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  • Inhibition of nuclear translocation of notch intracellular domain (NICD) by diosgenin prevented atherosclerotic
    Biochimie (IF 3.112) Pub Date : 2018-02-24
    Ambika Binesh, Sivasithambaram Niranjali Devaraj, Halagowder Devaraj

    Notch signaling plays a pivotal role in homeostasis and cardiovascular development. The role of Notch signaling in atherosclerosis cannot be complete without analysing the key role of Notch in macrophages, which trigger the inflammatory response and subsequent plaque formation in atherosclerosis. Diosgenin showed its anti-atherosclerotic property by the unifying mechanism of suppressing the expression of Notch Signaling pathway, particularly the nuclear translocation of notch intracellular domain (NICD) in aorta and in differentiated macrophage cells. It is further confirmed by the inhibition of NICD by DAPT (N-[N-(3, 5-difluorophenacetyl)-l-alanyl]-S-phenylglycine t-butyl ester), which also restricted the differentiation of macrophage. Hence, inhibition of nuclear translocation of NICD by diosgenin aids in preventing atherosclerosis.

  • 更新日期:2018-02-21
  • Profile of CYP19A1 mRNA expression and aromatase activity during syncytialization of primary human villous trophoblast cells at term
    Biochimie (IF 3.112) Pub Date : 2018-02-21
    Andrée-Anne Hudon Thibeault, Cathy Vaillancourt, J. Thomas Sanderson

    Estrogen production by the human villous trophoblast is dependent on the biosynthetic enzyme aromatase (CYP19; CYP19A1) and is crucial for successful placental development and pregnancy outcome. Using villous cytotrophoblast cells (vCTs) freshly isolated from normal term placenta, we characterized the promoter-specific expression of CYP19A1 mRNA (derived from promoters I.1, I.4, I.8 or total transcript) and aromatase activity during villous trophoblast syncytialization. CYP19A1 mRNA levels and aromatase activity in vCTs reached a maximum after about 48 h of culture. The cAMP inducer forskolin (10 μM) and protein kinase C stimulant phorbol myristate acetate (1 μM) increased CYP19A1 mRNA levels by 1.8- and 1.6-fold, respectively, as well as inducing aromatase catalytic activity. Dexamethasone (100 nM) and vascular endothelial growth factor (5 ng/mL) decreased CYP19A1 mRNA levels, while having no effect on aromatase activity. Our results emphasize the importance of not solely studying CYP19A1 regulation and function at the mRNA level but also by considering posttranslational mechanisms that alter the final catalytic activity of aromatase.

  • Activated CXCL5-CXCR2 axis promotes the migration, invasion and EMT of papillary thyroid carcinoma cells via modulation of β-catenin pathway
    Biochimie (IF 3.112) Pub Date : 2018-02-20
    Dong Cui, Yongfu Zhao, Jingchao Xu

    Initiation of epithelial-to-mesenchymal transition (EMT) is common in papillary thyroid carcinoma (PTC) and may contribute to its metastasis. Aims of the present study are to investigate whether and how the C-X-C motif chemokine ligand (CXCL)-5/C-X-C motif receptor 2 (CXCR2) axis affects PTC metastasis, with a focus on the EMT process. Herein, two PTC cell lines, KTC-1 and B-CPAP cells, identified as CXCR2-positive cells were used as the cell model. We found that a 24-h stimulation of 1 or 10 nM recombinant human CXCL5 (rhCXCL5) enhanced the migration and invasion of both KTC-1 and B-CPAP cells without affecting their proliferation. The migration- and invasion-promoting effects of rhCXCL5 were attenuated if CXCR2 was silenced by its specific short hairpin RNAs (shRNAs). EMT initiation is defined as downregulation of epithelial-cadherin (E-cadherin) and upregulation of N-cadherin, Vimentin and Snail. Our data showed that rhCXCL5-induced EMT in PTC cells was suppressed by CXCR2 shRNA. Furthermore, the active CXCL5-CXCR2 axis enhanced the phosphorylation of Akt at Ser 473 residue and that of glycogen synthase kinase-3 (GSK-3β) at Ser 9 residue, and accelerated the nuclear accumulation of β-catenin in PTC cells. Re-expression of the active form of β-catenin in PTC cells rescued their impaired invasiveness caused by the blockade of CXCL5-CXCR2 axis. In addition, CXCL5 and CXCR2 were overexpressed in the metastatic lymph nodes obtained from 18 patients with PTC. In summary, our study demonstrates that the activated CXCL5-CXCR2 axis contributes to the metastatic phenotype of PTC cells by modulating Akt/GSK-3β/β-catenin pathway.

  • Modulation of Kv3.1b potassium channel level and intracellular potassium concentration in 158N murine oligodendrocytes and BV-2 murine microglial cells treated with 7-ketocholesterol, 24S-hydroxycholesterol or tetracosanoic acid (C24:0)
    Biochimie (IF 3.112) Pub Date : 2018-02-17
    Maryem Bezine, Sonia Maatoug, Rym Ben Khalifa, Meryam Debbabi, Amira Zarrouk, Yuqin Wang, William J. Griffiths, Thomas Nury, Mohammad Samadi, Anne Vejux, Jérôme de Sèze, Thibault Moreau, Riadh Kharrat, Mohamed El Ayeb, Gérard Lizard
  • Structural and biophysical insight into dual site binding of the protoberberine alkaloid palmatine to parallel G-quadruplex DNA using NMR, fluorescence and Circular Dichroism spectroscopy
    Biochimie (IF 3.112) Pub Date : 2018-02-17
    Kumar Padmapriya, Ritu Barthwal

    Plant derived small molecules, which interact with and stabilize G-quadruplex DNA, act as inhibitors of telomere elongation and oncogene expression in humans. The inhibition of telomerase enzyme has immense potential since it is over expressed in most cancer cells. Interaction of palmatine, an antitumor alkaloid, to parallel G-quadruplex DNA, [d(TTGGGGT)]4 and [d(TTAGGGT)]4, has been investigated using Nuclear Magnetic Resonance (NMR), fluorescence and Circular Dichroism (CD) spectroscopy. Titrations were monitored by 1H and 31P NMR spectra and solution structure of palmatine-[d(TTGGGGT)]4 complex was obtained by restrained Molecular Dynamics (rMD) simulations using distance restraints from 2D NOESY spectra. Thermal stabilization of DNA was determined by CD, 1H NMR and Differential Scanning Calorimetry (DSC). Binding of palmatine induces 98% enhancement of fluorescence accompanied by blue shift ∼8 nm. CD spectral bands of DNA show minor changes. Diffusion NMR studies confirm formation of a stable complex. Proton NMR signals of palmatine shift upfield upon binding and NOE cross peaks of H10, H3, H28, 5OCH3 protons with T2, A3/G3, G6 and T7 residues reveal dual recognition sites in both G-quadruplex DNA sequences, resulting in thermal stabilization of G-quadruplex by ∼13-17 °C. Restrained molecular dynamics simulations using NOE distance restraints for 2:1 palmatine-[d(TTGGGGT)]4 complex reveal end-stacking of palmatine at G6pT7 step and groove binding along T2pG3 step. Binding to [d(TTAGGGT)]4 takes place at T2pA3pG4 and G6pT7 steps. Structural features of molecular recognition of two different G-quadruplex DNA sequences by palmatine have relevance in rational drug development for anti-cancer therapy.

  • Temozolomide Affects Extracellular Vesicles Released by Glioblastoma Cells
    Biochimie (IF 3.112) Pub Date : 2018-02-15
    Gwennan André-Grégoire, Nicolas Bidère, Julie Gavard

    Glioblastoma multiforme (GBM) is the most aggressive primary tumour within the brain as well as the most common and lethal cerebral cancer, mainly because of treatment failure. Indeed, tumour recurrence is inevitable and fatal in a short period of time. Glioblastoma stem-like cells (GSCs) are thought to participate in tumour initiation, expansion, resistance to treatments, including to the alkylating chemotherapeutic agent temozolomide, and relapse. Here, we assessed whether extracellular vesicles (EVs) released by GSCs could disseminate factors involved in resistance mechanisms. We first characterized EVs either circulating in peripheral blood from newly diagnosed patients or released by patient-derived temozolomide-resistant GSCs. We found that EVs from both sources were mainly composed of particles homogeneous in size (50-100 nm), while they were more abundant in liquid biopsies from GBM patients, as compared to healthy donors. Further, mass spectrometry analysis from GSC-derived EVs unveiled that particles from control and temozolomide-treated cells share core components of EVs, as well as ribosome- and proteasome-associated networks. More strikingly, temozolomide treatment led to the enrichment of EVs with cargoes dedicated to cell adhesion processes. Thus, while relatively inefficient in killing GSCs in vitro, temozolomide could instead increase the release of pro-tumoral information.

  • Biophysical methods: complementary tools to study the influence of human steroid hormones on the liposome membrane properties
    Biochimie (IF 3.112) Pub Date : 2018-02-13
    Rola Abboud, Catherine Charcosset, Hélène Greige-Gerges
  • G-quadruplexes in Prague: a Bohemian Rhapsody
    Biochimie (IF 3.112) Pub Date : 2018-02-13
    Michael O’Hagan, Jean-Louis Mergny, Zoë Ann Ella Waller

    The Sixth International Meeting on Quadruplex Nucleic Acids was held at the Hotel Internationale in Prague, Czech Republic from 31 May – 3 June 2017. A vibrant interdisciplinary community of almost over 300 scientists gathered to share their newest results in this exciting field and exchange ideas for further investigations.

  • Sticholysin II-mediated cytotoxicity involves the activation of regulated intracellular responses that anticipates cell death
    Biochimie (IF 3.112) Pub Date : 2018-02-13
    Carmen Soto, Gretchen Bergado, Rancés Blanco, Tania Griñán, Hermis Rodríguez, Uris Ros, Fabiola Pazos, María Eliana Lanio, Ana María Hernández, Carlos Álvarez

    Sticholysin II (StII) is a pore-forming toxin of biomedical interest that belongs to the actinoporin protein family. Sticholysins are currently under examination as an active immunomodulating component of a vaccinal platform against tumoral cells and as a key element of a nucleic acids delivery system to cell cytosol. These proteins form pores in the plasma membrane leading to ion imbalance and cell lysis. However, the intracellular mechanisms triggered by actinoporins upon binding to membranes and its consequences for cell death are barely understood. Here, we have examined the cytotoxicity and intracellular responses induced by StII upon binding to human B-cell lymphoma Raji in vitro. StII cytotoxicity involves a functional actin cytoskeleton, induces cellular swelling, lysis and the concomitant release of cytosol content. In addition, StII induces calcium release mainly from the Endoplasmic Reticulum, activates Mitogen-Activated Protein Kinase ERK and impairs mitochondrial membrane potential. Furthermore, StII stimulates the expression of receptor interacting protein kinase 1 (RIP1), normally related to different forms of regulated cell death such as apoptosis and necroptosis. In correspondence, necrostatin-1, an inhibitor of this kinase, reduces StII cytotoxicity. However, the mechanism of cell death activated by StII does not involve caspases activation, typical molecular features of apoptosis and pyroptosis. Our results suggest that, beyond pore-formation and cell lysis, StII-induced cytotoxicity could involve other regulated intracellular mechanisms connected to RIP1-MEK1/2 –ERK1/2- pathways. This opens new perspectives and challenges the general point of view that these toxins induce a completely unregulated mechanism of necrotic cell death. This study contributes to a better understanding of the molecular mechanisms involved in toxin-cell interaction and the implications for cell functioning, with connotation for the exploitations of these toxins in clinical settings.

  • Oleic acid induces the novel apolipoprotein O and reduces mitochondrial membrane potential in chicken and human hepatoma cells.
    Biochimie (IF 3.112) Pub Date : 2018-02-10
    Anna M. Weijler, Barbara Schmidinger, Stylianos Kapiotis, Hilde Laggner, Marcela Hermann

    Non-alcoholic fatty liver disease (NAFLD) is marked by hepatic fat accumulation and reflects a spectrum of chronic liver diseases associated with obesity, impaired insulin sensitivity and dyslipidemia. Apolipoprotein O (ApoO) is a new member of the plasma apolipoprotein family that may play a role in lipid metabolism and electron transport activity of the mitochondrium. However, its physiological functions have not been elucidated yet. Based on our previous data in a non-mammalian experimental system [1], we hypothesized that hepatic expression of ApoO is tightly linked not only to diet-induced hepatosteatosis, but also to increased lipoprotein-production induced by, e.g., hormones and oxidative stress. To gain insight into a mammalian experimental system, we compared the effects of lipid loading on ApoO regulation in chicken hepatoma LMH cells with those in the human hepatoma cell line HepG2. Incubation of the cells with BSA-complexed oleic acid (OA-Alb) induced triglyceride accumulation, but did not affect cell viability. qPCR using specific primer pairs and Western blot analysis with in-house produced rabbit anti-ApoO antisera demonstrated significant increase in ApoO transcript and protein levels in both cell lines. ROS formation due to OA-Alb treatment was only slightly altered in LMH cells, indicating an intact antioxidant defense system of the cells. Oxidative stress applied by addition of H2O2 revealed induction of ApoO transcript and protein level in the same or even higher extent as monitored in the presence of OA-Alb. Upon treatment with estrogen for 24 h quantitative analysis of ApoO transcript and protein revealed increases of ApoO expression supporting the assumption that estrogen affects lipoprotein metabolism at various points. Furthermore, both cell lines showed a significant decrease of the mitochondrial membrane potential upon incubation with OA-Alb. Therefore, we assume that our findings support a role of ApoO as an effector of compromised mitochondrial function that likely accompanies the onset of non-alcoholic fatty liver disease.

  • NK-18, a promising antimicrobial peptide: anti-multidrug resistant leukemia cells and LPS neutralizing properties
    Biochimie (IF 3.112) Pub Date : 2018-02-07
    Jiexi Yan, Xiaolei Liang, Caijuan Bai, Lanxia Zhou, Juan Li, Kairong Wang, Yan Tang, Li Zhao

    With the increase of multidrug resistance, novel anti-leukemia agents with diverse mechanisms of action are required to address this challenge. NK-18, the core region of mammalian derived protein NK-lysin, effectively inhibited the viability of both multidrug resistant and sensitive leukemia cell lines. Meanwhile, this proliferation inhibition effect was not distinct between sensitive and multidrug resistant leukemia cell line. NK-18 showed selectivity between non-tumorigenic and tumorigenic cells. It preferentially bound to tumor cells whose outer leaflet with high phosphatidylserine content. NK-18 acted on the multidrug resistant leukemia cell line by a rapid pore formation on the cell membrane, it is not easy for K562/ADM cells developing resistance against NK-18. Furthermore, NK-18 could neutralize lipopolysaccharides by electrostatic attraction and reduce NO production. These research data demonstrated NK-18 possesses great advantage in the multidrug resistant leukemia treatment compared with conventional chemotherapies and it could be a potential candidate for further research.

  • Punicalagin, an active pomegranate component, is a new inhibitor of PDIA3 reductase activity
    Biochimie (IF 3.112) Pub Date : 2018-02-06
    Flavia Giamogante, Ilaria Marrocco, Laura Cervoni, Margherita Eufemi, Silvia Chichiarelli, Fabio Altieri

    Background Polyphenolic compounds isolated from pomegranate fruit possess several pharmacological activities including anti-inflammatory, hepatoprotective, antigenotoxic and anticoagulant activities. The present work focuses the attention on PDIA3 interaction with punicalagin and ellagic acid, the most predominant components of pomegranate extracts. PDIA3, a member of the protein disulfide isomerase family involved in several cellular functions, is associated with different human diseases and it has the potential to be a pharmacological target. Methods The interaction of polyphenols with PDIA3 purified protein was explored by fluorescence quenching and calorimetric techniques and their effect on PDIA3 activity was investigated. Results A higher affinity was observed for punicalagin which also strongly affects PDIA3 reductase activity in vitro as a non-competitive inhibitor. Isothermal titration calorimetry confirmed the high affinity of punicalagin for PDIA3. Considering the PDIA3 involvement in oxidative cellular stress response observed in neuroblastoma cells after treatment with hydrogen peroxide, a comparative study was conducted to evaluate the effect of punicalagin on wild type and PDIA3-silenced cells. Punicalagin increases the cell sensitivity to hydrogen peroxide in neuroblastoma cells, but this effect is drastically reduced in PDIA3-silenced cells treated in the same experimental conditions. Conclusions Punicalagin binds PDIA3 and inhibits its redox activity. Comparative experiments conducted on unsilenced and PDIA3-silenced neuroblastoma cells suggest the potential of punicalagin to modulate PDIA3 reductase activity also in a biological model. General significance Punicalagin can be used as a new PDIA3 inhibitor and this can provide information on the molecular mechanisms underlying the biological activities of PDIA3 and punicalagin.

  • Simulating the γ-secretase enzyme: recent advances and future directions
    Biochimie (IF 3.112) Pub Date : 2018-02-02
    Rodrigo Aguayo-Ortiz, Laura Dominguez

    γ-secretase is an intra-membrane aspartyl protease involved in the production of amyloid-β peptides. Aberrant cleavage of 99-residue C-terminal fragment of the amyloid precursor protein leads to the formation of a 42-amino acid length of Aβ. Further oligomerization and aggregation of this isoform is implicated in the onset and progression of Alzheimer’s disease. A recent elucidation of γ-secretase by cryo-electron microscopy techniques have opened a new horizon in the structural and dynamic characterization of the enzyme. Currently, only a few molecular dynamics studies have been carried out to explore the mechanism of substrate recognition and entry, or the transition between active and inactive states of the catalytic subunit. Herein, we briefly review the computational approaches and their most relevant findings. The general picture of the current GS simulation studies will open new questions to understand the behavior of the enzyme dynamics and explain the modulation mechanisms for the treatment of Alzheimer's disease.

  • Cloning and sequencing of three-finger toxins from the venom glands of four Micrurus species from Mexico and heterologous expression of an alpha-neurotoxin from Micrurus diastema
    Biochimie (IF 3.112) Pub Date : 2018-01-31
    Jaime Felipe Guerrero-Garzón, Melisa Bénard-Valle, Rita Restano-Cassulini, Fernando Zamudio, Gerardo Corzo, Alejandro Alagón, Alejandro Olvera-Rodríguez

    The three-finger toxins (3FTxs) represent an extremely diverse protein family in elapid venoms, where the short chain α-neurotoxins are the most relevant toxin group from the clinical point of view. Essentially, the 3FTxs variability and the low proportions of α-neurotoxins in the venoms of North American coral snakes make it difficult to obtain effective elapid antivenoms against the envenomation symptoms caused mainly by these α-neurotoxins. In this work, thirty 3FTx transcript sequences were obtained from the venom glands of four coral snake species from Mexico (M. diastema, M. laticollaris, M. browni and M. tener). The transcripts were mined using a forward oligonucleotide based on the highly conserved signal peptide from the 3FTxs, and four of these transcripts, named MlatA1, B.D, B.E and D.H, encoded for short-chain α-neurotoxins. Additionally, one isoform of the D.H α-neurotoxin transcript was identified in the venom of M. diastema. The mature α-neurotoxin coded in the D.H transcript was heterologously expressed, and it was found soluble (4.2 mg/L) in the cytoplasm of a bacterial system. The recombinant D.H (rD.H) had an IC50 value of 31.5 ± 4.4 nM on nicotinic acetylcholine receptors of the muscular type expressed in rhabdomyosarcoma cells (TE671). The rDH also had an LD50 of 0.15 mg/kg mice, and it was evaluated as a potential immunogen in New Zealand rabbits. The protective capacity of rabbit sera was tested against two native coral snake α-neurotoxins, and against rD.H. One of the anti-rD.H rabbit sera was able to neutralize the lethality of all three neurotoxins when tested in groups of CD1 mice. This work contributes to the increasing understanding of the high diversity of 3FTxs, and shows that recombinant coral snake α-neurotoxins are promising supplements for hyperimmunization protocols for coral snake antivenom production.

  • Functional attribution of LdISP, an endogenous serine protease inhibitor from Leishmania donovani in promoting infection
    Biochimie (IF 3.112) Pub Date : 2018-01-31
    Md Nur Alam, Sajal Chakraborti, Dibyendu Paik, Angshuman Bagchi, Tapati Chakraborti

    Leishmaniasis, a parasitic disease caused by unicellular eukaryotic protozoa of the genus Leishmania, affects more than 12 million people worldwide. Events of leishmaniasis are based on the infection of the mammalian host, precisely macrophages, where both host and parasite derived proteases and endogenous inhibitors are significant. Pathogen derived protease inhibitors have generated considerable interest as they often act as an agent promoting infection and parasitic survivability. An endogenous serine protease inhibitor from Indian strain of Leishmania donovani was previously identified by our group and named as LdISP. It has been found to inhibit neutrophil elastase (NE), responsible for natural inflammation process. However, LdISP’s role in progression of infection or the proteomics based structural exposition has not been explored. The present study is aimed to localize and validate the potential role of LdISP in infectivity. We found that LdISP localized endogenously and treatment of infected host cells with LdISP curbs ROS and NO production. Additionally, in silico studies are carried out to predict the putative amino acid residues of LdISP involved in the inhibition process. Taken together, our results demonstrate that LdISP eventually exerts a pronounced role in L.donovani infection.

  • MiR-143-3p inhibits the proliferation, cell migration and invasion of human breast cancer cells by modulating the expression of MAPK7
    Biochimie (IF 3.112) Pub Date : 2018-01-31
    Chongsheng Xia, Ya Yang, Fanhua Kong, Qingli Kong, Changping Shan
  • Biochemical characterization of Campylobacter jejuni PNPase, an exoribonuclease important for bacterial pathogenicity
    Biochimie (IF 3.112) Pub Date : 2018-01-13
    Jorge Casinhas, Rute G. Matos, Nabila Haddad, Cecília M. Arraiano

    Bacteria need to promptly respond to environmental changes. Ribonucleases (RNases) are key factors in the adaptation to new environments by enabling a rapid adjustment in RNA levels. The exoribonuclease polynucleotide phosphorylase (PNPase) is essential for low-temperature cell survival, affects the synthesis of proteins involved in virulence and has an important role in swimming, cell adhesion/invasion ability, and chick colonization in C. jejuni. However, the mechanism of action of this ribonuclease is not yet known. In this work we have characterized the biochemical activity of C. jejuni PNPase. Our results demonstrate that Cj-PNP is a processive 3' to 5' exoribonuclease that degrades single-stranded RNAs. Its activity is regulated according to the temperature and divalent ions. We have also shown that the KH and S1 domains are important for trimerization, RNA binding, and, consequently, for the activity of Cj-PNP. These findings will be helpful to develop new strategies for fighting against C. jejuni and may be extrapolated to other foodborne pathogens.

  • Selection of PD1/PD-L1 X-Aptamers
    Biochimie (IF 3.112) Pub Date : 2017-09-11
    Hongyu Wang, Curtis H. Lam, Xin Li, Derek L. West, Xianbin Yang

    Specific, chemically modified aptamers (X-Aptamers) were identified against two immune checkpoint proteins, recombinant Programmed Death 1 (PD-1) and Programmed Death Ligand 1 (PD-L1). Selections were performed using a bead-based X-Aptamer (XA) library containing several different amino acid functional groups attached to dU at the 5-position. The binding affinities and specificities of the selected XA-PD1 and XA-PDL1 were validated by hPD-1 and hPD-L1 expression cells, as well as by binding to human pancreatic ductal adenocarcinoma tissue. The selected PD1 and PDL1 XAs can mimic antibody functions in in vitro assays.

  • Biosensors for Alzheimer's disease biomarker detection: A review
    Biochimie (IF 3.112) Pub Date : 2018-01-04
    Bingqing Shui, Dan Tao, Anca Florea, Jing Cheng, Qin Zhao, Yingying Gu, Wen Li, Nicole Jaffrezic-Renault, Yong Mei, Zhenzhong Guo

    Alzheimer's disease (AD) is a chronic disease amongst people aged 65 and older. Increasing evidence has illustrated that early diagnosis holds the key to effective treatment of AD. A variety of detection techniques have been developed. Biosensors are excellent analytical tools which have applications in detecting the biomarkers of AD. This review includes appropriate bioreceptors to achieve highly sensitive and selective quantification of AD biomarkers by using transducers. AD biomarkers such as tau protein, amyloid β peptides and apolipoprotein E4, are firstly summarized. The most commonly used bioreceptors, including aptamers and antibodies, are also reviewed. We introduce aptamers specific to AD biomarkers, list the sequences of aptamers designed to capture AD biomarkers and compare the properties of aptamers with those of antibodies with regard to their efficiency as bio-recognition elements. We discuss the recent progress of aptamer systems' applications in AD biomarkers in biosensing. The review also discusses novel strategies used for signal amplification in sensing AD biomarkers.

  • Direct visualization of the oligomeric state of hemagglutinins of influenza virus by high-resolution atomic force microscopy
    Biochimie (IF 3.112) Pub Date : 2018-01-02
    Nikolay Barinov, Nikita Ivanov, Alexey Kopylov, Dmitry Klinov, Elena Zavyalova

    High-resolution atomic force microscopy (AFM) is a powerful technique for the direct visualization of single molecules. Here, AFM is applied to characterize the oligomeric state of hemagglutinins of the influenza virus. Hemagglutinins are known to be present in a trimeric form inside the viral envelope. However, recombinant hemagglutinins are also present as large oligomers, which impair the functional activity of the protein. Five commercial recombinant hemagglutinins from the viral strains H1, H3, H5, H7, and H9 were studied with high-resolution AFM. Functionally inactive hemagglutinins were shown to have a higher percentage of large oligomers compared with the proteins with functional activity. Large oligomers were revealed to be unstable; the oligomeric state of hemagglutinin was affected by pH or the presence of ligands. Antibody binding shifts the balance to small oligomers, whereas DNA aptamer induced the formation of large associates.

  • Inhibition of autophagy reverses alcohol-induced hepatic stellate cells activation through activation of Nrf2-Keap1-ARE signaling pathway
    Biochimie (IF 3.112) Pub Date : 2018-01-02
    Zheng-Yuan Xie, Zhi-Hua Xiao, Fen-Fen Wang

    Background Numerous documents have indicated a critical role of autophagy in alcoholic liver fibrosis (ALF), but few papers have reported its function in hepatic stellate cells (HSCs) activation. The current study aimed to investigate the regulation effect of autophagy in HSCs activation, in further to explore the underlying mechanism involved. Methods HSC-T6 cells were treated with ethanol, 3-MA (autophagy inhibitor) or rapamycin (autophagy inducer), and cells were also transfected with si-Nrf2 or si-Keap1. Moreover, ALF animal model was established and Nrf-2(-/-), Keap1 (-/-) mice were purchased. The level of autophagy, the expression of α-SMA and CoL1A1, and Nrf2 antioxidant response were evaluated in stellate cells and livers. Results Ethanol treatment in cultured cells increased autophagy, oxidative stress level and promoted HSCs activation. Inhibition of autophagy reversed alcohol-induced HSCs activation and suppressed HSCs oxidative stress. Nrf2-Keap1-ARE pathway was involved in HSCs activation and oxidative stress regulated by autophagy. In addition, through in vivo study, we found that inhibition of autophagy could alleviate alcoholic fatty liver injury in ALF model mice and Nrf2 signaling was involved in autophagy regulated HSCs activation. Conclusion These data implicated mechanisms underlying autophagy in regulating the fibrogenic response in HSCs activation.

  • ssDNA Hybridization Facilitated by T7 ssDNA Binding Protein (gp2.5) Rapidly Initiates from the Strand Terminus or Internally Followed by a Slow Zippering Step
    Biochimie (IF 3.112) Pub Date : 2017-12-30
    Zhenyu Zou, Siying Wu, Jingyuan Xiong, Huangyuan Li, Yiguo Jiang, Huidong Zhang

    The hybridization of two complementary ssDNA is essential for molecular biology and biological physics. T7 ssDNA binding protein (gp2.5) can rapidly facilitate this hybridization, but the mechanism and kinetic process remain unknown. As determined by fluorescence resonance energy transfer (FRET) and rapid kinetic analysis methods, gp2.5 binding coiling ssDNA to form gp2.5-ssDNA complex is the rate-limiting step for the entire DNA hybridization process. Afterward, the hybridization initiates from either the terminus or the internal part of ssDNA at a nucleation rate of 0.45 s-1. The remaining DNA strands are hybridized in a zippering mode at a rate of 0.07 s-1, limited by the dissociation of gp2.5 from ssDNA. The gp2.5-faciliated hybridization rate constant (74 μM-1s-1) is much higher than the spontaneous hybridization rate (1.7 μM-1s-1) in the absence of gp2.5. These hybridization mechanism and kinetic process are different from those by other ssDNA binding proteins, such as T4 gp32, Escherichia coli SSB protein and recA protein. Compare with E. coli SSB, the relatively slower association of gp2.5 to ssDNA and faster dissociation of gp2.5 from ssDNA are probably the major reasons to facilitate the rapid hybridization. This study provides valuable insights into the molecular mechanism of the recombination and repair processes and proposes a basis for improvement in their associated biotechnologies.

  • L-ascorbic acid: a true substrate for HIF proly hydroxylase?
    Biochimie (IF 3.112) Pub Date : 2017-12-28
    A.I. Osipyants, A.A. Poloznikov, N.A. Smirnova, D.M. Hushpulian, A.Yu. Khristichenko, T.A. Chubar, A.A. Zakhariants, M. Ahuja, I.N. Gaisina, B. Thomas, A.M. Brown, I.G. Gazaryan, V.I. Tishkov

    L-Ascorbate (L-Asc), but not D-isoascorbate (D-Asc) and N-acetylcysteine (NAC) suppress HIF1 ODD-luc reporter activation induced by various inhibitors of HIF prolyl hydroxylase (PHD). The efficiency of suppression by L-Asc was sensitive to the nature of HIF PHD inhibitor chosen for reporter activation. In particular, the inhibitors developed to compete with alpha-ketoglutarate (αKG), were less sensitive to suppression by the physiological range of L-Asc (40-100 μM) than those having a strong iron chelation motif. Challenging those HIF activators in the reporter system with D-Asc demonstrated that the D-isomer, despite exhibiting the same reducing potency with respect to ferric iron, had almost no effect compared to L-Asc. Similarly, no effect on reporter activation was observed with cell-permeable reducing agent NAC up to 1 mM. Docking of L-Asc and D-Asc acid into the HIF PHD2 crystal structure showed interference of Tyr310 with respect to D-Asc. This suggests that L-Asc is not merely a reducing agent preventing enzyme inactivation. Rather, the overall results identify L-Asc as a co-substrate of HIF PHD that may compete for the binding site of αKG in the enzyme active center. This conclusion is in agreement with the results obtained recently in cell-based systems for TET enzymes and jumonji histone demethylases, where L-Asc has been proposed to act as a co-substrate and not as a reducing agent preventing enzyme inactivation.

  • The gene product of a Trypanosoma equiperdum ortholog of the cAMP-dependent protein kinase regulatory subunit is a monomeric protein that is not capable of binding cyclic nucleotides
    Biochimie (IF 3.112) Pub Date : 2017-12-27
    José Bubis, Juan Carlos Martínez, Maritza Calabokis, Joilyneth Ferreira, Carlos E. Sanz-Rodríguez, Victoria Navas, José Leonardo Escalona, Yurong Guo, Susan S. Taylor

    The full gene sequence encoding for the Trypanosoma equiperdum ortholog of the cAMP-dependent protein kinase (PKA) regulatory (R) subunits was cloned. A poly-His tagged construct was generated [TeqR-like(His)8], and the protein was expressed in bacteria and purified to homogeneity. The size of the purified TeqR-like(His)8 was determined to be ∼ 57,000 Da by molecular exclusion chromatography indicating that the parasite protein is a monomer. Limited proteolysis with various proteases showed that the T. equiperdum R-like protein possesses a hinge region very susceptible to proteolysis. The recombinant TeqR-like(His)8 did not bind either [3H] cAMP or [3H] cGMP up to concentrations of 0.40 and 0.65 μM, respectively, and neither the parasite protein nor its proteolytically generated carboxy-terminal large fragments were capable of binding to a cAMP-Sepharose affinity column. Bioinformatics analyses predicted that the carboxy-terminal region of the trypanosomal R-like protein appears to fold similarly to the analogous region of all known PKA R subunits. However, the protein amino-terminal portion seems to be unrelated and shows homology with proteins that contained Leu-rich repeats, a folding motif that is particularly appropriate for protein-protein interactions. In addition, the three-dimensional structure of the T. equiperdum protein was modeled using the crystal structure of the bovine PKA RIα subunit as template. Molecular docking experiments predicted critical changes in the environment of the two putative nucleotide binding clefts of the parasite protein, and the resulting binding energy differences support the lack of cyclic nucleotide binding in the trypanosomal R-like protein.

  • 更新日期:2017-12-27
  • Effect of dC → d(m5C) Substitutions on the Folding of Intramolecular Triplexes with Mixed TAT and C+GC Base Triplets
    Biochimie (IF 3.112) Pub Date : 2017-12-24
    Carolyn E. Carr, Rajkumar Ganugula, Ronald Shikiya, Ana Maria Soto, Luis A. Marky

    Oligonucleotide-directed triple helix formation has been recognized as a potential tool for targeting genes with high specificity. Cystosine methylation in the 5’ position is both ubiquitous and a stable regulatory modification, which could potentially stabilize triple helix formation. In this work, we have used a combination of calorimetric and spectroscopic techniques to study the intramolecular unfolding of four triplexes and two duplexes. We used the following triplex control sequence, named Control Tri, d(AGAGAC5TCTCTC5TCTCT), where C5 are loops of five cytosines. From this sequence, we studied three other sequences with dC → d(m5C) substitutions on the Hoogsteen strand (2MeH), Crick strand (2MeC) and both strands (4MeHC). Calorimetric studies determined that methylation does increase the thermal and enthalpic stability, leading to an overall favorable free energy, and that this increased stability is cumulative, i.e. methylation on both the Hoogsteen and Crick strands yields the largest favorable free energy. The differential uptake of protons, counterions and water was determined. It was found that methylation increases cytosine protonation by shifting the apparent pKa value to a higher pH; this increase in proton uptake coincides with a release of counterions during folding of the triplex, likely due to repulsion from the increased positive charge from the protonated cytosines. The immobilization of water was not affected for triplexes with methylated cytosines on their Hoogsteen or Crick strands, but was seen for the triplex where both strands are methylated. This may be due to the alignment in the major groove of the methyl groups on the cytosines with the methyl groups on the thymines which causes an increase in structural water along the spine of the triplex.

  • Aptamers as therapeutic middle molecules
    Biochimie (IF 3.112) Pub Date : 2017-10-16
    Yoshikazu Nakamura

    Therapeutic molecules can be classified as low-, middle- and high-molecular weight drugs depending on their molecular masses. Antibodies represent high-molecular weight drugs and their clinical applications have been developing rapidly. Aptamers, on the other hand, are middle-molecular weight molecules that are short, single-stranded nucleic acid sequences that are selected in vitro from large oligonucleotide libraries based on their high affinity to a target molecule. Hence, aptamers can be thought of as a nucleic acid analog to antibodies. However, several viewpoints hold that the potential of aptamers arises from interesting characteristics that are distinct from, or in some cases, superior to those of antibodies. Recently, therapeutic middle molecules gain considerable attention as protein-protein interaction (PPI) inhibitors. This review summarizes the recent achievements in aptamer development in our laboratory in terms of PPI and non-PPI inhibitors.

  • In silico approaches to RNA aptamer design
    Biochimie (IF 3.112) Pub Date : 2017-10-12
    Michiaki Hamada

    RNA aptamers are ribonucleic acids that bind to specific target molecules. An RNA aptamer for a disease-related protein has great potential for development into a new drug. However, huge time and cost investments are required to develop an RNA aptamer into a pharmaceutical. Recently, SELEX combined with high-throughput sequencers (i.e., HT-SELEX) has been widely used to select candidate RNA aptamers that bind to a target protein with high affinity and specificity. After candidate selection, further optimizations such as shortening and modifying candidate sequences are performed. In these steps, in silico approaches are expected to reduce the time and cost associated with aptamer drug development. In this article, we review existing in silico approaches to RNA aptamer development, including a method for ranking the candidates of RNA aptamers from HT-SELEX data, clustering a huge number of aptamer sequences, and finding motifs amidst a set of significant RNA aptamers. It is expected that further studies in addition to these methods will be utilized for in silico RNA aptamer design, permitting a minimal number of experiments to be performed through the utilization of sophisticated computational methods.

  • Challenging cancer targets for aptamer delivery
    Biochimie (IF 3.112) Pub Date : 2017-09-28
    Vittorio de Franciscis

    The extraordinary boost in the understanding of the genetic and epigenetic mechanisms underlying the development and progression of different types of cancer, is offering an unprecedented hope for the development of precise therapeutics able to interfere or replace the expression of target genes. In the last decade, the design of stable, safe and effective RNA-based therapeutics has been significantly improved increasing the number of molecules now in preclinical or in clinical trials for cancer gene therapy. However, with few exclusions as liver and hematological malignancies which are easy accessible to drugs, the development of effective systemic approaches for the delivery of RNA therapeutics to target cells is still unmet. To be effective, targeting carriers must be able to overcome both functional and physical barriers to safely carry and accumulate the therapeutic through the organism selectively to the tumor site, penetrate the target cancer mass, promote the uptake and localization in the appropriate intracellular compartment ultimately leading to the effective modulation of gene expression. Nucleic acid aptamers are folded single stranded oligonucleotides that bind at high affinity and high specificity their targets (proteins, lipids, small molecules etc), coupling the advantages of binding specificity proper of antibodies to the chemical nature of nucleic acids, sometimes also termed “nucleic acid antibodies”. In several cases, aptamers targeting cell surface receptors are recycled into the cell together with the bound receptor enabling to drive conjugated therapeutics to cancer cells in a receptor-dependent manner. Therefore, besides other in vivo delivery strategies, the use of aptamers as precise and effective targeting moieties for anticancer RNA-based therapeutics has rapidly emerged and has been successfully addressed by several laboratories. In this Review, we will focus on the most recent and challenging progresses in the field that highlights the precision and flexibility of aptamer-based chimeras paving the way to the development of safe and effective carriers for cancer gene therapeutics.

  • Complex formation with protamine prolongs the thrombin-inhibiting effect of DNA aptamer in vivo
    Biochimie (IF 3.112) Pub Date : 2017-09-19
    V.A. Spiridonova, T.M. Novikova, D.M. Nikulina, T.A. Shishkina, E.V. Golubkina, O.S. Dyukareva, N.N. Trizno

    Antithrombin DNA aptamersRE31 are single-chain oligonucleotides that fold into three-dimensional forms allowing them to bind the enzyme with high affinity and inhibit its activity in vivo. They are rapidly degraded by a nonspecific nuclease, and, to prolong the lifetime of the aptamer DNA in the bloodstream, it is necessary to coat it with a polymer envelope. A new approach to solving this problem based on preparation of DNA–polyelectrolyte complexes with a minimal particle size that can circulate with blood flow. In our experiments, the negatively charged aptamer DNA RE31 was coated step-by-step with positively charged protamine. They had protamine/aptamer ratios of 0.2/1 and 0.4/1 by charge, with particle size being determined by dynamic light scattering. The aptamer DNA–protamine complexes were administered to rats, followed by ex vivo analysis of blood samples. The results showed that prothrombin time (PT) increased by a factor of 5.6–6.7 within 2 h after injection and remained at approximately the same level for 6 h, while injections of pure protamine did not lead to any noticeable change in clotting time. Thus, complexation with protamine proved to prolong the inhibitory activity of the RE31 DNA aptamer.

  • DNA aptamer generation by ExSELEX using genetic alphabet expansion with a mini-hairpin DNA stabilization method
    Biochimie (IF 3.112) Pub Date : 2017-09-13
    Ichiro Hirao, Michiko Kimoto, Kyung Hyun Lee

    A novel aptamer generation method to greatly augment the affinity and stability of DNA aptamers was developed by genetic alphabet expansion combined with mini-hairpin DNA technology. The genetic alphabet expansion increases the physicochemical and structural diversities of DNA aptamers by introducing extra components, unnatural bases, as a fifth base, allowing for the enhancement of DNA aptamer affinities. Furthermore, the mini-hairpin DNA technology stabilizes DNA aptamers against nuclease digestion and thermal denaturation, by introducing an extraordinarily stable mini-hairpin DNA containing a GCGAAGC sequence. This novel method provides stabilized high-affinity DNA aptamers for diagnostic and therapeutic applications.

  • Deoxynucleoside 5-monophosphate N-glycosidase from a phylogenetically distant metazoa, sponge
    Biochimie (IF 3.112) Pub Date : 2017-12-19
    Nele Aas-Valleriani, Tõnu Reintamm, Merike Kelve

    Deoxynucleoside 5-monophosphate N-glycosidase or DNPH1 (former name Rcl) is a nucleotide hydrolase whose expression in mammalian cancer tissues has been associated with its tumorigenic potential. Therefore, the enzyme has been studied principally in rat and human models. We found the corresponding gene also in the freshwater sponge Ephydatia muelleri, an animal phylogenetically very distant from mammals. Here we report the expression and characterization of the recombinant DNPH1 from E. muelleri. The ancient homolog of mammalian enzyme in a sponge showed the substrate specificity and catalytic efficiency similar to that in higher animals. E. muelleri DNPH1 is inhibited by the purine nucleotides with different numbers of 5’-phosphate groups (n = 1-4). Our results demonstrate that GTP but also dGTP are the best inhibitors, followed by all other purine nucleotides that were tested. Hence, the functioning of DNPH1 in cells where the natural ATP and GTP concentrations are much higher than those of the substrates, dNMPs, should normally be downregulated. We demonstrate for the first time the existence of biologically relevant natural inhibitors of DNPH1, namely ATP and GTP.

  • An archaeal aminoacyl-tRNA synthetase complex for improved substrate quality control
    Biochimie (IF 3.112) Pub Date : 2017-12-19
    Ana Crnković, Mirela Čavužić, Vlatka Godinić-Mikulčić, Gregor Anderluh, Ivana Weygand-Đurašević, Ita Gruić-Sovulj

    Aminoacyl-tRNA synthetases (aaRS) decode genetic information by coupling tRNAs with cognate amino acids. In the archaeon Methanothermobacter thermautotrophicus arginyl- and seryl-tRNA synthetase (ArgRS and SerRS, respectively) form a complex which enhances serylation and facilitates tRNASer recycling through its association with the ribosome. Yet, the way by which complex formation participates in Arg-tRNAArg synthesis is still unresolved. Here we utilized pull down and surface plasmon resonance experiments with truncated ArgRS variants to demonstrate that ArgRS uses its N-terminal domain to establish analogous interactions with both SerRS and cognate tRNAArg, providing a rationale for the lack of detectable SerRS•[ArgRS•tRNAArg] complex. In contrast, stable ternary ArgRS•[SerRS•tRNASer] complex was easily detected supporting the model wherein ArgRS operates in serylation by modulating SerRS affinity toward tRNASer. We also found that the interaction with SerRS suppresses arginylation of unmodified tRNAArg by ArgRS, which, by itself, does not discriminate against tRNAArg substrates lacking posttranscriptional modifications. Hence, there is a fundamentally different participation of the protein partners in Arg-tRNA and Ser-tRNA synthesis. Propensity of the ArgRS•SerRS complex to exclude unmodified tRNAs from translation leads to an attractive hypothesis that SerRS•ArgRS complex might act in vivo as a safeguarding switch that improves translation accuracy.

  • Chicken GRIFIN: Structural characterization in crystals and in solution
    Biochimie (IF 3.112) Pub Date : 2017-12-15
    Federico M. Ruiz, Ulrich Gilles, Anna-Kristin Ludwig, Celia Sehad, Tze Chieh Shiao, Gabriel García Caballero, Herbert Kaltner, Ingo Lindner, René Roy, Dietmar Reusch, Antonio Romero, Hans-Joachim Gabius

    Despite its natural abundance in lenses of vertebrates the physiological function(s) of the galectin-related inter-fiber protein (GRIFIN) is (are) still unclear. The same holds true for the significance of the unique interspecies (fish/birds vs mammals) variability in the capacity to bind lactose. In solution, ultracentrifugation and small angle X-ray scattering (at concentrations up to 9 mg/mL) characterize the protein as compact and stable homodimer without evidence for aggregation. The crystal structure of chicken (C-)GRIFIN at seven pH values from 4.2 to 8.5 is reported, revealing compelling stability. Binding of lactose despite the Arg71Val deviation from the sequence signature of galectins matched the otherwise canonical contact pattern with thermodynamics of an enthalpically driven process. Upon lactose accommodation, the side chain of Arg50 is shifted for hydrogen bonding to the 3-hydroxyl of glucose. No evidence for a further ligand-dependent structural alteration was obtained in solution by measuring hydrogen/deuterium exchange mass spectrometrically in peptic fingerprints. The introduction of the Asn48Lys mutation, characteristic for mammalian GRIFINs that have lost lectin activity, lets labeled C-GRIFIN maintain capacity to stain tissue sections. Binding is no longer inhibitable by lactose, as seen for the wild-type protein. These results establish the basis for detailed structure-activity considerations and are a step to complete the structural description of all seven members of the galectin network in chicken.

  • Toluidine blue O modifies hippocampal amyloid pathology in a transgenic mouse model of Alzheimer’s disease
    Biochimie (IF 3.112) Pub Date : 2017-12-14
    Melike Yuksel, Kevser Biberoglu, Seda Onder, K. Gonca Akbulut, Ozden Tacal

    Recently, we demonstrated that toluidine blue O (TBO), a phenothiazine dye, shows inhibitory effects on both cholinesterases and amyloid pathology in Alzheimer’s disease (AD) cellular model. In the present study, we aimed to determine the effects of TBO (in a purity of 85%) on amyloid and tau pathologies in a triple transgenic mouse model of AD (3xTg-AD). Beginning at 7.5 (mild pathology) or 13 (severe pathology) months of age, 3xTg-AD mice were treated intraperitoneally with 4 mg/kg TBO or vehicle daily for 30 days. TBO treatment significantly reduced the levels of insoluble Aβ40 and Aβ42 in the hippocampi of mild and severe pathology groups compared to vehicle-treated counterparts. When the levels of full-length amyloid precursor protein (APP) and β-site APP-cleaving enzyme 1 (BACE1) were assessed in 3xTg-AD mice at late pathological stage, no significant changes were observed after TBO treatment. Similarly, TBO did not recover hyperphosphorylation of tau at residues Thr181 and Ser202/Thr205 significantly in soluble and insoluble hippocampal fractions of 3xTg-AD mice. Taken together, the current study is the first in vivo report, to our knowledge, demonstrating that TBO mitigates amyloid pathology in 3xTg-AD mice with no apparent change on tau phosphorylation. Overall, the preliminary data presented here support the possible use of TBO as a disease-modifying drug for AD treatment.

  • Secretory lipase from the human pathogen Leishmania major: Heterologous expression in the yeast Pichia pastoris and biochemical characterization
    Biochimie (IF 3.112) Pub Date : 2017-12-13
    Saoussen Ben Ayed, Madiha Bou Ali, Aymen Bali, Youssef Gargouri, Dhafer Laouini, Yassine Ben Ali

    Leishmaniasis is a parasitic reticuloendotheliosis whose pathogen is a zooflagellate belonging to the genus Leishmania transmitted by the bite of an infected phlebotome. Recently, a unique secretory lipase from the human pathogen Leishmania donovani Ldlip3 has been identified and characterized. This lipase has a high identity with a putative triacylglycerol lipase of Leishmania major (Lmlip2). In the present study, Lmlip2 was expressed in the eukaryotic heterologous expression system Pichia pastoris as tagged enzyme of 308 amino acids. Maximal protein production was reached after 2 days of fermentation. Optimal Lmlip2 lipase activity was measured using the pH stat technique at pH 8 at 26°C using vinyl esters and triacylglycerols (true lipids) as substrates. Moreover, biochemical characterization of Lmlip2 contained in culture supernatant, illustrates that L. major secreted lipase is active and stable at low temperatures especially 26°and prefer neutral pH; concerning substrate specificityLmlip2 presents a preference for short chains lipid substrates vinyl esters such as VC2, VC3 and VC4 likewise, it is capable to hydrolyze long chain triacylglycerols like olive oil. Metal ions and surfactants tested in this study decrease Lmlip2 activity. Further studies are needed to clarify the relation between the lipase activity and the virulence. Thus, it could lead to the identification of novel targets to block cutaneous Leishmaniasis in human hosts.

  • Aptamers as potential therapeutic agents for ovarian cancer
    Biochimie (IF 3.112) Pub Date : 2017-12-07
    Justin Liam Henri, Joanna Macdonald, Mia Strom, Wei Duan, Sarah Shigdar
  • Multi-targeted effects of G4-aptamers and their antiproliferative activity against cancer cells
    Biochimie (IF 3.112) Pub Date : 2017-12-05
    Anna M. Ogloblina, Alexandra N. Khristich, Natalia Y. Karpechenko, Svetlana E. Semina, Gennady A. Belitsky, Nina G. Dolinnaya, Marianna G. Yakubovskaya
  • Nobiletin induces brown adipocyte-like phenotype and ameliorates stress in 3T3-L1 adipocytes
    Biochimie (IF 3.112) Pub Date : 2017-12-05
    Jameel Lone, Hilal Ahmad Parray, Jong Won Yun

    Browning of white adipocytes (beiging) is an attractive therapeutic strategy against obesity and its associated metabolic complications. Nobiletin (NOB) is a polymethoxylated flavone present in Citrus fruits and has been reported to have anti-obesity effects. Here, we report that nobiletin exerts dual modulatory effects on adipocytes via induction of browning in 3T3-L1 white adipocytes and amelioration of stress in adipocytes. Nobiletin-induced beiging was investigated by determining expression levels of beige-specific genes and proteins by RT-PCR and immunoblot analysis, respectively. Nobiletin treatment rapidly elevated the expression levels of beige-specific genes such as Cd137, Cidea, Tbx1, and Tmem26. Further, nobiletin enhanced expression of the key transcription factors C/EBPβ, PPARδ, and PPARα, which are responsible for remodeling of white adipocytes. Nobiletin also strikingly activated HIB1B brown adipocytes and induced mitochondrial biogenesis in 3T3-L1 white adipocytes. In addition, nobiletin altered the expression of several lipid metabolism-related proteins such as ACOX1, CPT1, FAS, p-PLIN, SREBP and SIRT1. Moreover, nobiletin ameliorated stress in adipocytes by inhibiting expression levels of key stress molecules such as JNK and c-JUN. Nobiletin-induced browning could be mediated by tight regulation of kinases, as nobiletin induced PKA and p-AMPK at the protein expression level, and inhibition of PKA and p-AMPK by H-89 and dorsomorphin, respectively, abolished expression of the thermogenic markers PGC-1α and UCP1. Taken together, our findings suggest that nobiletin plays a modulatory role in adipocytes via induction of browning in 3T3-L1 white adipocytes and activation of HIB1B brown adipocytes combined with amelioration of stress in adipocytes, thereby exhibiting therapeutic potential against obesity.

  • Aptamers targeting cell surface proteins
    Biochimie (IF 3.112) Pub Date : 2017-12-02
    Masaki Takahashi

    High affinity binders targeting specific cell surface proteins are vital for development of basic and applied biosciences. However, despite sustained efforts to generate such binders by chemicals and antibodies, there are still many cell surface proteins that lack high affinity binders. Nucleic acid aptamers have potential as binding molecules for cell surface proteins, because they form distinct structures that have high affinity and specificity for a wide range of targets. Aptamers are isolated from large combinatorial libraries using a unique iterative selection-amplification process known as systematic evolution of ligands by exponential enrichment (SELEX). Among advantages of this method, purified and complex heterogeneous targets, such as bacteria, viruses, and whole-living cells, can be used for selection of aptamers. Moreover, SELEX allows generation of cell-surface-specific aptamers without prior knowledge of expression profiles in target cells. Therefore, the technology has been widely used as a valid and feasible method to generate aptamers binding to cell surface proteins with intact structure. Herein, this review summarizes and updates iconic SELEX technologies that target membrane proteins.

  • Insulin resistance in 3T3-L1 adipocytes by TNF-α is improved by punicic acid through upregulation of insulin signalling pathway and endocrine function, and downregulation of proinflammatory cytokines
    Biochimie (IF 3.112) Pub Date : 2017-11-26
    S.S. Anusree, G. Sindhu, M.R. Preetha Rani, K.G. Raghu

    Insulin resistance (IR) has become a major threat to public health due to its role in metabolic syndrome. Inflammation associated with IR is an interesting area of biomedical researchers in recent years and is expected to affect insulin signalling pathway via downregulating glucose transporters. In the present study, we evaluate the potential of punicic acid (PA), a nutraceutical found in pomegranate seed oil, against TNF-α induced alteration in 3T3-L1 adipocytes on glucose metabolism, endocrine function and inflammation. IR was induced in 3T3-L1 adipocytes by treating with TNF-α (10 ng/mL) and various concentrations of PA (5, 10, 30 μM) were incubated simultaneously. After 24 h, we found that TNF-α treatment increased mRNA expression of SOCS3, PTP1B and a decrease in IRS1 causing diminished glucose uptake. Further, it showed significantly increased transcriptional activity of NFκB and leptin secretion while PA maintained leptin levels normal. Additionally, PA prevented the over-expression of phosphorylated JNK in a dose dependent manner during IR. PA also ameliorated significantly the upregulation of proinflammatory cytokines. From the results, we conclude that PA is effective to ameliorate TNF-α induced IR and also we recommend the intake of PA for control and management of IR and its associated complications.

  • Serine 51 residue of Citrobacter freundii tyrosine phenol-lyase assists in C-α-proton abstraction and transfer in the reaction with substrate
    Biochimie (IF 3.112) Pub Date : 2017-11-26
    Maria V. Barbolina, Vitalia V. Kulikova, Marina A. Tsvetikova, Natalia V. Anufrieva, Svetlana V. Revtovich, Robert S. Phillips, Paul D. Gollnick, Tatyana V. Demidkina, Nicolai G. Faleev

    In the spatial structure of tyrosine phenol-lyase, the Ser51 residue is located in the active site of the enzyme. The replacement of Ser51 with Ala by site-directed mutagenesis led to a decrease of the kcat/Km parameter for reactions with l-tyrosine and 3-fluoro-l-tyrosine by three orders of magnitude, compared to wild type enzyme. For the elimination reactions of S-alkylcysteines, the values of kcat/Km decreased by an average of two orders of magnitude. The results of spectral studies of the mutant enzyme gave evidence for a considerable change of the chiral properties of the active site as a result of the replacement. Fast kinetic studies for the complexes of the mutant form with competitive inhibitors allowed us to conclude that the Ser51 residue interacts with the side chain amino group of Lys257 at the stage of C-α-proton abstraction. This interaction ensures the correct orientation of the side chain of Lys257 accepting the C-α-proton of the external aldimine and stabilizes its ammonium form. Also, it is probable that Ser51 takes part in formation of a chain of hydrogen bonds which is necessary to perform the transfer of the C-α-proton to the C-4′-position of the leaving phenol group in the reaction with the natural substrate.

  • Aptamers in Bordeaux 2017: An exceptional “millésime”
    Biochimie (IF 3.112) Pub Date : 2017-11-24
    Jean-Jacques Toulmé, Laurent Azéma, Fabien Darfeuille, Eric Dausse, Guillaume Durand, Olivier Paurelle

    About 150 participants attended the symposium organised at the Palais de la Bourse in Bordeaux, France on September 22–23, 2017. Thirty speakers from all over the world delivered lectures covering selection processes, aptamer chemistry and innovative applications of these powerful tools that display major advantages over antibodies. Beyond the remarkable science presented, lively discussion and fruitful exchange between participants made this meeting a great success. A series of lectures were focused on synthetic biology (riboswitches, new synthetic base pairs, mutated polymerases). Innovative selection procedures including functional screening of oligonucleotide pools were described. Examples of aptasensors for the detection of pathogens were reported. The potential of aptamers for the diagnostic and the treatment of diseases was also presented. Brief summaries of the lectures presented during the symposium are given in this report. The third edition of this symposium will take place in Boulder, Colorado in Summer 2018 (information available at http://www.aptamers-in-bordeaux.com/).

  • DNA mismatch repair proteins MLH1 and PMS2 can be imported to the nucleus by a classical nuclear import pathway
    Biochimie (IF 3.112) Pub Date : 2017-11-24
    Andrea C. de Barros, Agnes A.S. Takeda, Thiago R. Dreyer, Adrian Velazquez-Campoy, Boštjan Kobe, Marcos R.M. Fontes

    MLH1 and PMS2 proteins form the MutLα heterodimer, which plays a major role in DNA mismatch repair (MMR) in humans. Mutations in MMR-related proteins are associated with cancer, especially with colon cancer. The N-terminal region of MutLα comprises the N-termini of PMS2 and MLH1 and, similarly, the C-terminal region of MutLα is composed by the C-termini of PMS2 and MLH1, and the two are connected by linker region. The nuclear localization sequences (NLSs) necessary for the nuclear transport of the two proteins are found in this linker region. However, the exact NLS sequences have been controversial, with different sequences reported, particularly for MLH1. The individual components are not imported efficiently, presumably due to their C-termini masking their NLSs. In order to gain insights into the nuclear transport of these proteins, we solved the crystal structures of importin-α bound to peptides corresponding to the supposed NLSs of MLH1 and PMS2 and performed isothermal titration calorimetry to study their binding affinities. Both putative MLH1 and PMS2 NLSs can bind to importin-α as monopartite NLSs, which is in agreement with some previous studies. However, MLH1-NLS has the highest affinity already measured by a natural NLS peptide, suggesting a major role of MLH1 protein in nuclear import compared to PMS2. Finally, the role of MLH1 and PMS2 in the nuclear transport of the MutLα heterodimer is discussed.

  • Structural features of the interaction of the 3′-untranslated region of mRNA containing exosomal RNA-specific motifs with YB-1, a potential mediator of mRNA sorting
    Biochimie (IF 3.112) Pub Date : 2017-11-11
    Darya D. Yanshina, Olga A. Kossinova, Alexander V. Gopanenko, Olga A. Krasheninina, Alexey A. Malygin, Alia G. Ven'yaminova, Galina G. Karpova

    We have previously shown that YB-1 is the only protein of the HEK293 cell cytoplasmic (S100) extract that specifically interacts with RNA hairpins each containing one of the motifs ACCAGCCU (1), CAGUGAGC (2) and UAAUCCCA (3), which had been identified as often found in exosomal RNA and proposed as potential cis-acting elements targeting RNAs into exosomes. Here we explored the interactions of YB-1 with a fragment of the 3′-untranslated region (UTR) of septin 14 mRNA (SEPT14 RNA), which contains all three motifs. We demonstrated the occurrence of YB-1 among proteins pulled down from the HEK293 S100 extract using biotinylated SEPT14 RNA. With recombinant YB-1, it was found that SEPT14 RNA can bind up to 5 moles of protein per mole of RNA in a cooperative manner, which was shown to be mainly facilitated by the presence of the above motifs. RNA hairpins with motifs 1 and 2 competed with SEPT14 RNA for binding to the protein, whereas that with motif 3 was less competitive, in accordance with the affinity of YB-1 for these RNA hairpins. With YB-1-bound RNA, nucleotides protected from attack by hydroxyl radicals were revealed in all three motifs, although hairpins with motif 2 and especially with motif 1 contained many protected nucleotides outside the motifs, suggesting that the specific environments of these motifs contribute significantly to the YB-1 binding. An analysis of the environments of motifs 1–3 in the HEK293 cell mRNA 3′ UTRs gained from RNA-seq data led us to conclude that the primary binding sites of YB-1 in the 3′ UTRs are hairpins containing some part of the motif along with its specific surroundings; the consensus sequences of these hairpins were derived. Thus, our findings provide a new understanding of the structural basis of the interactions between YB-1 and mRNAs carrying the aforementioned motifs.

  • Fluorescent light-up acridine orange derivatives bind and stabilize KRAS-22RT G-quadruplex
    Biochimie (IF 3.112) Pub Date : 2017-11-10
    Josué Carvalho, Edgar Pereira, Julien Marquevielle, Maria P.C. Campello, Jean-Louis Mergny, António Paulo, Gilmar F. Salgado, João A. Queiroz, Carla Cruz

    KRAS is often found mutated in lethal cancers and should be an important target for anticancer drug development. However, no effective inhibitor has been reported so far, prompting the scientific community to describe the RAS proteins as nearly “undruggable”. Recent approaches developed to modulate KRAS protein expression comprises the targeting of G-quadruplex (G4) structures formed within the nuclease hypersensitive element of KRAS promoter region, by designing small and specific ligands to stabilize the tertiary fold and reduce gene expression. In this work, we report in vitro and in silico studies of novel acridine orange (AO) derivatives (C3-C8), developed as G4 stabilizing agents. The results show that the ligands bind with high affinity and stabilize KRAS22-RT G4 with modest specificity over duplex DNA. The most promising ligand C8 stabilizes the structure by ≈ 40 °C. Molecular docking using NMR-derived distance restraints reveal atomic details about the ligand structural features in the interaction with KRAS22-RT G4. In vitro studies with HeLa cells show that the ligands are cytotoxic with IC50 values between 0.9 μM and 5.7 μM. Moreover, the ligands tend to localize in the nucleus as shown by confocal fluorescence microscopy. Overall, these results show that the reported AO ligands display favourable properties as G4 ligands and this study provides structural detail for the development of lead KRAS G4 ligands.

  • Upregulation of aquaporin 3 expression by diterpenoids in Euphorbia pekinensis is associated with activation of the NF-κB signaling pathway in the co-culture system of HT-29 and RAW 264.7 cells
    Biochimie (IF 3.112) Pub Date : 2017-11-09
    Hongli Yu, Lian Liu, Kuilong Wang, Hao Wu, Wei Wang, Xingde Zhang, Guojing Cui, Xiaobing Cui, Jianyu Huang

    This study was designed to evaluate the toxic effects of diterpenoids separated from the roots of Euphorbia pekinensis, a type of widely used traditional Chinese medicine. This herb has intestinal toxicity associated with its complex diterpenoids. In this study, the diterpenoids (pekinenin A, pekinenin C, pekinenin F, pekinenin G, yuexiandajisu A, (−)-(1S)-15-hydroxy-18-carboxycembrene) elevated the expression of interleukin 1 beta and tumor necrosis factor alpha in a dose-dependent manner at doses of 6.25, 12.5, and 25 μM in RAW264.7 monocultures. Pekinenin C increased the expression of phosphorylated IκB and phosphorylated p65 in RAW264.7 monocultures, indicating that it stimulated a substantial inflammatory response and activated the nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) signaling pathway. A co-culture model of RAW 264.7 mouse macrophage cells and HT-29 human intestinal epithelial cells was established to study the correlation between inflammation and aquaporin (AQP) expression and to evaluate the toxicity of different diterpenoids from E. pekinensis. Pekinenin C (6.25, 12.5, and 25 μM) increased AQP3 mRNA and protein expression of HT-29 cells in the co-culture system in a dose-dependent manner but not in HT-29 monocultures. AQP3 mRNA and protein expression peaked at 2 and 3 h of HT-29 cells in the co-culture system, respectively. In contrast, their expression peaked more slowly in the monoculture system. After the specific NF-κB inhibitor BAY11-7082 (5, 10, and 20 μM) was added to the co-culture system, the release of cytokines and increased AQP3 expression caused by pekinenin C were inhibited. Comparisons of the representative monomeric compound pekinenin C, diterpenoid monomer mixtures, and total diterpenoids from E. pekinensis showed that the monomer mixtures had the most toxicity. In conclusion, this study demonstrated that E. pekinensis induces inflammation and increases the expression of AQP3, causing disorders of water metabolism, which may lead to gastrointestinal side effects such as diarrhea.

  • Aptamer-mediated Plasmodium-specific diagnosis of malaria
    Biochimie (IF 3.112) Pub Date : 2017-11-08
    Yee-Wai Cheung, Roderick M. Dirkzwager, Wai-Chung Wong, Josiane Cardoso, Joana D'Arc Neves Costa, Julian A. Tanner

    There is a critical need for better malaria rapid diagnostic tests to discriminate Plasmodium falciparum and Plasmodium vivax infection given the recent observation of HRP2 deletions in P. falciparum parasites. We previously identified a DNA aptamer, 2008s, that targets P. falciparum lactate dehydrogenase (PfLDH) and developed a sensitive aptamer-tethered enzyme capture (APTEC) assay. Here, we characterise two different LDH-binding DNA aptamers in their species-specific activities, then integrate within biochemical diagnostic assays and test in clinical samples. An enzyme-linked oligonucleotide assay demonstrated that aptamer pL1 bound with high affinity to both PfLDH and P. vivax lactate dehydrogenase (PvLDH), whereas aptamer 2008s was specific to PfLDH. An aptamer-tethered enzyme capture (APTEC) assay confirmed the specificity of 2008s in binding and capturing the enzyme activity of PfLDH which could be observed colorimetrically. In malaria patient samples, the 2008s APTEC assay was specific for P. falciparum blood samples and could discriminate against P. vivax blood samples. An aptamer for specific detection of falciparum malaria holds promise as a new strategy for species-specific malaria diagnosis rather than the conventional HRP2 immuno-assay.

  • Alkaline-tolerant RNA aptamers useful to purify acid-sensitive antibodies in neutral conditions
    Biochimie (IF 3.112) Pub Date : 2017-11-03
    Emire Inomata, Erika Tashiro, Shin Miyakawa, Yoshikazu Nakamura, Kazumasa Akita

    Recently, several oligonucleotides have been launched for clinical use and a number of therapeutic oligonucleotides are under clinical trials. Aptamer is one of the oligonucleotide therapeutics and has received a lot of attention as a new technology and an efficacious pharmaceutical compound comparable to antibody. Aptamer could be used for various purposes, not only therapeutics but also diagnostics, and applicable to affinity chromatography as a carrier molecule to purify proteins of interest. Here we demonstrate the usage and advantages of RNA aptamer to Fc region of human IgG (i.e., IgG aptamer) for purification of human antibodies. IgG aptamer requires divalent cations for binding to IgG and bound IgG dissociates easily upon treatment with chelating reagent, such as EDTA, under neutral conditions. This elution step is very mild and advantageous for maintaining active conformations of therapeutic antibodies compared to the widely used affinity purification with Protein A/G, which requires acidic elution that often damages the active conformation of antibodies. In fact, of several monoclonal antibodies tested, three antibodies were prone to aggregate on acidic elution from the Protein A/G resin, while remained fully active upon neutral elution from the IgG aptamer resin. The IgG aptamer was fully manipulated to alkaline resistant by ribose 2′-modifications, and thereby reusable numerous times with 1 N NaOH washing. The capacity of the aptamer resin to bind IgG was equivalent to that of the Protein A/G resin. Therefore, the IgG aptamer will provide us with a unique tool to uncover and purify human monoclonal antibodies, which hold therapeutic potential but lose the activity upon acidic elution from Protein A/G-based affinity resin.

  • Nucleic acid aptamers for neurodegenerative diseases
    Biochimie (IF 3.112) Pub Date : 2017-11-03
    Alix Bouvier-Müller, Frédéric Ducongé

    The increased incidence of neurodegenerative diseases represents a huge challenge for societies. These diseases are characterized by neuronal death and include several different pathologies, such as Alzheimer's disease, Parkinson's disease, multiple sclerosis, Huntington's disease and transmissible spongiform encephalopathies. Most of these pathologies are often associated with the aggregation of misfolded proteins, such as amyloid-ß, tau, α-synuclein, huntingtin and prion proteins. However, the precise mechanisms that lead to neuronal dysfunction and death in these diseases remain poorly understood. Nucleic acid aptamers represent a new class of ligands that could be useful to better understand these diseases and develop better diagnosis and therapy. In this review, several of these aptamers are presented as well as their applications for neurodegenerative diseases.

  • SDA and IDA – Two aptamers to inhibit cancer cell adhesion
    Biochimie (IF 3.112) Pub Date : 2017-11-02
    Ulrich Hahn

    Aptamers which bind to proteins involved in cell-cell interactions could have significant value to directly affect cancer cell adhesion or for directed cargo delivery. Here, I discuss two aptamers: aptamer SDA which binds to E- and P-selectin, and aptamer IDA which binds to α6β4 integrin. Both aptamers (SDA 91 nt and IDA 77 nt) bind their target proteins with dissociation constants in the 100–150 nM range and substantially inhibit special cellular adhesion, possibly a first and pivotal step in transendothelial migration during metastasis formation. The aptamers' half-lives in cell culture media are between two and six hours. IDA is internalized by integrin presenting cells within minutes thus possibly serving as vehicle for directed cargo delivery.

  • Systematic evaluation of cell-SELEX enriched aptamers binding to breast cancer cells
    Biochimie (IF 3.112) Pub Date : 2017-10-18
    Laia Civit, Seyed Mohammad Taghdisi, Anna Jonczyk, Silvana K. Haßel, Carsten Gröber, Michael Blank, H. James Stunden, Marc Beyer, Joachim Schultze, Eicke Latz, Günter Mayer

    The sensitive and specific detection of pathogenic cells is essential in clinical diagnostics. To achieve this, molecular tools are required that unequivocally recognise appropriate cell surface molecules, such as biomarkers that come along with disease onset and progression. Aptamers are short single-stranded oligonucleotides that interact with cognate target molecules with high affinity and specificity. Within the last years they have gained an increased attention as cell-recognition tools. Here, we report a systematic analysis of a cell-SELEX procedure, for the identification of aptamers that recognise breast cancer cells. Besides a comparison of conventional (Sanger) with high-throughput sequencing techniques (next-generation sequencing), three different screening techniques have been applied to characterise the binding properties of selected aptamer candidates. This method has been found to be beneficial in finding DNA aptamers, rarely enriched in the libraries. Finally, four DNA aptamers were identified that exhibit broad-spectrum interaction patterns to different cancer cell lines derived from solid tumours.

  • Thermodynamic study of aptamers binding to their target proteins
    Biochimie (IF 3.112) Pub Date : 2017-10-18
    Taiichi Sakamoto, Eric Ennifar, Yoshikazu Nakamura

    Aptamers are nucleic acids that bind to a target molecule with high affinity and specificity, which are selected from systematic evolution of ligands by exponential enrichment (SELEX). Aptamers feature high affinity and specificity to their target molecule and a large structural diversity; biophysical tools, together with structural studies, are essential to reveal the mechanism of aptamers recognition. Furthermore, understanding the mechanism of action would also contribute to their development for therapeutic applications. Isothermal titration calorimetry (ITC) is a fast and robust method to study the physical basis of molecular interactions. In a single experiment, it provides all thermodynamic parameters of a molecular interaction, including dissociation constant, Kd; Gibbs free energy change, ΔG; enthalpy change, ΔH; entropy change, ΔS; and stoichiometry, N. The development of modern microcalorimeters significantly contributed to the expansion of the ITC use in biological systems. Therefore, ITC has been applied to the development of small therapeutic agents that bind to target proteins and is increasingly being used to study aptamer-target protein interactions. This review focuses on thermodynamic approaches for understanding the molecular principles of aptamer–target interactions.

  • Aptamer affinity ligands in protein chromatography
    Biochimie (IF 3.112) Pub Date : 2017-10-18
    Gérald Perret, Egisto Boschetti

    The present review deals with the place of single chain oligonucleotide ligands (aptamers) in affinity chromatography applied to proteins. Aptamers are not the only affinity ligands available but they represent an emerging and highly promising route that advantageously competes with antibodies in immunopurification processes. A historical background of affinity chromatography from the beginning of the discipline to the most recent outcomes is first presented. Then the focus is centered on aptamers which represent the last step so far to the long quest for affinity ligands associating very high specificity, availability and strong stability against most harsh cleaning agents required in chromatography. Then technologies of ligand selection from large libraries followed by the most appropriate chemical grafting approaches are described and supported by a number of bibliographic references. Experimental results assembled from relevant published paper are reported; they are selected by their practical applicability and potential use at large scale. The review concludes with specific remarks and future developments that are expected in the near future to turn this technology into a large acceptance for preparative applications.

Some contents have been Reproduced with permission of the American Chemical Society.
Some contents have been Reproduced by permission of The Royal Society of Chemistry.
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