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author:("Ito, kensuke")
1.  Experimental detection of proteolytic activity in a signal peptide peptidase of Arabidopsis thaliana 
BMC Biochemistry  2013;14:16.
Background
Signal peptide peptidase (SPP) is a multi-transmembrane aspartic protease involved in intramembrane-regulated proteolysis (RIP). RIP proteases mediate various key life events by releasing bioactive peptides from the plane of the membrane region. We have previously isolated Arabidopsis SPP (AtSPP) and found that this protein is expressed in the ER. An AtSPP-knockout plant was found to be lethal because of abnormal pollen formation; however, there is negligible information describing the physiological function of AtSPP. In this study, we have investigated the proteolytic activity of AtSPP to define the function of SPPs in plants.
Results
We found that an n-dodecyl-ß-maltoside (DDM)-solubilized membrane fraction from Arabidopsis cells digested the myc-Prolactin-PP-Flag peptide, a human SPP substrate, and this activity was inhibited by (Z-LL)2-ketone, an SPP-specific inhibitor. The proteolytic activities from the membrane fractions solubilized by other detergents were not inhibited by (Z-LL)2-ketone. To confirm the proteolytic activity of AtSPP, the protein was expressed as either a GFP fusion protein or solely AtSPP in yeast. SDS-PAGE analysis showed that migration of the fragments that were cleaved by AtSPP were identical in size to the fragments produced by human SPP using the same substrate. These membrane-expressed proteins digested the substrate in a manner similar to that in Arabidopsis cells.
Conclusions
The data from the in vitro cell-free assay indicated that the membrane fraction of both Arabidopsis cells and AtSPP recombinantly expressed in yeast actually possessed proteolytic activity for a human SPP substrate. We concluded that plant SPP possesses proteolytic activity and may be involved in RIP.
doi:10.1186/1471-2091-14-16
PMCID: PMC3710259  PMID: 23829174
Signal peptide peptidase (SPP); Endoplasmic reticulum (ER); Aspartic protease; Regulated intramembrane proteolysis (RIP); Arabidopsis thaliana
2.  Systemic elevation of PTEN induces a tumor suppressive metabolic state 
Cell  2012;149(1):49-62.
SUMMARY
Decremental loss of PTEN results in cancer susceptibility and tumor progression. In turn this raises the possibility that PTEN elevation might be an attractive option for cancer prevention and therapy. We have generated several transgenic mouse lines with variably elevated PTEN expression levels, taking advantage of BAC (Bacterial Artificial Chromosome)-mediated transgenesis. Super-PTEN mutants are viable and show reduced body size due to decreased cell number, with no effect on cell size. Unexpectedly, PTEN elevation at the organism level results in healthy metabolism characterized by increased energy expenditure and reduced body fat accumulation. Cells derived from these mice show reduced glucose and glutamine uptake, increased mitochondrial oxidative phosphorylation, and are resistant to oncogenic transformation. Mechanistically we find that PTEN elevation orchestrates this metabolic switch by regulating PI3K-dependent and independent pathways, and negatively impacts two of the most pronounced metabolic features of tumor cells: glutaminolysis and the Warburg effect.
doi:10.1016/j.cell.2012.02.030
PMCID: PMC3319228  PMID: 22401813
3.  A PML-PPARδ pathway for fatty acid oxidation regulates haematopoietic stem cell maintenance 
Nature medicine  2012;18(9):1350-1358.
Stem cell function is an exquisitely regulated process. To date, however, the contribution of metabolic cues to stem cell function is poorly understood. Here we identify a novel PML - Peroxisome-proliferator activated receptor delta (PPARδ) - fatty acid oxidation (FAO) pathway for haematopoietic stem cell (HSC) maintenance. We have found that loss of Ppard profoundly affects the maintenance of HSCs. Moreover, treatment with PPARδ agonists improves these HSC functions, whereas, conversely, inhibition of mitochondrial FAO induces loss of the HSC compartment. Importantly, we demonstrate that PML exerts its essential role in HSC maintenance through regulation of PPAR signalling and FAO. Mechanistically, the PML-PPARδ-FAO pathway controls HSC asymmetric division. Depletion of Ppard or Pml, as well as FAO inhibition, results in symmetric commitment of HSC daughter cells while, conversely, PPARδ activation increases asymmetric division. Thus, our findings identify a new metabolic switch for the control of HSC cell fate with important therapeutic implications.
doi:10.1038/nm.2882
PMCID: PMC3566224  PMID: 22902876
4.  Newly Identified Roles of PML in Stem Cell Biology 
It has long been believed that the tumor suppressor promyelocytic leukemia (PML), the core component of the nuclear substructures known as the PML-nuclear bodies, plays a key part in acute PML (APL), as it is first cloned at the breakpoint of the t(15;17) translocation typical of that disease. Research over the past decade, however, has radically changed our view of how this tumor suppressor is regulated, how it can be therapeutically targeted, and how it functions in a number of tissue systems. One noteworthy recent study, for instance, revealed that PML regulates the activation of fatty acid metabolism, and that this metabolic reprograming plays an essential role in cancer biology and stem cell biology through the control it exerts over stem cell fate decisions. These findings sparked exciting new investigations of PML as a critical “rheostat” responsible for fine-tuning tissue homeostasis, and thus created at the intersection of cancer and stem cell biology a new field of study with important therapeutic implications.
doi:10.3389/fonc.2013.00050
PMCID: PMC3596805  PMID: 23504288
PML; stem cells; metabolism; stem cells and differentiation; breast cancer
5.  Crystallization and preliminary X-ray analysis of a glucansucrase from the dental caries pathogen Streptococcus mutans  
In this study, the glucansucrase from the dental caries pathogen S. mutans was purified and crystallized by the hanging-drop vapour-diffusion method using ammonium sulfate as a precipitant.
Glucansucrases encoded by Streptococcus mutans play essential roles in the synthesis of sticky dental plaques. Based on amino-acid sequence similarity, glucansucrases are classified as members of glycoside hydrolase family 70 (GH 70). Data on the crystal structure of GH 70 glucansucrases have yet to be reported. Here, the GH 70 glucansucrase GTF-SI from S. mutans was overexpressed in Escherichia coli strain BL21 (DE3), purified to homogeneity and crystallized using the hanging-drop vapour-diffusion method. Orthorhombic GTF-SI crystals belonging to space group P21212 were obtained. A diffraction data set was collected to 2.1 Å resolution.
doi:10.1107/S1744309110029714
PMCID: PMC2935234  PMID: 20823533
glucansucrase; dental caries; Streptococcus mutans
6.  Treatment of Moyamoya Syndrome Associated with Systemic Lupus Erythematosus and Hypothyroidism in an Adult by Encephaloduroarteriosynangiosis: A Case Report 
Case Reports in Medicine  2012;2012:120867.
A 54-year-old woman presented to our hospital with progressive motor weakness of the right arm. She had a medical history of systemic lupus erythematosus (SLE) and hypothyroidism. Magnetic resonance imaging indicated a watershed infarction of the left hemisphere. Cervical echogram indicated severe stenosis of the internal carotid artery (ICA) without wall thickening. Cerebral angiography indicated left ICA occlusion, development of unilateral moyamoya vessels, and leptomeningeal anastomosis. Encephaloduroarteriosynangiosis (EDAS) was performed after cerebral 99mTechnetium-ethyl-cysteinate-dimer single-photon emission computed tomography indicated a decreased cerebral blood flow, diminished cerebrovascular perfusion reserve. Motor weakness finally disappeared 6 months after surgery. Moyamoya syndrome is a rare complication of both SLE and hypothyroidism, and the surgical indication remains controversial. By evaluating the decreased cerebral perfusion reserve capacity and the existence of leptomeningeal anastomosis, EDAS could be an efficient method for the treatment of moyamoya syndrome associated with SLE and hypothyroidism.
doi:10.1155/2012/120867
PMCID: PMC3432552  PMID: 22966233
7.  A metabolic prosurvival role for PML in breast cancer  
The Journal of Clinical Investigation  2012;122(9):3088-3100.
Cancer cells exhibit an aberrant metabolism that facilitates more efficient production of biomass and hence tumor growth and progression. However, the genetic cues modulating this metabolic switch remain largely undetermined. We identified a metabolic function for the promyelocytic leukemia (PML) gene, uncovering an unexpected role for this bona fide tumor suppressor in breast cancer cell survival. We found that PML acted as both a negative regulator of PPARγ coactivator 1A (PGC1A) acetylation and a potent activator of PPAR signaling and fatty acid oxidation. We further showed that PML promoted ATP production and inhibited anoikis. Importantly, PML expression allowed luminal filling in 3D basement membrane breast culture models, an effect that was reverted by the pharmacological inhibition of fatty acid oxidation. Additionally, immunohistochemical analysis of breast cancer biopsies revealed that PML was overexpressed in a subset of breast cancers and enriched in triple-negative cases. Indeed, PML expression in breast cancer correlated strikingly with reduced time to recurrence, a gene signature of poor prognosis, and activated PPAR signaling. These findings have important therapeutic implications, as PML and its key role in fatty acid oxidation metabolism are amenable to pharmacological suppression, a potential future mode of cancer prevention and treatment.
doi:10.1172/JCI62129
PMCID: PMC3433768  PMID: 22886304
8.  PML Regulates Apoptosis at Endoplasmic Reticulum by Modulating Calcium Release 
Science (New York, N.Y.)  2010;330(6008):1247-1251.
The promyelocytic leukemia (PML) tumor suppressor is a pleiotropic modulator of apoptosis. However, the molecular basis for such a diverse proapoptotic role is currently unknown. We show that extranuclear Pml was specifically enriched at the endoplasmic reticulum (ER) and at the mitochondria-associated membranes, signaling domains involved in ER-to-mitochondria calcium ion (Ca2+) transport and in induction of apoptosis. We found Pml in complexes of large molecular size with the inositol 1,4,5-trisphosphate receptor (IP3R), protein kinase Akt, and protein phosphatase 2a (PP2a). Pml was essential for Akt- and PP2a-dependent modulation of IP3R phosphorylation and in turn for IP3R-mediated Ca2+ release from ER. Our findings provide a mechanistic explanation for the pleiotropic role of Pml in apoptosis and identify a pharmacological target for the modulation of Ca2+ signals.
doi:10.1126/science.1189157
PMCID: PMC3017677  PMID: 21030605
9.  Posttraumatic Cranial Cystic Fibrous Dysplasia 
Case Reports in Medicine  2011;2011:680401.
A 14-year-old was girl admitted to our hospital with a subcutaneous mass of the occipital head. The mass had grown for 6 years, after she had sustained a head injury at the age of 6, and was located directly under a previous wound. Skull X-ray Photograph (xp), computed tomography (CT), and magnetic resonance imaging (MRI) showed a bony defect and cystic changes in the skull corresponding to a subcutaneous mass. Bone scintigraphy revealed partial accumulation. The patient underwent total removal of the skull mass, and the diagnosis from the pathological findings of the cyst wall was fibrous dysplasia (FD). The radiographic findings for cystic cranial FD can be various. Progressive skull disease has been reported to be associated with head trauma, but the relationship between cranial FD and head trauma has not been previously reported. Previous studies have suggested that c-fos gene expression is a key mechanism in injury-induced FD.
doi:10.1155/2011/680401
PMCID: PMC3162981  PMID: 21876700
10.  LRF is an essential downstream target of GATA1 in erythroid development and regulates BIM-dependent apoptosis 
Developmental cell  2009;17(4):527-540.
SUMMARY
GATA-1-dependent transcription is essential for erythroid differentiation and maturation. Suppression of programmed cell death is also thought to be critical for this process; however, the link between these two features of erythropoiesis has remained elusive. Here, we show that the POZ-Krüppel family transcription factor, LRF (also known as Zbtb7a/Pokemon), is a direct target of GATA1 and plays an essential anti-apoptotic role during terminal erythroid differentiation. We find that loss of Lrf leads to lethal anemia in embryos, due to increased apoptosis of late stage erythroblasts. This programmed cell death is Arf- and p53-independent and is instead mediated by up-regulation of the pro-apoptotic factor Bim. We identify Lrf as a direct repressor of Bim transcription. In strong support of this mechanism, genetic Bim-loss delays the lethality of Lrf-deficient embryos and rescues their anemia-phenotype. Thus, our data defines a key transcriptional cascade for effective erythropoiesis, whereby GATA-1 suppresses BIM-mediated apoptosis via LRF.
doi:10.1016/j.devcel.2009.09.005
PMCID: PMC3134301  PMID: 19853566
11.  The nuclear bodies inside out: PML conquers the cytoplasm 
Current opinion in cell biology  2011;23(3):360-366.
The promyelocytic leukemia (PML) protein is the core component of nuclear substructures that host more than 70 proteins, termed nuclear domains 10 or PML-nuclear bodies. PML was first identified as the gene participating in the translocation responsible for the pathogenesis of acute promyelocytic leukemia (APL). The notion that PML is a tumor suppressor gene was soon extrapolated from leukemia to solid tumors. The last decade has radically changed the view of how this tumor suppressor is regulated, how it can be therapeutically targeted, and how it functions. Notably, one of the most recent and striking features uncovered is how PML regulates cellular homeostasis outside its original niche in the nucleus. These new findings open an exciting new area of research in extra-nuclear PML functions.
doi:10.1016/j.ceb.2011.03.011
PMCID: PMC3109131  PMID: 21501958
12.  Identification and Modulation of the Key Amino Acid Residue Responsible for the pH Sensitivity of Neoculin, a Taste-Modifying Protein 
PLoS ONE  2011;6(4):e19448.
Neoculin occurring in the tropical fruit of Curculigo latifolia is currently the only protein that possesses both a sweet taste and a taste-modifying activity of converting sourness into sweetness. Structurally, this protein is a heterodimer consisting of a neoculin acidic subunit (NAS) and a neoculin basic subunit (NBS). Recently, we found that a neoculin variant in which all five histidine residues are replaced with alanine elicits intense sweetness at both neutral and acidic pH but has no taste-modifying activity. To identify the critical histidine residue(s) responsible for this activity, we produced a series of His-to-Ala neoculin variants and evaluated their sweetness levels using cell-based calcium imaging and a human sensory test. Our results suggest that NBS His11 functions as a primary pH sensor for neoculin to elicit taste modification. Neoculin variants with substitutions other than His-to-Ala were further analyzed to clarify the role of the NBS position 11 in the taste-modifying activity. We found that the aromatic character of the amino acid side chain is necessary to elicit the pH-dependent sweetness. Interestingly, since the His-to-Tyr variant is a novel taste-modifying protein with alternative pH sensitivity, the position 11 in NBS can be critical to modulate the pH-dependent activity of neoculin. These findings are important for understanding the pH-sensitive functional changes in proteinaceous ligands in general and the interaction of taste receptor–taste substance in particular.
doi:10.1371/journal.pone.0019448
PMCID: PMC3084864  PMID: 21559382
13.  Evaluation of the Pichia pastoris expression system for the production of GPCRs for structural analysis 
Background
Various protein expression systems, such as Escherichia coli (E. coli), Saccharomyces cerevisiae (S. cerevisiae), Pichia pastoris (P. pastoris), insect cells and mammalian cell lines, have been developed for the synthesis of G protein-coupled receptors (GPCRs) for structural studies. Recently, the crystal structures of four recombinant human GPCRs, namely β2 adrenergic receptor, adenosine A2a receptor, CXCR4 and dopamine D3 receptor, were successfully determined using an insect cell expression system. GPCRs expressed in insect cells are believed to undergo mammalian-like posttranscriptional modifications and have similar functional properties than in mammals. Crystal structures of GPCRs have not yet been solved using yeast expression systems. In the present study, P. pastoris and insect cell expression systems for the human muscarinic acetylcholine receptor M2 subtype (CHRM2) were developed and the quantity and quality of CHRM2 synthesized by both expression systems were compared for the application in structural studies.
Results
The ideal conditions for the expression of CHRM2 in P. pastoris were 60 hr at 20°C in a buffer of pH 7.0. The specific activity of the expressed CHRM2 was 28.9 pmol/mg of membrane protein as determined by binding assays using [3H]-quinuclidinyl benzilate (QNB). Although the specific activity of the protein produced by P. pastoris was lower than that of Sf9 insect cells, CHRM2 yield in P. pastoris was 2-fold higher than in Sf9 insect cells because P. pastoris was cultured at high cell density. The dissociation constant (Kd) for QNB in P. pastoris was 101.14 ± 15.07 pM, which was similar to that in Sf9 insect cells (86.23 ± 8.57 pM). There were no differences in the binding affinity of CHRM2 for QNB between P. pastoris and Sf9 insect cells.
Conclusion
Compared to insect cells, P. pastoris is easier to handle, can be grown at lower cost, and can be expressed quicker at a large scale. Yeast, P. pastoris, and insect cells are all effective expression systems for GPCRs. The results of the present study strongly suggested that protein expression in P. pastoris can be applied to the structural and biochemical studies of GPCRs.
doi:10.1186/1475-2859-10-24
PMCID: PMC3094209  PMID: 21513509
14.  Characterization of the β-d-Glucopyranoside Binding Site of the Human Bitter Taste Receptor hTAS2R16* 
The Journal of Biological Chemistry  2010;285(36):28373-28378.
G-protein-coupled receptors mediate the senses of taste, smell, and vision in mammals. Humans recognize thousands of compounds as bitter, and this response is mediated by the hTAS2R family, which is one of the G-protein-coupled receptors composed of only 25 receptors. However, structural information on these receptors is limited. To address the molecular basis of bitter tastant discrimination by the hTAS2Rs, we performed ligand docking simulation and functional analysis using a series of point mutants of hTAS2R16 to identify its binding sites. The docking simulation predicted two candidate binding structures for a salicin-hTAS2R16 complex, and at least seven amino acid residues in transmembrane 3 (TM3), TM5, and TM6 were shown to be involved in ligand recognition. We also identified the probable salicin-hTAS2R16 binding mode using a mutated receptor experiment. This study characterizes the molecular interaction between hTAS2R16 and β-d-glucopyranoside and will also facilitate rational design of bitter blockers.
doi:10.1074/jbc.M110.144444
PMCID: PMC2934701  PMID: 20605788
Calcium Imaging; G-protein-coupled Receptors (GPCR); Membrane Proteins; Receptor Structure-Function; Signal Transduction; Bitter; Taste Receptor; Binding Site; Molecular Dynamics; Molecular Modeling
15.  A novel signaling network as a critical rheostat for the biology and maintenance of the normal stem cell and the cancer-initiating cell 
Summary of recent advances
Recent advances from our own group and others have defined a novel PML/PTEN/Akt/mTOR/FoxO signaling network, and highlighted its critical importance in oncogenesis as well as in the functional regulation of normal stem cell and cancer-initiating cell (CIC) biology. These findings are of great importance in cancer therapy in view of the fact that this network is amenable to pharmacological modulation at multiple levels. The integrated analysis of these data allows us to propose a new provocative working model whereby the aberrant super-activation of Akt/mTOR signaling elicits built-in cellular fail-safe mechanisms that could be effectively utilized for cancer treatment to extinguish the CICs pool. In this review, we will discuss these recent findings, this working model, and their therapeutic implications.
doi:10.1016/j.gde.2009.01.004
PMCID: PMC2677410  PMID: 19216069
16.  PML targeting eradicates quiescent leukaemia-initiating cells 
Nature  2008;453(7198):1072-1078.
The existence of a small population of ‘cancer initiating cells (CICs)’ responsible for tumour maintenance has been firmly demonstrated in leukaemia. This concept is currently being tested in solid tumours. Leukaemia-initiating cells (LICs), particularly those which are in a quiescent state, are thought to be resistant to chemotherapy and targeted therapies resulting in disease relapse. Chronic myeloid leukaemia (CML) is a paradigmatic haematopietic stem cell (HSC) disease in which the LIC pool is not eradicated by current therapy, leading to disease relapse upon drug discontinuation. Here we define the critical role of the promyelocytic leukaemia protein (PML) tumour suppressor in HSC maintenance and present a new therapeutic approach for targeting quiescent LICs and possibly CICs by pharmacological inhibition of PML.
doi:10.1038/nature07016
PMCID: PMC2712082  PMID: 18469801
17.  Reactive oxygen species induce chondrocyte hypertrophy in endochondral ossification 
The Journal of Experimental Medicine  2007;204(7):1613-1623.
Chondrocyte hypertrophy during endochondral ossification is a well-controlled process in which proliferating chondrocytes stop proliferating and differentiate into hypertrophic chondrocytes, which then undergo apoptosis. Chondrocyte hypertrophy induces angiogenesis and mineralization. This step is crucial for the longitudinal growth and development of long bones, but what triggers the process is unknown. Reactive oxygen species (ROS) have been implicated in cellular damage; however, the physiological role of ROS in chondrogenesis is not well characterized. We demonstrate that increasing ROS levels induce chondrocyte hypertrophy. Elevated ROS levels are detected in hypertrophic chondrocytes. In vivo and in vitro treatment with N-acetyl cysteine, which enhances endogenous antioxidant levels and protects cells from oxidative stress, inhibits chondrocyte hypertrophy. In ataxia telangiectasia mutated (Atm)–deficient (Atm−/−) mice, ROS levels were elevated in chondrocytes of growth plates, accompanied by a proliferation defect and stimulation of chondrocyte hypertrophy. Decreased proliferation and excessive hypertrophy in Atm−/− mice were also rescued by antioxidant treatment. These findings indicate that ROS levels regulate inhibition of proliferation and modulate initiation of the hypertrophic changes in chondrocytes.
doi:10.1084/jem.20062525
PMCID: PMC2118643  PMID: 17576777
18.  Analysing the substrate multispecificity of a proton-coupled oligopeptide transporter using a dipeptide library 
Nature Communications  2013;4:2502.
Peptide uptake systems that involve members of the proton-coupled oligopeptide transporter (POT) family are conserved across all organisms. POT proteins have characteristic substrate multispecificity, with which one transporter can recognize as many as 8,400 types of di/tripeptides and certain peptide-like drugs. Here we characterize the substrate multispecificity of Ptr2p, a major peptide transporter of Saccharomyces cerevisiae, using a dipeptide library. The affinities (Ki) of di/tripeptides toward Ptr2p show a wide distribution range from 48 mM to 0.020 mM. This substrate multispecificity indicates that POT family members have an important role in the preferential uptake of vital amino acids. In addition, we successfully establish high performance ligand affinity prediction models (97% accuracy) using our comprehensive dipeptide screening data in conjunction with simple property indices for describing ligand molecules. Our results provide an important clue to the development of highly absorbable peptides and their derivatives including peptide-like drugs.
Proton-coupled oligopeptide transporters (POTs) can recognize and mediate the uptake of up to 8,400 di/tripeptides or peptide-like drugs. Ito et al. comprehensively map the substrate specificity of the yeast POT Ptr2p, and use this information to construct models for the prediction of ligand affinity.
doi:10.1038/ncomms3502
PMCID: PMC3791473  PMID: 24060756

Results 1-18 (18)