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1.  Reminiscence of our research on membrane phospholipids in mammalian cells by using the novel technology 
By using “our devised up-to-the-second technique” over 30 years ago, we succeeded in the first isolation in the world of the three different kinds of mammalian cell mutants defective in the biosynthesis on each of phosphatidylserine (PS), cardiolipin (CL) and sphingomyelin (SM) from the parental CHO cells. As the results, we found that during the biosyntheses of PS and SM, the biosynthetic precursor or the final lipids are transported from their synthesized intracellular organelles to the plasma membranes via the other intracellular organelles. We further clarified the presence of the reversed routes for PS and SM from the plasma membranes to their synthesized organelles too. Our first epoch-making finding is not only the cycling inter-conversion reactions between PS and PE catalyzed by PSS-II and PSD but also their simultaneous transferring between MAM and Mit (found by O. Kuge). Our second finding is “the ceramide-trafficking protein (CERT)” working as the specific transfer protein of ceramide from the ER to the Golgi apparatus, during the SM biosynthesis (by K. Hanada).
As for their new biological roles, we clarified possible contribution of PS and/or PE to the fusion process between viral envelope and endosomal membrane, releasing the genetic information of the virus to the host cytoplasm. CL is contributing to the functional NADH-ubiquinone reductase activity by keeping the right structure of Coenzyme Q9 for its functioning. SM and cholesterol form the microdomain within the plasma membrane, so-called “the raft structure” where the GPI-anchored proteins are specifically located for their functioning.
doi:10.2183/pjab.88.536
PMCID: PMC3552046  PMID: 23229749
membrane phospholipids (PS, CL and SM); mammalian cell mutants; biosynthetic regulation; biological roles; lipid transport; intracellular organelles
2.  Therapeutic targets in the ASK1-dependent stress signaling pathways 
Apoptosis signal-regulating kinase 1 (ASK1) is a member of the mitogen-activated protein kinase kinase kinase (MAP3K) family that activates downstream MAP kinases (MAPKs), c-Jun N-terminal kinases (JNKs) and p38 MAPKs, in response to various stresses, such as reactive oxygen species (ROS), endoplasmic reticulum (ER) stress, lipopolysaccharide, and calcium overload. Activation of the JNK and p38 pathways induces stress responses such as cell death, differentiation, and the production of inflammatory cytokines. A series of studies using ASK1-deficient mice have indicated that ASK1 plays important roles in many stress-related diseases, including cardiovascular and neurodegenerative diseases, suggesting that small compounds that inhibit ASK1 activity could possibly be used for the amelioration of the development and/or progression of these diseases. In this review, we provide an overview of the pathophysiological roles of ASK1-dependent signaling pathways and discuss the mechanistic basis for how these could serve as potential therapeutic targets.
doi:10.2183/pjab.88.434
PMCID: PMC3491083  PMID: 23060232
ASK1; inhibitors; MAP kinase; signal transduction; stress
3.  Synthesis of neoproteoglycans using the transglycosylation reaction as a reverse reaction of endo-glycosidases 
A method for the synthesis of carbohydrate chains (glycosaminoglycans) and their coupling to peptides was investigated using proteoglycans. Glycosidases generally catalyze a hydrolytic reaction, but can also mediate the reverse reaction, which in this case is a transglycosylation. In the transglycosylation reaction of bovine testicular hyaluronidase, which is an endoglycosidase, glycosaminoglycans (hyaluronan and chondroitin sulfates) release disaccharide (uronic acid-N-acetylhexosamine) moieties from non-reducing terminal sites, and then the liberated disaccharides are transferred immediately to the non-reducing termini of other glycosaminoglycan chains. Using such continuous reactions, it is possible to synthesize glycosaminoglycan chains according to a specific design. It then becomes possible to transfer glycosaminoglycan chains synthesized on a peptide to other peptides using the transglycosylation reaction of endo-β-xylosidase acting on the linkage region between a peptide and glycosaminoglycan chains of proteoglycans. We believe this approach will open a new field for the synthesis of homogeneous proteoglycans or their corresponding analogues.
doi:10.2183/pjab.88.327
PMCID: PMC3422686  PMID: 22850725
neoproteoglycan; glycosaminoglycan; hyaluronidase; endo-β-xylosidase; transglycosylation; sugar chain reconstruction
4.  Unnatural base pair systems toward the expansion of the genetic alphabet in the central dogma 
Toward the expansion of the genetic alphabet of DNA, several artificial third base pairs (unnatural base pairs) have been created. Synthetic DNAs containing the unnatural base pairs can be amplified faithfully by PCR, along with the natural A–T and G–C pairs, and transcribed into RNA. The unnatural base pair systems now have high potential to open the door to next generation biotechnology. The creation of unnatural base pairs is a consequence of repeating “proof of concept” experiments. In the process, initially designed base pairs were modified to address their weak points. Some of them were artificially evolved to ones with higher efficiency and selectivity in polymerase reactions, while others were eliminated from the analysis. Here, we describe the process of unnatural base pair development, as well as the tests of their applications.
doi:10.2183/pjab.88.345
PMCID: PMC3422687  PMID: 22850726
unnatural base pair; genetic alphabet; replication; transcription; translation; PCR
5.  Immunochemistry of pathogenic yeast, Candida species, focusing on mannan 
This review describes recent findings based on structural and immunochemical analyses of the cell wall mannan of Candida albicans, and other medically important Candida species. Mannan has been shown to consist of α-1,2-, α-1,3-, α-1,6-, and β-1,2-linked mannopyranose units with few phosphate groups. Each Candida species has a unique mannan structure biosynthesized by sequential collaboration between species-specific mannosyltransferases. In particular, the β-1,2-linked mannose units have been shown to comprise a characteristic oligomannosyl side chain that is strongly antigenic. For these pathogenic Candida species, cell-surface mannan was also found to participate in the adhesion to the epithelial cells, recognition by innate immune receptors and development of pathogenicity. Therefore, clarification of the precise chemical structure of Candida mannan is indispensable for understanding the mechanism of pathogenicity, and for development of new antifungal drugs and immunotherapeutic procedures.
doi:10.2183/pjab.88.250
PMCID: PMC3410142  PMID: 22728440
Candida; mannan; 1H NMR; mannosyltransferase; pathogenicity; Dectin-2
6.  Health-promoting effects of green tea 
Green tea is manufactured from the leaves of the plant Camellia sinensis Theaceae and has been regarded to possess anti-cancer, anti-obesity, anti-atherosclerotic, anti-diabetic, anti-bacterial, and anti-viral effects. Many of the beneficial effects of green tea are related to the activities of (−)-epigallocatechin gallate (EGCG), a major component of green tea catechins. For about 20 years, we have engaged in studies to reveal the biological activities and action mechanisms of green tea and EGCG. This review summarizes several lines of evidence to indicate the health-promoting properties of green tea mainly based on our own experimental findings.
doi:10.2183/pjab.88.88
PMCID: PMC3365247  PMID: 22450537
green tea; catechin; health promotion; molecular mechanism; gene expression
7.  Peculiarity of methoxy group-substituted phenylhydrazones in Fischer indole synthesis 
We found that the Fischer indole synthesis of ethyl pyruvate 2-methoxyphenylhydrazone (5) with HCl/EtOH gave an abnormal product, ethyl 6-chloroindole-2-carboxylate (7), as the main product, with a smaller amount of ethyl 7-methoxyindole-2-carboxylate (6) as the normal product. This abnormal reaction was the result of a cyclization on the side with the substituent (methoxy group) of a benzene ring on phenylhydrazone, which was not previously observed. In this initial investigation, we focused on 1) the application of the above-mentioned abnormal Fischer indole synthesis, 2) the details of this reaction of phenylhydrazone with other kinds of substituents, 3) the mechanism of the first step of the Fischer indole synthesis, 4) the abnormal reaction in methoxydiphenylhydrazones, and 5) a synthetic device to avoid an abnormal reaction. The results of these studies are summarized herein.
doi:10.2183/pjab.88.1
PMCID: PMC3278968  PMID: 22241067
Fischer indole synthesis; methoxy group; abnormal reaction; phenylhydrazone; reaction mechanism; natural product
8.  Comparative gene expression profiling of placentas from patients with severe pre-eclampsia and unexplained fetal growth restriction 
Background
It has been well documented that pre-eclampsia and unexplained fetal growth restriction (FGR) have a common etiological background, but little is known about their linkage at the molecular level. The aim of this study was to further investigate the mechanisms underlying pre-eclampsia and unexplained FGR.
Methods
We analyzed differentially expressed genes in placental tissue from severe pre-eclamptic pregnancies (n = 8) and normotensive pregnancies with or (n = 8) without FGR (n = 8) using a microarray method.
Results
A subset of the FGR samples showed a high correlation coefficient overall in the microarray data from the pre-eclampsia samples. Many genes that are known to be up-regulated in pre-eclampsia are also up-regulated in FGR, including the anti-angiogenic factors, FLT1 and ENG, believed to be associated with the onset of maternal symptoms of pre-eclampsia. A total of 62 genes were found to be differentially expressed in both disorders. However, gene set enrichment analysis for these differentially expressed genes further revealed higher expression of TP53-downstream genes in pre-eclampsia compared with FGR. TP53-downstream apoptosis-related genes, such as BCL6 and BAX, were found to be significantly more up-regulated in pre-eclampsia than in FGR, although the caspases are expressed at equivalent levels.
Conclusions
Our current data indicate a common pathophysiology for FGR and pre-eclampsia, leading to an up-regulation of placental anti-angiogenic factors. However, our findings also suggest that it may possibly be the excretion of these factors into the maternal circulation through the TP53-mediated early-stage apoptosis of trophoblasts that leads to the maternal symptoms of pre-eclampsia.
doi:10.1186/1477-7827-9-107
PMCID: PMC3199758  PMID: 21810232
9.  2-Aminophenoxazine-3-one and 2-amino-4,4α-dihydro-4α,7-dimethyl-3H-phenoxazine-3-one cause cellular apoptosis by reducing higher intracellular pH in cancer cells 
We examined intracellular pH (pHi) of ten cancer cell lines derived from different organs and two normal cell lines including human embryonic lung fibroblast cells (HEL) and human umbilical vein endothelial cells (HUVEC) in vitro, and found that pHi of most of these cancer cells was evidently higher (pH 7.5 to 7.7) than that of normal cells (7.32 and 7.44 for HEL and HUVEC, respectively) and that of primary leukemic cells and erythrocytes hitherto reported (≤7.2). Higher pHi in these cancer cells could be related to the Warburg effect in cancer cells with enhanced glycolytic metabolism. Since reversal of the Warburg effect may perturb intracellular homeostasis in cancer cells, we looked for compounds that cause extensive reduction of pHi, a major regulator of the glycolytic pathway and its associated metabolic pathway. We found that phenoxazine compounds, 2-aminophenoxazine-3-one (Phx-3) and 2-amino-4,4α-dihydro-4α,7-dimethyl-3H-phenoxazine-3-one (Phx-1) caused a rapid and drastic dose-dependent decrease of pHi in ten different cancer cells within 30 min, though the extent of the decrease of pHi was significantly larger for Phx-3 (ΔpHi = 0.6 pH units or more for 100 µM Phx-3) than for Phx-1 (ΔpHi = 0.1 pH units or more for 100 µM Phx-1). This rapid and drastic decrease of pHi in a variety of cancer cells caused by Phx-3 and Phx-1 possibly perturbed their intracellular homeostasis, and extensively affected the subsequent cell death, because these phenoxazines exerted dose-dependent proapoptotic and cytotoxic effects on these cells during 72 h incubation, confirming a causal relationship between ΔpHi and cytotoxic effects due to Phx-3 and Phx-1. Phx-3 and Phx-1 also reduced pHi of normal cells including HEL and HUVEC, although they exerted less proapoptotic and cytotoxic effects on these cells than on cancer cells. Drugs such as Phx-3 and Phx-1 that reduce pHi and thereby induce cellular apoptosis might serve as benevolent anticancer drugs.
doi:10.2183/pjab.87.199
PMCID: PMC3149379  PMID: 21558757
phenoxazines; cancer cells; intracellular pH; apoptosis
10.  Development of modified nucleosides that have supremely high anti-HIV activity and low toxicity and prevent the emergence of resistant HIV mutants 
An idea to use 4′-C-substituted-2′-deoxynucleoside derivatives was proposed based on a working hypothesis to solve the problems of existing acquired immune deficiency syndrome chemotherapy (highly active antiretroviral therapy). Subsequent studies have successfully proved the validity of the idea and resulted in the development of 2′-deoxy-4′-C-ethynyl-2-fluoroadenosine and 2′-deoxy-4′-C-ethynyl-2-chloroadenosine, nucleoside reverse transcriptase inhibitors, which have supremely high activity against all human immunodeficiency viruses including multidrug-resistant HIV and low toxicity.
doi:10.2183/pjab.87.53
PMCID: PMC3066546  PMID: 21422739
AIDS; anti-HIV agent; nucleoside reverse transcriptase inhibitor; drug-resistant HIV; 4′-C-substituted-2′-deoxynucleoside
11.  Structure-based development of specific inhibitors for individual cathepsins and their medical applications 
Specific inhibitors for individual cathepsins have been developed based on their tertiary structures of X-ray crystallography. Cathepsin B-specific inhibitors, CA-074 and CA-030, and cathepsin L specific inhibitors, CLIK-148 and CLIK-195, were designed as the epoxysuccinate derivatives. Cathepsin S inhibitor, CLIK-060, and cathepsin K inhibitor, CLIK-166, were synthesized. These inhibitors can use in vitro and also in vivo, and show no toxicity for experimental animals by the amounts used as the cathepsin inhibitor.
Various cathepsins are used in the processing of antigenic proteins. The CLIK-060 treatment to the autoimmune disease, Sjögren model mice, led to strongly suppress the expression of the pathological symptoms. Cathepsins L or K participates to the degradation of bone collagen. The CLIK-148 protects osteoporosis in animals and also protects the bone metastasis of cancer cells. Cathepsin L also enhances insulin-induced glucose uptake into 3T3-L1 adipocytes, suggesting cathepsin L plays the roles in adipogenesis and glucose tolerance in type 2 diabetes.
doi:10.2183/pjab.87.29
PMCID: PMC3043741  PMID: 21321479
cathepsin; inhibitor; cystatin; autoimmune diseases; osteoporosis; Sjögren syndrome
12.  Molecules participating in insect immunity of Sarcophaga peregrina 
Pricking the body wall of Sarcophaga peregrina (flesh fly) larvae with a needle activated the immune system of this insect and induced various immune molecules, including antibacterial proteins, in the hemolymph. In this review, I summarize and discuss the functions of these immune molecules, with particular emphasis on the dual roles of some of these molecules in defense and development.
doi:10.2183/pjab.86.927
PMCID: PMC3035055  PMID: 21157125
insect immunity; ontogeny; antibacterial proteins; dual roles of an immune protein
13.  Development of fluorescent probes for bioimaging applications 
Fluorescent probes, which allow visualization of cations such as Ca2+, Zn2+ etc., small biomolecules such as nitric oxide (NO) or enzyme activities in living cells by means of fluorescence microscopy, have become indispensable tools for clarifying functions in biological systems. This review deals with the general principles for the design of bioimaging fluorescent probes by modulating the fluorescence properties of fluorophores, employing mechanisms such as acceptor-excited Photoinduced electron Transfer (a-PeT), donor-excited Photoinduced electron Transfer (d-PeT), and spirocyclization, which have been established by our group. The a-PeT and d-PeT mechanisms are widely applicable for the design of bioimaging probes based on many fluorophores and the spirocyclization process is also expected to be useful as a fluorescence off/on switching mechanism. Fluorescence modulation mechanisms are essential for the rational design of novel fluorescence probes for target molecules. Based on these mechanisms, we have developed more than fifty bioimaging probes, of which fourteen are commercially available. The review also describes some applications of the probes developed by our group to in vitro and in vivo systems.
doi:10.2183/pjab.86.837
PMCID: PMC3037519  PMID: 20948177
probe; bioimaging; photoinduced electron transfer; fluorescence; spirocyclization
14.  Semaphorins and their receptors: Novel features of neural guidance molecules 
Semaphorins were originally identified as axon guidance cues involved in the development of the nervous system. In recent years, it is emerging that they also participate in various biological systems, including physiological and pathological processes. In this review, we primarily focus on our cumulative findings for the role of semaphorins and their receptors in the regulation of the immune system, while also summarizing recent progress in the context of cardiovascular system.
doi:10.2183/pjab.86.611
PMCID: PMC3081170  PMID: 20551597
Semaphorin; immune cell interactions; cardiac morphogenesis; plexins
15.  The trail of my studies on glycoproteins from enterokinase to tumor markers 
This review describes the results of the author’s studies on glycoproteins which have been carried out for more than 50 years. Starting from the elucidation of basic structures of glycoproteins, i.e. the structure of the linkage between an amino acid and a sugar and the occurrence of the β-mannosidic linkage as the common structure of glycoproteins, the author became interested in the cell membrane glycoproteins focused on the comparison of cancer cells versus normal cells. These studies were then extended to the establishment of sugar-directed and cancer-associated monoclonal antibodies. Some of the monoclonal antibodies are useful for cancer diagnosis.
doi:10.2183/pjab.86.578
PMCID: PMC3081172  PMID: 20551595
mucin; cell membrane; glycopeptide; glycosylamine; monoclonal antibody; cancer diagnosis
16.  Phosphoinositide-binding interface proteins involved in shaping cell membranes 
The mechanism by which cell and cell membrane shapes are created has long been a subject of great interest. Among the phosphoinositide-binding proteins, a group of proteins that can change the shape of membranes, in addition to the phosphoinositide-binding ability, has been found. These proteins, which contain membrane-deforming domains such as the BAR, EFC/F-BAR, and the IMD/I-BAR domains, led to inward-invaginated tubes or outward protrusions of the membrane, resulting in a variety of membrane shapes. Furthermore, these proteins not only bind to phosphoinositide, but also to the N-WASP/WAVE complex and the actin polymerization machinery, which generates a driving force to shape the membranes.
doi:10.2183/pjab.86.509
PMCID: PMC3108299  PMID: 20467216
phosphoinositide; membrane-deforming proteins; N-WASP; WAVE; BAR domain; F-BAR domain
17.  Hbo1 Links p53-Dependent Stress Signaling to DNA Replication Licensing▿  
Molecular and Cellular Biology  2007;28(1):140-153.
Hbo1 is a histone acetyltransferase (HAT) that is required for global histone H4 acetylation, steroid-dependent transcription, and chromatin loading of MCM2-7 during DNA replication licensing. It is the catalytic subunit of protein complexes that include ING and JADE proteins, growth regulatory factors and candidate tumor suppressors. These complexes are thought to act via tumor suppressor p53, but the molecular mechanisms and links between stress signaling and chromatin, are currently unknown. Here, we show that p53 physically interacts with Hbo1 and negatively regulates its HAT activity in vitro and in cells. Two physiological stresses that stabilize p53, hyperosmotic shock and DNA replication fork arrest, also inhibit Hbo1 HAT activity in a p53-dependent manner. Hyperosmotic stress during G1 phase specifically inhibits the loading of the MCM2-7 complex, providing an example of the chromatin output of this pathway. These results reveal a direct regulatory connection between p53-responsive stress signaling and Hbo1-dependent chromatin pathways.
doi:10.1128/MCB.00662-07
PMCID: PMC2223294  PMID: 17954561
18.  A ρ-dependent termination site in the gene coding for tyrosine tRNA su3 of Escherichia coli 
Nature  1978;272(5652):423-428.
A set of partially overlapping DNA restriction fragments that support promoter-dependent transcription of the tRNA1Tyr gene of Escherichia coli has been used to study site-specific termination in vitro. Transcription termination occurs at a specific site 224–226 nucleotides beyond the end of the structural gene and is completely dependent on ρ-factor. Certain features of this site suggest differences from other termination sites previously studied. A role for specific sequence recognition is suggested.
PMCID: PMC1994828  PMID: 345126
19.  Heterogeneity in the modification and involvement of chromatin components of the CpG island of the silenced human CDH1 gene in cancer cells 
Nucleic Acids Research  2002;30(21):4770-4780.
The structural alteration of chromatin has a key role in regulating gene expression. The alteration of chromatin is mediated by modification of its components. Detailed understanding of the relationship between these modifications, notably, methylation of the full-length CpG island, the association of methyl-CpG binding proteins (MBPs), and the acetylation and methylation of histones in gene silencing is vitally important. Currently, however, the manner in which chromatin components, associated with a specific gene, are modified is poorly understood. Here we provide in vivo evidence in cancer cells of the differential association between CpG methylation, MBPs, and histone modification in the entire CpG island of the human E-cadherin (CDH1) gene. Of the cell lines with CDH1 transcriptional repression, the distribution of methyl-CpGs in the CpG island differed markedly. In a cell line with gene silencing, the promoter region was almost methylation-free. Chromatin immunoprecipitation analysis revealed that the acetylation status of histone H4 differed between cell lines. However, deacetylated histone H3 was associated with the CpG island in all silenced cell lines. Binding of MeCP2 was also detected in all silenced cell lines. Additional binding of MBD1 protein was detected in a cell line in which the promoter region was poorly methylated and only histone H3 was deacetylated. Binding of MBD2 protein was detected in all other silenced cell lines. Histone H3 lysine 9 was methylated in all silenced cells, while histone H3 lysine 4 was methylated in some silenced cell lines. These results demonstrate that chromatin components associated with inactive CDH1 chromatin is heterogeneously modified and suggests the presence of multiple pathways for the formation of inactive chromatin.
PMCID: PMC135805  PMID: 12409468
20.  Sequence of the gene for isoleucine tRNA1 and the surrounding region in a ribosomal RNA operon of Escherichia coli 
Nucleic Acids Research  1979;6(2):575-592.
A DNA fragment of about 2000 base pairs carrying the gene for tRNA1Ile has been cloned from a total Eco RI endonuclease digest of Escherichia coli DNA. Sequence analyses revealed that about the first 850 base pairs from one end of the fragment contain a nucleotide sequence corresponding to that in the 3'-end of 16S rRNA. The gene for tRNAIle follows the 16S rRNA gene and both genes flank a spacer sequence of 68 base pairs. The spacer region contains a repeating, a hair pin and a symmetrical structure when the sequence is viewed in the single stranded form. A notable hair pin structure is also observed in the region adjacent to the 3'-end of the tRNA1Ile gene. In addition, about 850 base pairs from the other end of the DNA fragment have been found to contain the nucleotide sequence of the 5'-end of 23S rRNA. The presence of the genes for tRNA1Ile, 16S and 23S rRNA and the hybridization to tRNA1Ala suggest that this cloned DNA is part of one of the E. coli rRNA operons carrying these two tRNA genes as a spacer.
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PMCID: PMC327714  PMID: 370791

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