Characterization of Filarial Phosphoglycerate kinase Biochimie (IF 3.362) Pub Date : 2019-08-22 Ranjeet Kumar, Faiyaz Ahmad, Sushma Rathaur
Phosphoglycerate kinase (PGK) is a key enzyme of glycolysis which also acts as a mediator of DNA replication and repair in the nucleus. We have cloned and expressed PGK in Brugia malayi. The rBmPGK was found to be 415 amino acid residues long having 45kDa subunit molecular weight. This enzyme was also identified in different life stages of bovine filarial parasite Setaria cervi. The enzyme activity was highest in microfilarial stage followed by adult female and male as also shown by real time PCR in the present study. Further using BmPGK primers the cDNA prepared from S. cervi was amplified and sequenced which showed 100% homology with Brugia malayi PGK. B. malayi and S. cervi, PGK consists of conserved calmodulin binding domain (CaMBD) having 21 amino acids. In the present study we have shown the CaMBD binds to calcium-calmodulin and regulates its activity. The binding of calmodulin (CaM) with CaMBD was confirmed using calmodulin agarose binding pull down assay, which showed that the rBmPGK binds to CaM agarose-calcium dependent manner. The effect of CaM-Ca2+on the activity of rBmPGK was studied at different concentration of CaM (0.01-5.0 μM) and calcium chloride (0.01-100 μM). The rBmPGK was activated up to 85 % in the presence of CaM at 1 μM and 10 μM concentration of CaCl2. Interestingly this activation was abrogated by metal chelator EDTA. Similar results were shown in case of Setaria cervi PGK. A significant increase (90±10) % in ScPGK activity was observed in the presence of CaM and CaCl2 at 1.0 μM and 1.0 mM respectively, further increase in the conc. of CaCl2, the activity of ScPGK was found to be decreased like rBmPGK. Bioinformatics studies have also confirmed the interaction between CaMBD and CaM which showed CaM interacted to Phe 206, Gln 220, Arg 223 and Asn 224 of rBmPGK CaM binding domain. On the basis of these findings, it has been suggested that the activity of filarial PGK could be regulated in cells by Ca2+-CaM depending upon the concentration of calcium. To the best of our knowledge this is first report in filarial parasite.
Antithrombin is incorporated into exosomes produced by antithrombin non-expressing cells Biochimie (IF 3.362) Pub Date : 2019-08-21 Ginés Luengo-Gil, Antonio Bernardino García-Andreo, Carmen Ortega-Sabater, Nataliya Bohdan, Salvador Espín, Julia Peñas-Martínez, Elena Martínez-Planes, Álvaro García-Hernández, Vicente Vicente, Miguel Quintanilla, Irene Martínez-Martínez
Antithrombin is a serine protease inhibitor that exerts a crucial role in hemostasis as the main inhibitor of the coagulation cascade. It plays also critical roles in other processes, such as inflammation and cancer. Here we show that exosomes released by Madin-Darby canine kidney (MDCK) cells cultured in the presence of heparin incorporate antithrombin from the serum. Exosomal antithrombin is found complexed with the serine protease high temperature requirement A1 (HTRA1), whose cellular levels are increased after serum deprival, the condition used to collect exosomes. Although the biological relevance of the presence of antithrombin in exosomes remains to be investigated, our results suggest a functional interplay between antithrombin and HTRA1.
Modulating DNA by polyamides to regulate transcription factor PU.1-DNA binding interactions Biochimie (IF 3.362) Pub Date : 2019-08-21 Beibei Liu, James K. Bashkin, Gregory M.K. Poon, Shuo Wang, Siming Wang, W. David Wilson
Identification of 2H phosphoesterase superfamily proteins with 2´-CPDase activity Biochimie (IF 3.362) Pub Date : 2019-08-15 Shuhei Mitsutomi, Nobuyoshi Akimitsu, Kazuhisa Sekimizu, Chikara Kaito
The 2H phosphoesterase superfamily (2H family) proteins are widely conserved among organisms. The 2H family is classified into several subgroups, including YjcG-like proteins whose enzymatic activity has not been reported. In the present study, we found that two YjcG-like proteins (Staphylococcus aureus SA0873 and Bacillus subtilis YjcG) have 2´-CPDase activity that hydrolyzes a 2´,3´-cyclic nucleotide, thereby producing a nucleotide with a 3´-phosphate. The SA0873 protein selectively hydrolyzes a 2´,3´-cyclic nucleotide with a purine base. Four SA0873 mutant proteins (H34A, T36A, H115A, and T117A), in which alanine was substituted for amino acid residues in the HxT/Sx motifs that are conserved in the 2H family, abolished the 2´-CPDase activity. Comparison of three-dimensional structures between the YjcG-like proteins with 2´-CPDase activity and another 2H family subgroup, LigT/2´-5´ RNA ligase-like proteins with 3´-CPDase activity, revealed that the orientation of the substrate binding pocket is reversed between the two groups. Our findings revealed that YjcG-like proteins not only have a substrate-binding pocket different from that of LigT/2´-5´ RNA ligase-like proteins, but they also have 2´-CPDase activity.
Comparative effects of trehalose and 2-hydroxypropyl-β-cyclodextrin on aggregation of UV-irradiated muscle glycogen phosphorylase b Biochimie (IF 3.362) Pub Date : 2019-08-10 Tatiana B. Eronina, Valeriya V. Mikhaylova, Natalia A. Chebotareva, Vladimir V. Shubin, Nikolai N. Sluchanko, Boris I. Kurganov
Chemical chaperones are a class of small molecules which enhance folding and prevent aggregation of proteins. Investigation of their effects on the processes of protein aggregation is of importance for further understanding of implication of protein aggregation in neurodegenerative diseases, as well as for solving biotechnological tasks. The effects of chemical chaperones trehalose and 2-hydroxypropyl-β-cyclodextrin (HP-β-CD) on the kinetics of aggregation of UV-irradiated muscle glycogen phosphorylase b (UV-Phb) at 37 °C have been studied. The process of thermal aggregation of UV-Phb includes a slow stage of structural reorganization of the UV-Phb molecule, nucleation stage and fast attachment of structurally reorganized UV-Phb molecules to nuclei formed during the nucleation stage. It was shown that both trehalose and HP-β-CD increased the duration of the nucleation phase and slowed down the rate of structural reorganization of the UV-Phb molecule. This conclusion has been confirmed by the circular dichroism data. In the absence of chaperones, 82% UV-Phb aggregates, whereas in the presence of HP-β-CD or trehalose the portion of aggregated protein decreases to 70 and 66%, respectively. The data on analytical ultracentrifugation demonstrated that in the presence of these additives the size of protein aggregates decreased. Analysis of the combined effect of trehalose and HP-β-CD on UV-Phb aggregation showed that protein aggregation was independently affected by trehalose and HP-β-CD.
Unfolded Protein Response Supports Endothelial Barrier Function Biochimie (IF 3.362) Pub Date : 2019-08-09 Nektarios Barabutis
Ongoing efforts are oriented towards the development of novel therapeutic agents to repress lung hyper permeability responses due to inflammation. The endothelial barrier dysfunction due to such events, may eventually lead to severe cardiovascular complications, such as the Acute Respiratory Distress Syndrome. Hsp90 inhibitors are anticancer compounds, associated with strong anti-inflammatory responses in the endothelium. Our latest observations in experimental models of Acute Lung Injury suggest that P53 orchestrates, at least in part, such responses. Remarkably, both Hsp90 inhibition and P53 induction are associated with the activation of the Unfolded Protein Response element. The purpose of the current manuscript, is to introduce the hypotheses that UPR induction protects the vasculature against inflammation.
Protein-protein interactions regulate the activity of Adipose Triglyceride Lipase in intracellular lipolysis Biochimie (IF 3.362) Pub Date : 2019-08-09 Natalia Kulminskaya, Monika Oberer
Carefully regulated lipid homeostastis generates an optimal physiological, non-toxic environment. Imbalances in lipid metabolism lead to obesity and are associated with type-2 diabetes, hepatic steatosis, hypertension and cardiovascular disease. Mammals store energy in lipid droplets predominantly in white adipose tissue. This energy reservoir builds up during periods of energy excess and is mobilized during energy deprivation. Triacylglycerols (TAGs) are unable to cross cell membranes for cell nutrition; they have to be cleaved before further transportation within the body. Lipolysis describes the cleavage of TAG and is carried out with the help of lipases. Adipose triglyceride lipase (ATGL) catalyzes the first step of intracellular lipolysis to mobilize TAG stores. In this minireview, we set the focus on molecular mechanism and interfaces behind co-activation and inhibition of ATGL, namely via its regulation by the co-activating protein CGI-58, the inhibitory proteins G0S2 and HILPDA, as well as the regulatory effect of fatty acid binding proteins and the perilipin protein family.
Apolipoprotein A-I improves hepatic autophagy through the AMPK pathway Biochimie (IF 3.362) Pub Date : 2019-08-08 Xia Rao, Yutong Wang
Dysfunction in lipid metabolism may result in a decrease in hepatic autophagy, which contributes to the pathogenesis of non-alcoholic steatohepatitis. ATP-binding cassette transporter A1 transports free cholesterol and phospholipids to apolipoprotein A-I (apoA-I) to form nascent high-density lipoprotein particles. Results from previous studies showed that the overexpression of apoA-I significantly reduced levels of hepatic lipids and endoplasmic reticulum stress by modifying lipid transport. Here, we investigated the effects of apoA-I overexpression on hepatic autophagy in cultured hepatocytes and mice. The overexpression of apoA-I in HepG2 cells resulted in an increase in the levels of autophagy as well as the phosphorylation of AMP-activated protein kinase α (AMPKα) and ULK1 and a decrease in the phosphorylation of mammalian target of rapamycin (mTOR). An AMPK inhibitor and siRNA eliminated this apoA-1 effect. Consistently, apoA-I transgenic mice showed increased autophagy and AMPKα phosphorylation. These results suggest that apoA-I overexpression alleviates steatohepatitis by increasing hepatic autophagy through the AMPK-mTOR-ULK1 pathway.
Role of AKT and mTOR Signaling Pathways in the Induction of Epithelial-Mesenchymal Transition (EMT) Process Biochimie (IF 3.362) Pub Date : 2019-08-08 Mostafa Karimi Roshan, Arash Soltani, Anvar Soleimani, Kolsoum Rezaie Kahkhaie, Amir R. Afshari, Mohammad Soukhtanloo
Epithelial-mesenchymal transition (EMT) is a critical process in the development of many tissues and organs in multicellular organisms that its important role in the pathogenesis of metastasis and tumor cell migration has been firmly established. Decreased adhesive capacity, cytoskeletal reorganization, and increased mobility are hallmarks of the EMT. Several molecular mechanisms promote EMT, Including regulation of the levels of specific cell-surface proteins, ECM-degrading enzymes, and altering the expression of certain transcription factors and microRNAs. EMT process is modulated through multiple signaling pathways including the AKT/mTOR pathway. AKT is a key component in numerous processes which was recently shown to regulate the EMT through suppression of the expression of E-cadherin via EMT transcription factors. On the other hand, mTOR complexes can also regulate the EMT through the regulation of cell’s actin cytoskeleton by altering the PKC phosphorylation state and direct phosphorylation and activation of Akt. Here we review the effect of AKT and mTOR on EMT and consequently metastasis and cell motility.
LIPUS promotes FOXO1 accumulation by downregulating miR-182 to enhance osteogenic differentiation in hPDLCs Biochimie (IF 3.362) Pub Date : 2019-08-08 Duanjing Chen, Mingli Xiang, Yuanyuan Gong, Ling Xu, Tingwei Zhang, Yao He, Mengjiao Zhou, Liangjing Xin, Jie Li, Jinlin Song
Low intensity pulsed ultrasound (LIPUS) promotes bone fracture healing in clinical therapy. Transcription factor Forkhead box O1 (FOXO1) is crucial for bone differentiation. But whether FOXO1 is involved in LIPUS-promoted bone differentiation is largely unknown. In the current study, treatment of human primary periodontal ligament cells (hPDLCs) with LIPUS promoted total and nucleus FOXO1 protein accumulation. LIPUS-induced activation of FOXO1 further lead to higher alkaline phosphatase (ALP) and runt-related transcription factor 2 (Runx2) expression and matrix mineralization. LIPUS inhibited miR-182 expression, which functioned as a repressor of FOXO1 through post-transcriptional regulation. Overexpression of miR-182 reversed the LIPUS-enhanced FOXO1 expression and osteogenic differentiation. Moreover, LIPUS enhanced Akt phosphorylation, which functioned in preventing active FOXO1 excessive accumulation via inducing the cytoplasm translocation of nucleus FOXO1. In conclusion, our study revealed that FOXO1, which was a target gene of miR-182, played an essential role in LIPUS-promoted osteogenic differentiation. This new molecular insight throws light upon the application of LIPUS therapy on periodontal bone defect.
Mouse Fat-Specific Protein 27 (FSP27) expressed in plant cells localizes to lipid droplets and promotes lipid droplet accumulation and fusion Biochimie (IF 3.362) Pub Date : 2019-08-07 Ann M. Price, Nathan M. Doner, Satinder K. Gidda, Srikarthika Jambunathan, Christopher N. James, Alyssa Schami, Olga Yurchenko, Robert T. Mullen, John M. Dyer, Vishwajeet Puri, Kent D. Chapman
The case for class II bacteriocins: a biophysical approach using “suicide probes” in receptor-free hosts to study their mechanism of action Biochimie (IF 3.362) Pub Date : 2019-08-02 N.S. Ríos Colombo, M.C. Chalón, F.G. Dupuy, C.F. Gonzalez, A. Bellomio
in silico prediction of protein flexibility with local structure approach Biochimie (IF 3.362) Pub Date : 2019-08-01 Tarun J. Narwani, Catherine Etchebest, Pierrick Craveur, Sylvain Léonard, Joseph Rebehmed, Narayanaswamy Srinivasan, Aurélie Bornot, Jean-Christophe Gelly, Alexandre G. de Brevern
Flexibility is an intrinsic essential feature of protein structures, directly linked to their functions. To this day, most of the prediction methods use the crystallographic data (namely B-factors) as the only indicator of protein’s inner flexibility and predicts them as rigid or flexible.PredyFlexy stands differently from other approaches as it relies on the definition of protein flexibility (i) not only taken from crystallographic data, but also (ii) from Root Mean Square Fluctuation (RMSFs) observed in Molecular Dynamics simulations. It also uses a specific representation of protein structures, named Long Structural Prototypes (LSPs). From Position-Specific Scoring Matrix, the 120 LSPs are predicted with a good accuracy and directly used to predict (i) the protein flexibility in three categories (flexible, intermediate and rigid), (ii) the normalized B-factors, (iii) the normalized RMSFs, and (iv) a confidence index. Prediction accuracy among these three classes is equivalent to the best two class prediction methods, while the normalized B-factors and normalized RMSFs have a good correlation with experimental and in silico values. Thus, PredyFlexy is a unique approach, which is of major utility for the scientific community. It support parallelization features and can be run on a local cluster using multiple cores.
Improved hepatic MRP2/ABCC2 transport activity in LPS-induced cholestasis by aquaporin-1 gene transfer Biochimie (IF 3.362) Pub Date : 2019-08-01 Julieta Marrone, Guillermo N. Tocchetti, Mauro Danielli, Aldo D. Mottino, Raúl A. Marinelli
Multidrug resistance-associated protein 2 (MRP2/ABCC2), a hepatocyte canalicular transporter involved in bile secretion, is downregulated in cholestasis triggered by lipopolysaccharide. The human aquaporin-1 (hAQP1) adenovirus-mediated gene transfer to liver improves cholestasis by incompletely defined mechanisms. Here we found that hAQP1 did not affect MRP2/ABCC2 expression, but significantly increased its transport activity assessed in situ with endogenous and exogenous substrates, likely by a hAQP1-induced increase in canalicular membrane cholesterol amount. Our results suggest that hAQP1-induced MRP2/ABCC2 activation contributes to the cholestasis improvement.
ATP synthase, an essential enzyme in growth and multiplication is modulated by Protein Tyrosine Phosphatase in Mycobacterium tuberculosis H37Ra Biochimie (IF 3.362) Pub Date : 2019-08-01 Aditi Chatterjee, Sapna Pandey, Ekta Dhamija, Swati Jaiswal, Shivraj M. Yabaji, Kishore K. Srivastava
Mycobacterium tuberculosis (Mtb) protein tyrosine phosphatase (PtpA) has so far been known to control intracellular survival of mycobacteria; whereas the ATP synthase which is essential for mycobacterial growth has recently been contemplated in developing a breakthrough anti-TB drug, diarylquinoline. Since both of these enzymes have been established as validated drug targets; we report a robust and functional relationship between these two enzymes through a series of experiments using Mtb H37Ra. In the present study we report that the mycobacterial ATP synthase alpha subunit is regulated by PtpA. We generated gene knockouts for the enzyme PtpA and subjected to determine the mycobacterial replication and the proteome profile of wild type, mutant (ΔptpA) and complemented (ΔptpA::ptpA) strains of Mtb H37Ra. A substantial amount of decrease in the protein level of ATP synthase alpha subunit (AtpA) in case of mutant H37Ra was observed, while the levels of the enzyme were either increased or remained unchanged, in wild type and in the complemented strains.
Targeting a viral DNA sequence with a deoxyribozyme in a preparative scale Biochimie (IF 3.362) Pub Date : 2019-08-01 Parisa Dastjerdi-Khorzoghi, Fatemeh Javadi-Zarnaghi, Zohreh Hojati
Origins of peptidases Biochimie (IF 3.362) Pub Date : 2019-08-01 Neil D. Rawlings, Alex Bateman
The distribution of all peptidase homologues across all phyla of organisms was analysed to determine within which kingdom each of the 271 families originated. No family was found to be ubiquitous and even peptidases thought to be essential for life, such as signal peptidase and methionyl aminopeptides are missing from some clades. There are 33 peptidase families common to archaea, bacteria and eukaryotes and are assumed to have originated in the last universal common ancestor (LUCA). These include peptidases with different catalytic types, exo- and endopeptidases, peptidases with different tertiary structures and peptidases from different families but with similar structures. This implies that the different catalytic types and structures pre-date LUCA. Other families have had their origins in the ancestors of viruses, archaea, bacteria, fungi, plants and animals, and a number of families have had their origins in the ancestors of particular phyla. The evolution of peptidases is compared to recent hypotheses about the evolution of organisms.
DNA Binding Thermodynamics and Site Stoichiometry as a Function of Polyamide Size Biochimie (IF 3.362) Pub Date : 2019-07-31 Yang Song, Jacquelyn Niederschulte, Kristin N. Bales, Andrew H. Park, James K. Bashkin, Cynthia M. Dupureur
MicroRNA-25-5p counteracts oxidized LDL-induced pathological changes by targeting neuronal growth regulator 1 (NEGR1) in human brain micro-vessel endothelial cells Biochimie (IF 3.362) Pub Date : 2019-07-28 Qi Zhang, Chun Liu, Qiang Li, Jianan Li, Yina Wu, Jianmin Liu
MicroRNA-25-5p (miR-25-5p) may be involved in the pathogenesis and processes of vascular diseases. The aim of this study was to investigate the role of miR-25-5p in oxidized low-density lipoprotein (ox-LDL)-treated human brain microvessel endothelial cells (HBMECs) and the underlying mechanisms. RT-qPCR and/or western blot were used to detect the expression levels of miR-25-5p and neuronal growth regulator 1 (NEGR1). The effect of miR-25-5p overexpression and NEGR1 silencing on cell proliferation, migration, apoptosis and reactive oxygen species (ROS) production of HBMECs were measured by using CCK-8 assay, transwell assay and flow cytometry, respectively. The expression levels of apoptosis-related protein (cleaved caspase-3 and pro-caspase-3) were detected using western blot, and the nitric oxide (NO) production was measured by a nitric oxide assay kit. The expression level of miR-25-5p was decreased in HBMECs treated with ox-LDL. Compared with the control group, miR-25-5p overexpression significantly promoted the proliferation and migration of HBMECs treated with ox-LDL (p<0.01). Overexpression of miR-25-5p significantly suppressed cell apoptosis, ROS production and NO reduction of ox-LDL-induced HBMECs (p<0.01). In addition, the target gene of miR-25-5p was predicted to be NEGR1 through Targetscan online analysis. The effect of NEGR1 silencing on cell proliferation, migration, apoptosis, ROS and NO production of ox-LDL-induced HBMECs was similar to that of miR-25-5p overexpression. Furthermore, miR-25-5p overexpression and NEGR1 silencing significantly downregulated the protein expression levels of JAK2 and STAT3. Thus, miR-25-5p neutralizes the effects of ox-LDL on multiple functions of HBMECs through suppressing the expression of NEGR1 via regulating the JAK/STA signaling pathway.
Matrix metalloproteinase-2: Not (just) a “hero” of the past Biochimie (IF 3.362) Pub Date : 2019-07-27 Patrick Henriet, Hervé Emonard
The 72-kDa type IV collagenase or gelatinase A is the second member of the matrix metalloproteinase family, MMP-2. Since the discovery of its first two substrates within components of the extracellular matrix, denatured interstitial type I collagen and native type IV collagen, the roles and various levels of regulation of MMP-2 have been intensively studied, mainly in vitro. Its (over)expression in most if not all tumors was considered a hallmark of cancer aggressiveness and boosted investigations aiming at its inhibition. Unfortunately, the enthusiasm subsided like a soufflé after clinical trial failures, mostly because of insufficient knowledge of in vivo MMP-2 activities and detrimental side effects of broad-spectrum MMP inhibition. Nowadays, MMP-2 remains a major topic of interest in research, the second in the MMP family after MMP-9. This review presents a broad overview of the major features of this protease. This knowledge is crucial to identify diagnostic or therapeutic strategies focusing on MMP-2. In this sense, recent publications and clinical trials underline the potential value of measuring circulating or tissular MMP-2 levels as diagnostic or prognostic tools, or as a useful secondary outcome for therapies against other primary targets. Direct MMP-2 inhibition has benefited from substantial progress in the design of more specific inhibitors but their in vivo application remains challenging but certainly worth the efforts it receives.
Transmembrane Channel-Like 5 (TMC5) promotes prostate cancer cell proliferation through cell cycle regulation Biochimie (IF 3.362) Pub Date : 2019-07-26 Wanfeng Zhang, Sen Wang, Xianqin Zhang, Kun Liu, Jing Song, Xue Leng, Ruihan Luo, Longke Ran
Background In this study, we aimed to investigate the biological functions of Transmembrane Channel-Like 5 (TMC5) by bioinformatics and molecular biology methods in prostate cancer (PCa). Methods We assessed the mRNA expression level of TMC5 in PCa with public database the Cancer Genome Atlas (TCGA) and Oncomine. The biological functions were demonstrated by bioinformatics methods and siRNA mediated knockdown experiments. Reverse transcription polymerase chain reaction (RT-PCR), immunohistochemical (IHC) experiments and microarray analysis were performed to confirm the results. Results TMC5 expression level was significantly up-regulated in 4 independent PCa cohorts compared to normal group. Moreover, TMC5 has higher diagnostic efficiency than PSA-KLK3 (AUC (Area Under Curve) =0.772, P<0.001). The high expression of TMC5 was associated with clinical Gleason score, prostate-specific antigen (PSA) level, androgen receptor (AR) activity score and the genes which were known frequently mutated in PCa progression (P<0.05). Functionally, Gene Otology (GO) analysis suggested that TMC5 was related to cell development; TMC5 knockdown significantly inhibited PCa cells proliferation by arresting cell cycle at G1 phase. Drug sensitivity experiments showed TMC5 knockdown significantly enhanced cells sensitivity to 5-Fluorouracil. Microarray analysis showed TMC5 knockdown significantly inhibited cell cycle and tumor progression. Conclusion Our findings revealed that TMC5 promoted PCa cell proliferation through cell cycle regulation and could be a powerful and hopeful target for PCa treatment.
Swainsonine induces autophagy via PI3K/AKT/mTOR signaling pathway to injure the Renal Tubular Epithelial cells Biochimie (IF 3.362) Pub Date : 2019-07-26 Shuai Wang, Jinglong Wang, Lin Yang, Rong Guo, Enxia Huang, Hanqi Yang, Yajing Zhang, Lu Sun, Runjie Song, Jingshu Chen, Yanan Tian, Baoyu Zhao, Qingyun Guo, Hao Lu
Swainsonine is a major toxic ingredients of locoweed plants, ingestion of these plants may cause locoism in livestock characterized by extensive cellular vacuolar degeneration of multiple tissues. However, so far, the mechanisms responsible for vacuolar degeneration induced by SW are not known. In this study, we investigated the role of autophagy in SW-induced TCMK-1 cells using Western blotting, transmission electron microscopy, immunofluorescent microscopy and qRT-PCR. The results showed that SW treatment increased the levels of LC3-II. The co-localization of LC3-II and lysosomal protein LAMP-2 results suggested that SW treatment does not interfere with fusion between autophagosome and lysosome. TEM results indicated that SW induced aggregation of the lysosome around the autophagosome. In addition, SW treatment suppressed p-PI3K, p-Akt, p-mTOR, p-p70S6K and p-4EBP1 level. In conclusion, SW induced autophagy via pI3K/AKT/mTOR signaling pathway and revealed the role of autophagy in causing the SW toxicity characterized by the vacuolar degeneration.
Dissection of TMEM165 function in Golgi glycosylation and its Mn2+ sensitivity Biochimie (IF 3.362) Pub Date : 2019-07-24 Elodie Lebredonchel, Marine Houdou, Sven Potelle, Geoffroy de Bettignies, Céline Schulz, Marie-Ange Krzewinski Recchi, Vladimir Lupashin, Dominique Legrand, André Klein, François Foulquier
Since 2012, the interest for TMEM165 increased due to its implication in a rare genetic human disease named TMEM165-CDG (Congenital Disorder(s) of Glycosylation). TMEM165 is a Golgi localized protein, highly conserved through evolution and belonging to the uncharacterized protein family 0016 (UPF0016). Although the precise function of TMEM165 in glycosylation is still controversial, our results highly suggest that TMEM165 would act as a Golgi Ca2+/Mn2+ transporter regulating both Ca2+ and Mn2+ Golgi homeostasis, the latter is required as a major cofactor of many Golgi glycosylation enzymes. Strikingly, we recently demonstrated that besides its role in regulating Golgi Mn2+ homeostasis and consequently Golgi glycosylation, TMEM165 is sensitive to high manganese exposure. Members of the UPF0016 family contain two particularly highly conserved consensus motifs E-φ-G-D-[KR]-[TS] predicted to be involved in the ions transport function of UPF0016 members. We investigate the contribution of these two specific motifs in the function of TMEM165 in Golgi glycosylation and in its Mn2+ sensitivity. Our results show the crucial importance of these two conserved motifs and underline the contribution of some specific amino acids in both Golgi glycosylation and Mn2+ sensitivity.
Oridonin enhances TRAIL-induced apoptosis through GALNT14-mediated DR5 glycosylation Biochimie (IF 3.362) Pub Date : 2019-07-20 Mi-Yeon Jeon, Seung Un Seo, Seon Min Woo, Kyoung-jin Min, Hee Sun Byun, Gang Min Hur, Sun Chul Kang, Taeg Kyu Kwon
Oridonin is a diterpenoid isolated from the Rabdosia rubescens and has multiple biological effects, such as anti-inflammation and anti-tumor activities. In present study, we revealed that the sensitizing effect of oridonin on tumor necrosis factor-related apoptosis-inducing ligand (TRAIL)-induced apoptosis in several cancer cells, but not in normal cells. Oridonin enhanced death-signaling inducing complexes (DISC) formation and DR5 glycosylation without affecting expression of downstream intracellular apoptosis-related proteins. Oridonin upregulated peptidyl O-glycosyltransferase GALNT14 in a dose- and time-dependent manner. Knockdown of GALNT14 by siRNA and Endo H treatment reduced oridonin-induced DR5 glycosylation. Furthermore, treatment with inhibitor of glycosylation (benzyl-α-GalNAc) blocked oridonin plus TRAIL-induced apoptosis. Collectively, our results suggest that oridonin-induced DR5 glycosylation contributes to TRAIL-induced apoptotic cell death in cancer cells.
Skeletal muscle atrogenes: from rodent models to human pathologies Biochimie (IF 3.362) Pub Date : 2019-07-17 Daniel Taillandier, Cécile Polge
Skeletal muscle atrophy is a common side effect of most human diseases. Muscle loss is not only detrimental for the quality of life but it also dramatically impairs physiological processes of the organism and decreases the efficiency of medical treatments. While hypothesized for years, the existence of an atrophying programme common to all pathologies is still incompletely solved despite the discovery of several actors and key regulators of muscle atrophy. More than a decade ago, the discovery of a set of genes, whose expression at the mRNA levels were similarly altered in different catabolic situations, opened the way of a new concept: the presence of atrogenes, i.e. atrophy-related genes. Importantly, the atrogenes are referred as such on the basis of their mRNA content in atrophying muscles, the regulation at the protein level being sometimes more complicate to elucidate. It should be noticed that the atrogenes are markers of atrophy and that their implication as active inducers of atrophy is still an open question for most of them. While the atrogene family has grown over the years, it has mostly been incremented based on data coming from rodent models. Whether the rodent atrogenes are valid for humans still remain to be established. An “atrogene” was originally defined as a gene systematically up- or down-regulated in several catabolic situations. Even if recent works often restrict this notion to the up-regulation of a limited number of proteolytic enzymes, it is important to keep in mind the big picture view. In this review, we provide an update of the validated and potential rodent atrogenes and the metabolic pathways they belong, and based on recent work, their relevance in human physio-pathological situations. We also propose a more precise definition of the atrogenes that integrates rapid recovery when catabolic stimuli are stopped or replaced by anabolic ones.
BRD4 contributes to high-glucose-induced podocyte injury by modulating Keap1/Nrf2/ARE signaling Biochimie (IF 3.362) Pub Date : 2019-07-17 Hong Zuo, Shujin Wang, Jia Feng, Xufeng Liu
Determination of the Crystal Structure and Substrate Specificity of Ananain Biochimie (IF 3.362) Pub Date : 2019-07-12 Tang Yongqing, Pascal G. Wilmann, Jing Pan, Michael L. West, Tracey J. Brown, Tracey Mynott, Robert N. Pike, Lakshmi C. Wijeyewickrema
Ananain (EC 188.8.131.52) accounts for less than 10% of the total enzyme in the crude pineapple stem extract known as bromelain, yet yields the majority of the proteolytic activity of bromelain. Despite a high degree of sequence identity between ananain and stem bromelain, the most abundant bromelain cysteine protease, ananain displays distinct chemical properties, substrate preference and inhibitory profile compared to stem bromelain. A tripeptidyl substrate library (REPLi) was used to further characterize the substrate specificity of ananain and identify two optimal substrates for cleavage by ananain. The optimal tripeptides, PLQ and VLR, both yielded a high kcat/KM value of 1.7 x 106 M-1s-1, with cleavage confirmed to occur after the Leu residue for each substrate. Crystal structures of unbound ananain and an inhibitory complex of ananain and E-64, solved at 1.73 and 1.98 Å, respectively, revealed a geometrically flat and open S1 subsite for ananain. This subsite accommodates diverse P1 substrate residues, while a narrow and deep hydrophobic pocket-like S2 subsite would accommodate a non-polar P2 residue, such as the preferred Leu residue observed in the specificity studies. A further illustration of the atomic interactions between E-64 and ananain explains the high inhibitory efficiency of E-64 toward ananain. These data reveal the first in depth structural and functional data for ananain and provide a basis for further study of the natural properties of the enzyme.
Treatment of rat thyrocytes in vitro with cathepsin B and L inhibitors results in disruption of primary cilia leading to redistribution of the trace amine associated receptor 1 to the endoplasmic reticulum Biochimie (IF 3.362) Pub Date : 2019-07-11 Joanna Szumska, Zaina Batool, Alaa Al-Hashimi, Vaishnavi Venugopalan, Vladislav Skripnik, Norbert Schaschke, Matthew Bogyo, Klaudia Brix
The relationship between molecular content of mesenchymal stem cells derived exosomes and their potentials: opening the way for exosomes based therapeutics Biochimie (IF 3.362) Pub Date : 2019-07-11 Davod Jafari, Sara Malih, Seyed Sadegh Eslami, Rasool Jafari, Leila Darzi, Parastoo Tarighi, Ali Samadikuchaksaraei
At least, more than half of our understanding of extracellular vesicles owes to the studies conducted over the past few years. When it became clear that the exosomes have various potentials in medicine, extensive research has focused on these potentials in a variety of areas including cancer, drug delivery, and regenerative medicine. The growing understanding of molecular structure and functions of exosomes causes the vision to become brighter in the exosomes complexity, and our attitude toward these vesicles has undergone changes accordingly. Proteomic and transcriptomic studies on exosomes have highlighted their molecular diversity. In this review, we explicitly examine the exosomes composition, molecular structure and their therapeutic potentials in some diseases. Due to the very heterogeneous nature of exosomes, the process of their use as a therapeutic agent in the clinic has been challenged. We are still at the beginning of recognizing the molecular composition of exosomes and mechanisms that affect their physiology and biology. The growing trend of engineering of exosomes has shown a promising future to further utilize them in a different field. Molecular profiling of exosomes and their content for their related potentials in regenerative medicine should be done exactly for further defining a minimum content for specific therapeutic potentials.
Stringent response protein as a potential target to intervene persistent bacterial infection Biochimie (IF 3.362) Pub Date : 2019-07-11 Gajraj Singh Kushwaha, Bolaji Fatai Oyeyemi, Neel Sarovar Bhavesh
Computational insights into the active structure of SGK1 and its implication for ligand design Biochimie (IF 3.362) Pub Date : 2019-07-11 Bashir A. Akhoon, Neha S. Gandhi, Rakesh Pandey
Serum and glucocorticoid-inducible kinase 1 (SGK1), a protein kinase, shares significant structural similarity with other members of the AGC protein kinase family. It has been reported that the inactive SGK1 structure lacks αC helix and this unique feature makes it distinct from other protein kinases. Activation of SGK1 by PDK1 requires phosphorylation at Thr256, but the structural insights of the activation remain unclear. The co-crystal structures of small molecule inhibitors, Magnesium (Mg+2) and ATP bound to the inactive SGK1 are reported however the important regulatory domains such as αC helix are missing in these crystal structures. We modelled the missing αC domain and employed computational molecular dynamics simulations to study the conformational changes in the WT and phosphorylated human SGK1 to systematically investigate how the individual domain motions are modulated by the binding of substrate and Mg+2. The MD results corroborate with the experiential findings and has shown that the inactive SGK1 lacks αC helix content. Surprisingly, we find that the active SGK1 structure closely resembles with other protein kinases and adopt the αC helix content up on SGK1 phosphorylation. However, the residues participating in αC helix formation are fewer than reported in protein kinase A structure, a close relative of SGK1. The computational binding analysis reveals that most of the SGK1 selective inhibitors have less binding affinity for active SGK1 than some FDA-approved kinase inhibitors such as Afatinib, Tofacitinib, Dabrafenib, and Palbociclib. Only EMD638683 was seen as a strong candidate for selective SGK1 inhibition. To our knowledge, this is the first dynamic study of SGK1 that provides new structural insights around the active site that would surely help the experimental biologists for the design of suitable selective ligands able to inhibit or activate SGK1 function.
Nutrigenomics and RNA methylation: role of micronutrients Biochimie (IF 3.362) Pub Date : 2019-07-11 Pauline Mosca, Bruno Leheup, Natacha Dreumont
RNA modifications regulate gene expression by impacting different steps in RNA processing. They are as diverse as they are important for the cell. Most of them have been identified around 1970 and the recent development of high-throughput techniques has shed some insights on their prevalence and function. They are present in all RNA types, but their regulation is still not fully understood. The most described RNA modification is methylation, which requires S-adenosylmethionine as a methyl donor, produced through the one carbon metabolism. Different micronutrients (i.e. folate and vitamin B12) are required to properly generate S-adenosylmethionine, making nutrition a strong regulating factor. Although micronutrients have been extensively described to affect epigenetic mechanisms such as DNA methylation, protein histone post-translational modifications or miRNAs, far less is known about RNA methylation. Here, we review what is known about the regulation of RNA methylation by micronutrients and the physiological consequences of deficiencies.
Relationship between acyl-lipid and sterol metabolisms in diatoms Biochimie (IF 3.362) Pub Date : 2019-07-07 Eric Maréchal, Josselin Lupette
Diatoms are a phylum of unicellular photosynthetic eukaryotes living in oceans and fresh waters, characterized by the complexity of their plastid, resulting from a secondary endosymbiosis event. In the model diatom Phaeodactylum tricornutum, fatty acids (FAs) are synthesized from acetyl-CoA in the stroma of the plastid, producing palmitic acid. FAs are elongated and desaturated to form very-long chain polyunsaturated fatty acids (VLC-PUFAs) in domains of the endomembrane system that need to be identified. Synthesis of VLC-PUFAs is coupled with their import to the core of the plastid via the so-called “omega” pathway. The biosynthesis of sterols in diatoms is likely to be localized in the endoplasmic reticulum as well as using precursors deriving from the mevalonate pathway, using acetyl-CoA as initial substrate. These metabolic modules can be characterized functionally by genetic analyzes or chemical treatments with appropriate inhibitors. Some ‘metabolic modules’ are characterized by a very low level of metabolic intermediates. Since some chemical treatments or genetic perturbation of lipid metabolism induce the accumulation of these intermediates, channeling processes are possibly involved, suggesting that protein-protein interactions might occur between enzymes within large size complexes or metabolons. At the junction of these modules, metabolic intermediates might therefore play dramatic roles in directing carbon fluxes from one direction to another. Here, acetyl-CoA seems determinant in the balance between TAGs and sterols. Future lines of research and potential utilization for biotechnological applications are discussed.
Mapping post-transcriptional modifications in Staphylococcus aureus tRNAs by nanoLC/MSMS Biochimie (IF 3.362) Pub Date : 2019-07-08 Laura Antoine, Philippe Wolff, Eric Westhof, Pascale Romby, Stefano Marzi
RNA modifications are involved in numerous biological processes. These modifications are constitutive or modulated in response to adaptive processes and can impact RNA base pairing formation, protein recognition, RNA structure and stability. tRNAs are the most abundantly modified RNA molecules. Analysis of the roles of their modifications in response to stress, environmental changes, and infections caused by pathogens, has fueled new research areas. Nevertheless, the detection of modified nucleotides in RNAs is still a challenging task. We present here a reliable method to identify and localize tRNA modifications, which was applied to the human pathogenic bacteria, Staphyloccocus aureus. The method is based on a separation of tRNA species on a two-dimensional polyacrylamide gel electrophoresis followed by nano liquid chromatography-mass spectrometry. We provided a list of modifications mapped on 25 out of the 40 tRNA species (one isoacceptor for each amino acid). This method can be easily used to monitor the dynamics of tRNA modifications in S. aureus in response to stress adaptation and during infection of the host, a relatively unexplored field.
An approach to recombinantly produce mature grape polyphenol oxidase Biochimie (IF 3.362) Pub Date : 2019-07-05 Yu Li, Mark-Anthony McLarin, Martin J. Middleditch, Stuart J. Morrow, Paul A. Kilmartin, Ivanhoe K.H. Leung
Polyphenol oxidases (PPOs) are important enzymes that are widely found in both prokaryotes and eukaryotes including grapes. Studies of grape PPO to date have mostly relied on enzymes extracted and purified from plants. In this work, we describe the production of the mature form of Shine Muscat grape PPO by using an Escherichia coli expression system. We have optimised the purification procedure to obtain pure and active recombinant enzymes and characterised the catalytic efficiency of the recombinant grape PPO by using ultraviolet/visible (UV/Vis) spectrophotometry. Our work provides a simple protocol of obtaining pure and active recombinant grape PPO that will enable further studies about the catalytic mechanism and inhibition of this enzyme.
Characterization of all the lipolytic activities in pancreatin and comparison with porcine and human pancreatic juices Biochimie (IF 3.362) Pub Date : 2019-07-06 Amal Salhi, Sawsan Amara, Pascal Mansuelle, Rémy Puppo, Régine Lebrun, Brigitte Gontero, Ahmed Aloulou, Frédéric Carrière
Porcine pancreatic extracts (PPE), also named pancreatin, are commonly used as a global source of pancreatic enzymes for enzyme replacement therapy in patients with exocrine pancreatic insufficiency. They are considered as a good substitute of human pancreatic enzymes and they have become a material of choice for in vitro models of digestion. Nevertheless, while the global PPE contents in lipase, protease and amylase activities are well characterized, little is known about individual enzymes. Here we characterized the lipase, phospholipase, cholesterol esterase and galactolipase activities of PPE and compared them with those of porcine (PPJ) and human (HPJ) pancreatic juices. The phospholipase to lipase activity ratio was similar in PPJ and HPJ, but was 4-fold lower in PPE. The galactolipase and cholesterol esterase activities were found at lower levels in PPJ compared to HPJ, and they were further reduced in PPE. The enzymes known to display these activities in HPJ, pancreatic lipase-related protein 2 (PLRP2) and carboxylester hydrolase/bile salt-stimulated lipase (CEH/BSSL), were identified in PPJ using gel filtration experiments, SDS-PAGE and LC-MS/MS analysis. The galactolipase and cholesterol esterase activities of PPE indicated that PLRP2 and CEH/BSSL are still present at low levels in this enzyme preparation, but they were not detected by mass spectrometry. Besides differences between porcine and human enzymes, the lower levels of phospholipase, galactolipase and cholesterol esterase activities in PPE are probably due to some proteolysis occurring during the production process. In conclusion, PPE do not provide a full substitution of the lipolytic enzymes present in HPJ.
Impact of proteolysis on cancer stem cell functions Biochimie (IF 3.362) Pub Date : 2019-03-12 Larissa E. Hillebrand, Thomas Reinheckel
Cancer cells within a tumor are heterogeneous and exist in a variety of functionally distinct cell states, which are thought to be hierarchically organized. The cell on top of this hierarchy, the cancer stem cell (CSC) or, alternatively, tumor initiating cell (TIC), is responsible for initiation, maintenance, progression, and relapse of tumors. For the execution of these functions, CSC are equipped with distinct molecular tools. Although proteolytic enzymes in cancers have been extensively studied in general, relatively few studies have addressed proteases in function and fate of CSC/TICs. Here we review protease involvement in cell biological hallmarks of CSC/TICs such as cellular self-renewal, extracellular matrix remodeling and cell motility, resistance to radio- and chemotherapies, as well as evasion of the immune system. In general, CSC/TICs are characterized by a comparatively high expression and activity of proteases. It appears that CSC/TICs install a high degree of pericellular proteolysis depending on metalloproteases such as ADAMs and MMPs but also on secreted serine- and cysteine proteases. Interestingly, it turned out that not all proteases promote the malignant behavior of CSC/TICs. In fact, some proteases, such as ADAM 23, cathepsin K, and granzyme B, have been shown to negatively regulate CSC/TIC functions, thereby exhibiting anti-tumor effects. Finally, we discuss how the enhanced proteolytic signature of CSC/TICs can be used for their therapeutic targeting in order to render this clinically decisive subpopulation of cancer cells harmless.
Upregulation of JHDM1D-AS1 protects PDLSCs from H2O2-induced apoptosis by decreasing DNAJC10 via phosphorylation of eIF2α Biochimie (IF 3.362) Pub Date : 2019-07-02 Bai Shi, Bingyi Shao, Chonshi Yang, Ye Guo, Xiaohui Fu, Ning Gan
Periodontal ligament stem cells (PDLSCs) are a promising tool for regenerative medicine in clinical periodontal ligament repair. However, clinical maintenance of high quality and large quantity of PDLSCs faces multiple obstacles. One of them is how PDLSCs respond to environmental stimuli such as reactive oxygen species. We aim to elucidate how PDLSCs react to oxidative stress and the underlying mechanisms.We utilized hydrogen peroxide-induced oxidative stress to mimic ROS increase in rat PDLSCs. Our data indicated a rapid downregulation of a long non-coding RNA, lncRNA JHDM1D antisense 1 (JHDM1D-AS1), when PDLSCs were treated with hydrogen peroxide, which was negatively associated with PDLSC apoptosis. Moreover, our data showed that JHDM1D-AS1 regulated PDLSC apoptosis via inhibition of DNAJC10, a heat shock protein 40 family member. Moreover, overexpressed DNAJC10 inhibited Bcl-2 protein level and eIF2α phosphorylation level, which, in turn, contributed to PDLSC apoptosis. Our results revealed a protective role of JHDM1D-AS1 in ROS-induced apoptosis, and validated that JHDM1D-AS1/DNAJC10/phosphorylated-eIF2α/Bcl-2 pathway works as an anti-apoptotic signaling axis in PDLSCs.These findings will facilitate the in vitro culturing of PDLSCs for clinical usage and promote stem cell-based therapy for periodontal tissue regeneration.
Implication of Homocysteine in protein quality control processes Biochimie (IF 3.362) Pub Date : 2019-06-30 V. Sudhakar Reddy, Jamma Trinath, G. Bhanuprakash Reddy
Homocysteine (Hcy) is a key metabolite generated during methionine metabolism. The elevated levels of Hcy in the blood is reffered as hyperhomocystenimeia (HHcy). The HHcy is caused by imapired metabolism/deficiency of either folate, or B12 or defects in Hcy metabolism. Accumulating evidence suggests that HHcy is associated with cardiovascular and brain diseases including atherosclerosis, endothelial injury, and stroke etc. Vitamin B12 (cobalamin; B12) is a water-soluble vitamin essential for two metabolic reactions. It acts as a co-factor for methionine synthase and L-methylmalonyl-CoA mutase. Besides, it is also vital for DNA synthesis and maturation of RBC. Deficiency of B12 is associated with haematological and neurological disorders. Hyperhomocysteinemia (HHcy)-induced toxicity is thought to be mediated by accumulation of Hcy and its metabolites, homocysteinylated proteins. Cellular protein quality control (PQC) is essential for the maintenance of proteome integrity, and cell viability and its failure contributes to the development of multiple diseases. Chaperones, unfolded protein response (UPR), ubiquitin-proteasome system (UPS), and autophagy are analogous strategies of PQC that maintain cellular proteome integrity. Recently, multiple studies reported that HHcy responsible for perturbation of PQC by reducing chaperone levels, activating UPR, and impairing autophagy. Besides, HHcy also induce cytotoxicity, inflammation, protein aggregation and apoptosis. It has been shown that some of the factors including altered SIRT1-HSF1 axis and irreversible homocysteinylation of proteins responsible for folate and/or B12 deficiency or HHcy-induced impairment of PQC. Therefore, this review highlights the current understanding of HHcy in the impairment of cellular PQC and their pathophysiological and clinical consequences, epigenomic changes, therapeutic implications of B12, and chemical chaperones based on cell culture and experimental animal models.
How are circRNAs translated by non-canonical initiation mechanisms? Biochimie (IF 3.362) Pub Date : 2019-06-29 Leïla Halidou Diallo, Florence Tatin, David Florian, Anne-Claire Godet, Audrey Zamora, Anne-Catherine Prats, Barbara Garmy-Susini, Eric Lacazette
Targeting TOR signaling for enhanced lipid productivity in algae Biochimie (IF 3.362) Pub Date : 2019-06-29 Laura Prioretti, Frédéric Carriere, Ben Field, Luisana Avilan, Marie-Hélène Montané, Benoît Menand, Brigitte Gontero
Microalgae can produce large quantities of triacylglycerols (TAGs) and other neutral lipids that are suitable for making biofuels and as feedstocks for green chemistry. However, TAGs accumulate under stress conditions that also stop growth, leading to a trade-off between biomass production and TAG yield. Recently, in the model marine diatom Phaeodactylum tricornutum it was shown that inhibition of the target of rapamycin (TOR) kinase boosts lipid productivity by promoting TAG production without stopping growth. We believe that basic knowledge in this emerging field is required to develop innovative strategies to improve neutral lipid accumulation in oleaginous microalgae. In this minireview, we discuss current research on the TOR signaling pathway with a focus on its control on lipid homeostasis. We first provide an overview of the well characterized roles of TOR in mammalian lipogenesis, adipogenesis and lipolysis. We then present evidence of a role for TOR in controlling TAG accumulation in microalgae, and draw parallels between the situation in animals, plants and microalgae to propose a model of TOR signaling for TAG accumulation in microalgae.
Increasing evidence of pathogenic role of the Mediator (MED) complex in the development of cardiovascular diseases Biochimie (IF 3.362) Pub Date : 2019-06-27 C. Napoli, C. Schiano, A. Soricelli
Cardiovascular diseases (CVDs) are the first cause of death in the World. Mediator (MED) is an evolutionarily conserved protein complex, which mediates distinct protein-protein interactions. Pathogenic events in MED subunit have been associated with human diseases. Novel increasing evidence showed that missense mutations in MED13L gene are associated with transposition of great arteries while MED12, MED13, MED15, and MED30, have been correlated with heart development. Moreover, MED23 and MED25 have been associated with heart malformations in humans. Relevantly, MED1, MED13, MED14, MED15, MED23, MED25, and CDK8, were found modify glucose and/or lipid metabolism. Indeed, MED1, MED15, MED25, and CDK8 interact in the PPAR- and SREBP-mediated signaling pathways. MED1, MED14 and MED23 are involved in adipocyte differentiation, whereas MED23 mediates smooth muscle cell differentiation. MED12, MED19, MED23, and MED30 regulate endothelial differentiation by alternative splicing mechanism. Thus, MEDs have a central role in early pathogenic events involved in CVDs representing novel targets for clinical prevention and therapeutic approaches.
Disturbances in H+ dynamics during environmental carcinogenesis Biochimie (IF 3.362) Pub Date : 2019-06-20 Dominique Lagadic-Gossmann, Kévin Hardonnière, Baharia Mograbi, Odile Sergent, Laurence Huc
Despite the improvement of diagnostic methods and anticancer therapeutics, the human population is still facing an increasing incidence of several types of cancers. According to the World Health Organization, this growing trend would be partly linked to our environment, with around 20% of cancers stemming from exposure to environmental contaminants, notably chemicals like polycyclic aromatic hydrocarbons (PAHs). PAHs are widespread pollutants in our environment resulting from incomplete combustion or pyrolysis of organic material, and thus produced by both natural and anthropic sources; notably benzo[a]pyrene (B[a]P), i.e. the prototypical molecule of this family, that can be detected in cigarette smoke, diesel exhaust particles, occupational-related fumes, and grilled food. This molecule is a well-recognized carcinogen belonging to group 1 carcinogens. Indeed, it can target the different steps of the carcinogenic process and all cancer hallmarks. Interestingly, H+ dynamics have been described as key parameters for the occurrence of several, if not all, of these hallmarks. However, information regarding the role of such parameters during environmental carcinogenesis is still very scarce. The present review will thus mainly give an overview of the impact of B[a]P on H+ dynamics in liver cells, and will show how such alterations might impact different aspects related to the finely-tuned balance between cell death and survival processes, thereby likely favoring environmental carcinogenesis. In total, the main objective of this review is to encourage further research in this poorly explored field of environmental molecular toxicology.
LncRNA THOR promotes tongue squamous cell carcinomas by stabilizing IGF2BP1 downstream targets Biochimie (IF 3.362) Pub Date : 2019-06-18 Haojie Yang, Ganglan Fu, Funing Liu, Chuwen Hu, Junjie Lin, Zicong Tan, Yanni Fu, Fengtao Ji, Minghui Cao
THOR, a highly conserved lncRNA, is potentially involved in various cancer development. However, its involvement in tongue squamous cell carcinoma (TSCC) remains unclear. The present study aims to explore the biological function and molecular mechanism of THOR in TSCC progression. The expressions of THOR and IGF2BP1 in TSCC tissues and adjacent non-cancerous tongue tissues (ANT) were examined through qRT-PCR. THOR levels were manipulated in TSCC cells to explore its function in cancer progression in vitro and in vivo, which were subsequently evaluated by CCK8, colony formation assay, flow cytometry, xenograft tumor assays. In situ hybridization, RIP and Western blot assay were performed to explore the underlying molecular mechanisms. We discovered that THOR and IGF2BP1 were dramatically upregulated in TSCC tissues. The expression of THOR is positively correlated with IGF2BP1 mRNA level. THOR mediated IGF2 expression via interacting with IGF2BP1, and affected the downstream MEK-ERK signaling pathway to regulate TSCC cells proliferation. THOR/IGF2BP1/IGF2-MEK-ERK axis regulated the proliferation of TSCC cells, implying that THOR would be a promising therapeutic target for TSCC patients.
Proteolytic processing and activation of gingipain zymogens secreted by T9SS of Porphyromonas gingivalis Biochimie (IF 3.362) Pub Date : 2019-06-15 Florian Veillard, Maryta Sztukowska, Zuzanna Nowakowska, Danuta Mizgalska, Ida B. Thøgersen, Jan J. Enghild, Matthew Bogyo, Barbara Potempa, Ky-Anh Nguyen, Jan Potempa
Porphyromonas gingivalis uses a type IX secretion system (T9SS) to deliver more than 30 proteins to the bacterial surface using a conserved C-terminal domain (CTD) as an outer membrane translocation signal. On the surface, the CTD is cleaved and an anionic lipopolysaccharide (A-PLS) is attached by PorU sortase. Among T9SS cargo proteins are cysteine proteases, gingipains, which are secreted as inactive zymogens requiring removal of an inhibiting N-terminal prodomain (PD) for activation. Here, we have shown that the gingipain proRgpB isolated from the periplasm of a T9SS-deficient P. gingivalis strain was stable and did not undergo autocatalytic activation. Addition of purified, active RgpA or RgpB, but not Lys-specific Kgp, efficiently cleaved the PD of proRgpB but catalytic activity remained inhibited because of inhibition of the catalytic domain in trans by the PD. In contrast, active RgpB was generated from the zymogen, although at a slow rate, by gingipain-null P. gingivalis lysate or intact bacterial cell suspension. This activation was dependent on the presence of the PorU sortase. Interestingly, maturation of proRgpB with the catalytic cysteine residues mutated to Ala expressed in the ΔRgpA mutant strain was indistinguishable from that in the parental strain. Cumulatively, this suggests that PorU not only has sortase activity but is also engaged in activation of gingipain zymogens on the bacterial cell surface.
Interplay between Primary cilia, Ubiquitin-Proteasome system and Autophagy Biochimie (IF 3.362) Pub Date : 2019-06-15 Asma Boukhalfa, Caterina Miceli, Yenniffer Ávalos, Etienne Morel, Nicolas Dupont
Cilia are microtubule-based organelles located at the cell surface of many eukaryotic cell types. Cilia control different cellular functions ranging from motility (for motile cilia) to signal transduction pathways (for primary cilia). A variety of signaling pathways are coordinated by this organelle during development, cell migration and cell differentiation. Interestingly, aberrant ciliogenesis or altered cilium signaling has been associated with human diseases, notably in cancer. Disruption of cilia through mutation of genes encoding cilia proteins has been also linked to multiple human disorders referred as ciliopathies. Recent studies highlight the interplay between cilia and proteostasis. Here we review findings regarding the crosstalk between cilia and two proteolytic systems, the ubiquitin proteasome system and the autophagy-lysosomal system and discuss the potential implications in human disease including ciliopathies.
Diversity of circular RNAs and RNA ligases in archaeal cells Biochimie (IF 3.362) Pub Date : 2019-06-15 Hubert F. Becker, C. L’Hermitte-Stead, H. Myllykallio
Circular RNAs (circRNAs) differ structurally from other types of RNAs and are resistant against exoribonucleases. Although they have been detected in all domains of life, it remains unclear how circularization affects or changes functions of these ubiquitous nucleic acid circles. The biogenesis of circRNAs has been mostly described as a backsplicing event, but in archaea, where RNA splicing is a rare phenomenon, a second pathway for circRNA formation was described in the cases of rRNAs processing, tRNA intron excision, and Box C/D RNAs formation. At least in some archaeal species, circRNAs are formed by a ligation step catalyzed by an atypic homodimeric RNA ligase belonging to Rnl3 family. In this review, we describe archaeal circRNA transcriptomes obtained using high throughput sequencing technologies on Sulfolobus solfataricus, Pyrococcus abyssi and Nanoarchaeum equitans cells. We will discuss the distribution of circular RNAs among the different RNA categories and present the Rnl3 ligase family implicated in the circularization activity. Special focus is given for the description of phylogenetic distributions, protein structures, and substrate specificities of archaeal RNA ligases.
Gangliosidome of human anencephaly: a high resolution multistage mass spectrometry study Biochimie (IF 3.362) Pub Date : 2019-06-13 Mirela Sarbu, Raluca Ica, Alina Petrut, Zeljka Vukelic;, Cristian V.A. Munteanu, Andrei J. Petrescu, Alina D. Zamfir
Widely dispersed throughout the entire body tissues, gangliosides (GGs) are essential components of neuronal cell membranes, where exhibit a vital role in neuronal function and brain development, directly influencing the neural tube formation, neurogenesis, neurotransmission, etc. Due to several factors, partial or complete closing faults of the fetal neural tube may occur in the first trimester of pregnancy, generating a series of neural tube defects (NTD), among which anencephaly. The absence in anencephaly of the forebrain and skull bones determines the exposure to the amniotic fluid of the remaining brain tissue and the spinal cord, causing the degeneration of the nervous system tissue. Based on the previously achieved information related to the direct alteration of neural development with deficient concentration of several GGs, a systematic and comparative mass spectrometry (MS) mapping assay on GGs originating from fetuses in different intrauterine developmental stages, i.e. the 29th (denoted An29), 35th (An35) and the 37th (An37) gestational weeks was here conducted. Our approach, based on Orbitrap MS under high sensitivity, resolution and mass accuracy conditions, enabled for the first time the nanoelectrospray ionization, detection and identification of over 150 glycoforms, mainly novel, polysialylated species. Such a pattern, specific for incipient developmental stages reliably documents the brain development stagnation, characteristic for anencephaly. Further, the fragmentation MS2-MS3 experiments by collision induced dissociation (CID) confirmed the incidence in all three samples of GT2(d18:1/16:2) as a potential biomarker. Therefore, this fingerprinting of the anencephalic gangliosidome may serve in development of approaches for routine screening and early diagnosis.
Overexpression of CKIP-1 alleviates hypoxia-induced cardiomyocyte injury by up-regulating Nrf2 antioxidant signaling via Keap1 inhibition Biochimie (IF 3.362) Pub Date : 2019-06-12 Jie Ren, Jingjin Li, Jingwen Hu, Hang Yu, Qian Yang, Jianjun Mu
Induction of endothelial dysfunction by oxidized low-density lipoproteins via downregulation of Erk-5/Mef2c/Klf2 signaling: Amelioration by fisetin Biochimie (IF 3.362) Pub Date : 2019-06-11 Rohit Patel, Johnna F. Varghese, Rana P. Singh, Umesh C.S. Yadav
Recombinant cystatins in plants Biochimie (IF 3.362) Pub Date : 2019-06-11 Jonathan Tremblay, Marie-Claire Goulet, Dominique Michaud
Dozens of studies have assessed the practical value of plant cystatins as ectopic inhibitors of Cys proteases in biological systems. The potential of these proteins in crop protection to control herbivorous pests and pathogens has been documented extensively over the past 25 years. Their usefulness to regulate endogenous Cys proteases in planta has also been considered recently, notably to implement novel traits of agronomic relevance in crops or to generate protease activity-depleted environments in plants or plant cells used as bioreactors for recombinant proteins. After a brief update on the basic structural characteristics of plant cystatins, we summarize recent advances on the use of these proteins in plant biotechnology. Attention is also paid to the molecular improvement of their structural properties for the improvement of their protease inhibitory effects or the fine-tuning of their biological target range.
Fibroblast deficiency of Insulin-Like Growth Factor 1 Receptor Type 1 (IGF1R) impairs initial steps of murine pheochromocytoma development Biochimie (IF 3.362) Pub Date : 2019-06-08 Martin Ayelen, Venara Marcela, Mathó Cecilia, Olea Fernanda Daniela, Fernández María Celia, Pennisi Patricia A
Insulin-like growth factor 1 (IGF1) has a critical role in maintaining tumor phenotype and survival of already transformed murine pheochromocytoma (pheo) cells (MPC4/30) and it is required for the initial establishment of these tumors. However, the role of local IGF1/IGF1R system in tumor microenvironment has not been fully understood. In vivo, by subcutaneous injection of pheo cells in heterozygous IGF1R knockout mice (L/n), we found that the time of noticeable tumor appearance was delayed, and incidence was decreased in L/n group compared to control (L/L) mice. Once established, tumor proliferation, vascularization or growth rate did not differ between groups. In vitro, fibroblast from L/n and L/L mice were cultured to generate conditioned media (CM) and differential matrixes on which pheo cells were seeded. Proliferation rate was higher when pheo cells were cultured with CM, or in differential matrix generated by L/L murine fibroblasts. A diminished fibronectin (FN) expression and secretion from L/n fibroblast was associated with decreased expression of integrin subunits in tumor cells. Also, soluble factors as IGF1 and insulin-like growth factor binding protein 2 (IGFBP2) were reduced. Our data suggest that IGF1 signaling through IGF1R may contribute to tumor cells anchorage and survival by interaction with both matrix and soluble factors produced by tumor microenvironment fibroblasts.
Phospho-peptide binding domains in S. cerevisiae model organism Biochimie (IF 3.362) Pub Date : 2019-06-10 Simona Panni
Protein phosphorylation is one of the main mechanisms by which signals are transmitted in eukaryotic cells, and it plays a crucial regulatory role in almost all cellular processes. In yeast, more than half of the proteins are phosphorylated in at least one site, and over 20,000 phosphopeptides have been experimentally verified. However, the functional consequences of these phosphorylation events for most of the identified phosphosites are unknown. A family of protein interaction domains selectively recognises phosphorylated motifs to recruit regulatory proteins and activate signalling pathways. Nine classes of dedicated modules are coded by the yeast genome: 14-3-3, FHA, WD40, BRCT, WW, PBD, and SH2. The recognition specificity relies on a few residues on the target protein and has coevolved with kinase specificity. In the present study, we review the current knowledge concerning yeast phospho-binding domains and their networks. We emphasise the relevance of both positive and negative amino acid selection to orchestrate the highly regulated outcomes of inter- and intra-molecular interactions. Finally, we hypothesise that only a small fraction of yeast phosphorylation events leads to the creation of a docking site on the target molecule, while many have a direct effect on the protein or, as has been proposed, have no function at all.
Mammalian legumain – a lysosomal cysteine protease with extracellular functions? Biochimie (IF 3.362) Pub Date : 2019-06-07 Ngoc Nguyen Lunde, Tatjana Bosnjak, Rigmor Solberg, Harald Thidemann Johansen
The cysteine protease legumain (asparaginyl endopeptidase, AEP) plays important roles in normal physiology but is also associated with several disorders, such as atherosclerosis, osteoporosis, cancer and neurodegenerative diseases. The functional roles of legumain have mainly been associated with the presence in lysosomes where legumain is active and mediates processing of multiple proteins, such as the conversion of single to double chain forms of cysteine cathepsins. However, in recent years, a number of studies point to extracellular roles of legumain in addition to the pivotal roles in the lysosomes. In this review, recent knowledge on novel extracellular functions of this protease will be addressed and new discoveries in relation to the diseases mentioned above will be presented.
A Novel Isothermal Method using Rolling Circle Reverse Transcription for Accurate Amplification of Small RNA sequences Biochimie (IF 3.362) Pub Date : 2019-06-07 Lufang Ning, Xingyu Wang, Ke Xu, Shixi Song, Qiao Li, Xingbin Yang
Ppn2 endopolyphosphatase overexpressed in Saccharomyces cerevisiae: comparison with Ppn1, Ppx1, and Ddp1 polyphosphatases Biochimie (IF 3.362) Pub Date : 2019-06-06 Nadeshda Andreeva, Larisa Ledova, Lubov Ryazanova, Alexander Tomashevsky, Tatiana Kulakovskaya, Mikhail Eldarov
Saccharomyces cerevisiae has high level of inorganic polyphosphate and a multicomponent system of its metabolism, including polyphosphatases Ppx1, Ppn1, Ddp1, and Ppn2. The aim of the study was to construct the yeast strain overexpressing Ppn2 and to compare the properties of Ppn2, Ppx1, Ppn1, and Ddp1 purified from overexpressing strains of S. cerevisiae. We overexpressed Ppn2 in S. cerevisiae under a strong constitutive promoter of the yeast glyceraldehyde-3-phosphate dehydrogenase-encoding gene and suggested biochemical criteria for distinguishing among yeast polyphosphatases, which is important for their identification and understanding of their functions. Ppn2, Ppn1, and Ddp1 had endopolyphosphatase activities, whereas Ppx1 did not. Ppx1 and Ppn1 exhibited high and Ddp1 and Ppn2 low exopolyphosphatase activity: 240, 500, 0.05 and 0.1 U/mg protein, respectively. The enzymes had distinct patterns of exopolyphosphatase activities stimulation by divalent metal ions. Ppn2, Ppn1 and Ddp1 displayed endopolyphosphatase activity in the presence of 1 mM Mg2+. The endopolyphosphatase activities of Ppn2 and Ppn1 were induced by 0.01 mM of Co2+ or Zn2+, whereas that of Ddp1 required 0.1 mM of these cations. The endopolyphosphatase activity of Ppn1 was inhibited by 0.01 mg mL-1 of heparin, while endopolphosphatase activity of Ppn2 was weakly sensitive to 0.25 mg mL-1 of heparin. The Ppx1 and Ppn1 activity with guanosine tetraphosphate was nearly 80% of activity with long-chain polyphosphates. The Ppn1 hydrolyzed dATP, while Ppx1 did not. The differences in the mode of polyphosphate hydrolysis, substrate specificity, metal ion dependence and cell localization suggest distinct roles of these enzymes in yeast.
Stefin A-Functionalized Liposomes As A System For Cathepsins S And L-Targeted Drug Delivery Biochimie (IF 3.362) Pub Date : 2019-06-01 A. Bratovs, L. Kramer, G. Mikhaylov, O. Vasiljeva, B. Turk
Proteolytic activity in the tumor microenvironment is one of the key elements supporting tumor development and metastasis. One of the key families of proteases that are overexpressed in various types of cancer and implicated in different stages of tumor progression are cysteine cathepsins. Among them, cathepsins S and L can be secreted into the tumor microenvironment by tumor and/or immune cells, making them promising drug delivery targets. Here we present a new system for cathepsin S/L targeting using a liposomal drug carrier system functionalized with the endogenous cysteine cathepsin inhibitor, stefin A. The selective targeting of cathepsins by stefin A-conjugated liposomes was confirmed in vitro and in vivo, demonstrating the potential of this approach for cancer diagnosis and treatment.
Linkage between EMT and stemness state through molecular association between TWIST1 and NY-ESO1 in esophageal squamous cell carcinoma Biochimie (IF 3.362) Pub Date : 2019-05-31 Sima Ardalan Khales, Mohammad Reza Abbaszadegan, Ahmad Majd, Mohammad Mahdi Forghanifard
Aberrant expression of cancer testis antigens (CTAs) is reported in tumors, especially those with stemness properties. A number of CTAs can induce epithelial mesenchymal transition (EMT) process and promote cancer stem cells (CSCs) characteristics. We aimed in this study to analyze the correlation between NY-ESO1 and TWIST1 in esophageal squamous cell carcinoma (ESCC), as well as their impact on EMT process. Gene expression profiling of NY-ESO1 and TWIST1 was performed in 43 esophageal tumors compared to their margin normal tissues of using qRT-PCR, and their correlation with clinicopathological variables of the patients was evaluated. In silico analysis of the NY-ESO1, epithelial and mesenchymal cell markers and also their promoter sequences was executed. ESCC cell lines KYSE-30 and YM-1 were transduced to ectopically express TWIST1 using a retroviral system, followed by qRT-PCR mRNA expression analysis to reveal the probable correlation among TWIST1, NY-ESO1 and EMT markers gene expression. Scratch assay was performed to estimate migration of TWIST1-induced cells. Overexpression of TWIST1 and NY-ESO1 mRNA was observed in 42% and 39.5% (P ˂ 0.05) of tumors, respectively. Expression of the genes was significantly correlated with each other (p=0.005). TWIST1 and NY-ESO1 overexpression was significantly associated with stage of progression and size of tumors, respectively. A direct association between TWIST1 and NY-ESO1 mRNA expression was confirmed by induced ectopic expression of TWIST1 in ESCC cell lines KYSE-30 and YM-1. TWIST1-induced cells led to increase migration in ESCC cell line. Furthermore, significant up-regulation of EMT markers was observed following ectopic expression of TWIST1 in these cells. Based on our findings, it may be proposed that a vital association is exist between the EMT and the acquisition of cancer stemness state in tumor cells through the TWIST1/NY-ESO1 axis and it can be a critical hallmark in ESCC tumorigenesis.
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