions above their cri...
Source: Journal of Biochemistry - May 30, 2016 Category: Biochemistry Authors: Shigeri, Y., Horie, M., Yoshida, T., Hagihara, Y., Imura, T., Inagaki, H., Haramoto, Y., Ito, Y., Asashima, M. Tags: Regular Papers Source Type: research
KIAA0368-deficiency affects disassembly of 26S proteasome under oxidative stress condition
Many cellular stresses cause damages of intracellular proteins, which are eventually degraded by the ubiquitin and proteasome system. The proteasome is a multicatalytic protease complex composed of 20S core particle and the proteasome activators that regulate the proteasome activity. Extracellular mutants 29 (Ecm29) is a 200 kDa protein encoded by KIAA0368 gene, associates with the proteasome, but its role is largely unknown. Here, we generated KIAA0368-deficient mice and investigated the function of Ecm29 in stress response. KIAA0368-deficient mice showed normal peptidase activity and proteasome formation at normal condit...
Source: Journal of Biochemistry - May 30, 2016 Category: Biochemistry Authors: Haratake, K., Sato, A., Tsuruta, F., Chiba, T. Tags: Regular Papers Source Type: research
Purification and characterization of recombinant sugarcane sucrose phosphate synthase expressed in E. coli and insect Sf9 cells: an importance of the N-terminal domain for an allosteric regulatory property
Sucrose phosphate synthase (SPS) catalyses the transfer of glycosyl group of uridine diphosphate glucose to fructose-6-phosphate to form sucrose-6-phosphate. Plant SPS plays a key role in photosynthetic carbon metabolisms, which activity is modulated by an allosteric activator glucose-6-phosphate (G6P). We produced recombinant sugarcane SPS using Escherichia coli and Sf9 insect cells to investigate its structure-function relationship. When expressed in E. coli, two forms of SPS with different sizes appeared; the larger was comparable in size with the authentic plant enzyme and the shorter was trimmed the N-terminal 20 kDa ...
Source: Journal of Biochemistry - May 30, 2016 Category: Biochemistry Authors: Sawitri, W. D., Narita, H., Ishizaka-Ikeda, E., Sugiharto, B., Hase, T., Nakagawa, A. Tags: Regular Papers Source Type: research
