Identification of 2H phosphoesterase superfamily proteins with 2 ´-CPDase activity.
Identification of 2H phosphoesterase superfamily proteins with 2´-CPDase activity. Biochimie. 2019 Aug 15;: Authors: Mitsutomi S, Akimitsu N, Sekimizu K, Kaito C Abstract 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, thereb...
Source: Biochimie - August 15, 2019 Category: Biochemistry Authors: Mitsutomi S, Akimitsu N, Sekimizu K, Kaito C Tags: Biochimie Source Type: research

Comparative effects of trehalose and 2-hydroxypropyl- β-cyclodextrin on aggregation of UV-irradiated muscle glycogen phosphorylase b.
Comparative effects of trehalose and 2-hydroxypropyl-β-cyclodextrin on aggregation of UV-irradiated muscle glycogen phosphorylase b. Biochimie. 2019 Aug 10;: Authors: Eronina TB, Mikhaylova VV, Chebotareva NA, Shubin VV, Sluchanko NN, Kurganov BI Abstract 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 eff...
Source: Biochimie - August 10, 2019 Category: Biochemistry Authors: Eronina TB, Mikhaylova VV, Chebotareva NA, Shubin VV, Sluchanko NN, Kurganov BI Tags: Biochimie Source Type: research

Protein-protein interactions regulate the activity of Adipose Triglyceride Lipase in intracellular lipolysis.
Abstract 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 cleava...
Source: Biochimie - August 9, 2019 Category: Biochemistry Authors: Kulminskaya N, Oberer M Tags: Biochimie Source Type: research

Unfolded Protein Response Supports Endothelial Barrier Function.
Abstract 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 a...
Source: Biochimie - August 9, 2019 Category: Biochemistry Authors: Barabutis N Tags: Biochimie Source Type: research

LIPUS promotes FOXO1 accumulation by downregulating miR-182 to enhance osteogenic differentiation in hPDLCs.
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. PMID: 31401188 [PubMed - as supplied by publisher] (Source: Biochimie)
Source: Biochimie - August 8, 2019 Category: Biochemistry Authors: Chen D, Xiang M, Gong Y, Xu L, Zhang T, He Y, Zhou M, Xin L, Li J, Song J Tags: Biochimie Source Type: research

Role of AKT and mTOR Signaling Pathways in the Induction of Epithelial-Mesenchymal Transition (EMT) Process.
Abstract 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 signa...
Source: Biochimie - August 8, 2019 Category: Biochemistry Authors: Roshan MK, Soltani A, Soleimani A, Kahkhaie KR, Afshari AR, Soukhtanloo M Tags: Biochimie Source Type: research

Apolipoprotein A-I improves hepatic autophagy through the AMPK pathway.
Abstract 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. T...
Source: Biochimie - August 8, 2019 Category: Biochemistry Authors: Rao X, Wang Y Tags: Biochimie Source Type: research

Mouse Fat-Specific Protein 27 (FSP27) expressed in plant cells localizes to lipid droplets and promotes lipid droplet accumulation and fusion.
In this study, we tested the function of mouse FSP27 in stably-transformed Arabidopsis thaliana leaves and seeds, as well as through transient expression in Nicotiana tabacum suspension-cultured cells and N. benthamiana leaves. Confocal microscopic analysis of plant cells revealed that, similar to ectopic expression in mammalian cells, FSP27 produced in plants 1) correctly localized to LDs, 2) accumulated at LD-LD contact sites, and 3) induced an increase in the number and size of LDs and also promoted LD clustering and fusion. Furthermore, FSP27 increased oil content in transgenic A. thaliana seeds. Given that plant oils ...
Source: Biochimie - August 7, 2019 Category: Biochemistry Authors: Price AM, Doner NM, Gidda SK, Jambunathan S, James CN, Schami A, Yurchenko O, Mullen RT, Dyer JM, Puri V, Chapman KD Tags: Biochimie Source Type: research

The case for class II bacteriocins: a biophysical approach using "suicide probes" in receptor-free hosts to study their mechanism of action.
The case for class II bacteriocins: a biophysical approach using "suicide probes" in receptor-free hosts to study their mechanism of action. Biochimie. 2019 Aug 02;: Authors: Ríos Colombo NS, Chalón MC, Dupuy FG, Gonzalez CF, Bellomio A Abstract Class II bacteriocins are unmodified membrane-active peptides that act over a narrow spectrum of target bacteria. They bind a specific receptor protein on the membrane to form a pore, leading to membrane permeabilization and cell death. However, little is known about the molecular events triggering the pore formation after the bacterioc...
Source: Biochimie - August 2, 2019 Category: Biochemistry Authors: Ríos Colombo NS, Chalón MC, Dupuy FG, Gonzalez CF, Bellomio A Tags: Biochimie Source Type: research

Targeting a viral DNA sequence with a deoxyribozyme in a preparative scale.
In this report, catalytic activity of an oxidizing DNA-cleaving deoxyribozyme, F-8(X), was comprehensively inspected in semi-preparative (10 μM substrate) scale. A 60 nucleotides long synthetic DNA sequence was selected as the target DNA for this study. The DNA sequence was originated from a single stranded DNA virus. Investigations revealed high yield in the presence of optimal concentration of oxidizing agents. The optimal conditions have been applied for scale-up of the reaction to preparative (40 μM substrate) and multi-turnover reactions to achieve highest amount of product in a cost-, time- and labor-effective ...
Source: Biochimie - August 1, 2019 Category: Biochemistry Authors: Dastjerdi-Khorzoghi P, Javadi-Zarnaghi F, Hojati Z Tags: Biochimie Source Type: research

ATP synthase, an essential enzyme in growth and multiplication is modulated by Protein Tyrosine Phosphatase in Mycobacterium tuberculosis H37Ra.
Abstract 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 gener...
Source: Biochimie - August 1, 2019 Category: Biochemistry Authors: Chatterjee A, Pandey S, Dhamija E, Jaiswal S, Yabaji SM, Srivastava KK Tags: Biochimie Source Type: research

in silico prediction of protein flexibility with local structure approach.
rn AG Abstract 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, ...
Source: Biochimie - August 1, 2019 Category: Biochemistry Authors: Narwani TJ, Etchebest C, Craveur P, Léonard S, Rebehmed J, Srinivasan N, Bornot A, Gelly JC, de Brevern AG Tags: Biochimie Source Type: research

Origins of peptidases.
Abstract 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 struct...
Source: Biochimie - August 1, 2019 Category: Biochemistry Authors: Rawlings ND, Bateman A Tags: Biochimie Source Type: research

Improved hepatic MRP2/ABCC2 transport activity in LPS-induced cholestasis by aquaporin-1 gene transfer.
Abstract 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/...
Source: Biochimie - August 1, 2019 Category: Biochemistry Authors: Marrone J, Tocchetti GN, Danielli M, Mottino AD, Marinelli RA Tags: Biochimie Source Type: research

DNA Binding Thermodynamics and Site Stoichiometry as a Function of Polyamide Size.
Abstract The interactions of 6-8 ring hairpin polyamides (PAs) with the minor groove of DNA have been investigated extensively. More recent studies of large antiviral PAs (14-20 rings) active against small DNA tumor viruses lead to questions regarding the extent to which the DNA binding behaviors of the well studied, smaller PAs can be reliably extrapolated to the larger ones. Described here is the first reported study of hairpin PA-DNA binding thermodynamics as a function of PA size (6 to 20 rings). All PAs exhibit binding affinity in the low nM to upper pM range, which indicates that affinity is not a discrimina...
Source: Biochimie - July 31, 2019 Category: Biochemistry Authors: Song Y, Niederschulte J, Bales KN, Park AH, Bashkin JK, Dupureur CM Tags: Biochimie Source Type: research

MicroRNA-25-5p counteracts oxidized LDL-induced pathological changes by targeting neuronal growth regulator 1 (NEGR1) in human brain micro-vessel endothelial cells.
Abstract 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 assa...
Source: Biochimie - July 28, 2019 Category: Biochemistry Authors: Zhang Q, Liu C, Li Q, Li J, Wu Y, Liu J Tags: Biochimie Source Type: research

Matrix metalloproteinase-2: Not (just) a "hero" of the past.
Matrix metalloproteinase-2: Not (just) a "hero" of the past. Biochimie. 2019 Jul 27;: Authors: Henriet P, Emonard H Abstract 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 aggressivene...
Source: Biochimie - July 27, 2019 Category: Biochemistry Authors: Henriet P, Emonard H Tags: Biochimie Source Type: research

Swainsonine induces autophagy via PI3K/AKT/mTOR signaling pathway to injure the Renal Tubular Epithelial cells.
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. PMID: 31356846 [PubMed - as supplied by publisher] (Source: Biochimie)
Source: Biochimie - July 26, 2019 Category: Biochemistry Authors: Wang S, Wang J, Yang L, Guo R, Huang E, Yang H, Zhang Y, Sun L, Song R, Chen J, Tian Y, Zhao B, Guo Q, Lu H Tags: Biochimie Source Type: research

Transmembrane Channel-Like 5 (TMC5) promotes prostate cancer cell proliferation through cell cycle regulation.
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 significan...
Source: Biochimie - July 26, 2019 Category: Biochemistry Authors: Zhang W, Wang S, Zhang X, Liu K, Song J, Leng X, Luo R, Ran L Tags: Biochimie Source Type: research

Dissection of TMEM165 function in Golgi glycosylation and its Mn2+ sensitivity.
Abstract 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...
Source: Biochimie - July 24, 2019 Category: Biochemistry Authors: Lebredonchel E, Houdou M, Potelle S, de Bettignies G, Schulz C, Krzewinski Recchi MA, Lupashin V, Legrand D, Klein A, Foulquier F Tags: Biochimie Source Type: research

Oridonin enhances TRAIL-induced apoptosis through GALNT14-mediated DR5 glycosylation.
Abstract 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 ti...
Source: Biochimie - July 20, 2019 Category: Biochemistry Authors: Jeon MY, Seo SU, Woo SM, Min KJ, Byun HS, Hur GM, Kang SC, Kwon TK Tags: Biochimie Source Type: research

"RNA structure, maturation, interactions and functions".
"RNA structure, maturation, interactions and functions". Biochimie. 2019 Jul 17;: Authors: Motorine Y, Massenet S PMID: 31325478 [PubMed - as supplied by publisher] (Source: Biochimie)
Source: Biochimie - July 17, 2019 Category: Biochemistry Authors: Motorine Y, Massenet S Tags: Biochimie Source Type: research

Skeletal muscle atrogenes: from rodent models to human pathologies.
Abstract 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, ...
Source: Biochimie - July 17, 2019 Category: Biochemistry Authors: Taillandier D, Polge C Tags: Biochimie Source Type: research

BRD4 contributes to high-glucose-induced podocyte injury by modulating Keap1/Nrf2/ARE signaling.
In this study, we aimed to explore the potential role of BRD4 in regulating HG-induced podocyte injury and its underlying molecular mechanism. HG exposure significantly upregulated BRD4 in podocytes. BRD4 inhibition by small interfering RNA or its chemical inhibitor (JQ1) markedly repressed HG-induced apoptosis and reactive oxygen species (ROS) production. By contrast, BRD4 overexpression exacerbated HG-induced podocyte injury. Moreover, BRD4 inhibition potentiated nuclear factor (erythroid-derived 2)-like 2 (Nrf2) signaling associated with suppression of Kelch-like ECH-associated protein (Keap1). BRD4 inhibition promoted ...
Source: Biochimie - July 17, 2019 Category: Biochemistry Authors: Zuo H, Wang S, Feng J, Liu X Tags: Biochimie Source Type: research

Determination of the Crystal Structure and Substrate Specificity of Ananain.
Abstract Ananain (EC 3.4.22.31) 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 ...
Source: Biochimie - July 12, 2019 Category: Biochemistry Authors: Yongqing T, Wilmann PG, Pan J, West ML, Brown TJ, Mynott T, Pike RN, Wijeyewickrema LC Tags: Biochimie Source Type: research

Computational insights into the active structure of SGK1 and its implication for ligand design.
Abstract 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 α...
Source: Biochimie - July 11, 2019 Category: Biochemistry Authors: Akhoon BA, Gandhi NS, Pandey R Tags: Biochimie Source Type: research

Nutrigenomics and RNA methylation: role of micronutrients.
Abstract 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...
Source: Biochimie - July 11, 2019 Category: Biochemistry Authors: Mosca P, Leheup B, Dreumont N Tags: Biochimie Source Type: research

The relationship between molecular content of mesenchymal stem cells derived exosomes and their potentials: opening the way for exosomes based therapeutics.
Abstract 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 highligh...
Source: Biochimie - July 11, 2019 Category: Biochemistry Authors: Jafari D, Malih S, Eslami SS, Jafari R, Darzi L, Tarighi P, Samadikuchaksaraei A Tags: Biochimie Source Type: research

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.
Abstract Taar1 is a G protein-coupled receptor (GPCR) confined to primary cilia of rodent thyroid epithelial cells. Taar1-deficient mouse thyroid follicles feature luminal accumulation of thyroglobulin suggesting that Taar1 acts as a regulator of extra- and pericellular thyroglobulin processing, which is mediated by cysteine cathepsin proteases present at the apical plasma membrane of rodent thyrocytes. Here, by immunostaining and confocal laser scanning microscopy, we demonstrated co-localization of cathepsin L, but only little cathepsin B, with Taar1 at primary cilia of rat thyrocytes, the FRT cells. Because pro...
Source: Biochimie - July 11, 2019 Category: Biochemistry Authors: Szumska J, Batool Z, Al-Hashimi A, Venugopalan V, Skripnik V, Schaschke N, Bogyo M, Brix K Tags: Biochimie Source Type: research

Stringent response protein as a potential target to intervene persistent bacterial infection.
Abstract More than half of the world's population is infected with persistent bacterial infections, consequently, persisters are gradually becoming a major public health concern. During the persistent phase, bacterial pathogens deploy many regulatory strategies to compensate unfavorable host environmental conditions. The stringent response is one of such gene regulatory mechanisms which is stimulated by nutrient starvation. It is regulated by the synthesis of highly phosphorylated signaling nucleotides, (p)ppGpp or alarmone. (p)ppGpp is synthesized by ppGpp synthetases, and these proteins are classified as RelA/Sp...
Source: Biochimie - July 11, 2019 Category: Biochemistry Authors: Kushwaha GS, Oyeyemi BF, Bhavesh NS Tags: Biochimie Source Type: research

Mapping post-transcriptional modifications in Staphylococcus aureus tRNAs by nanoLC/MSMS.
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. PM...
Source: Biochimie - July 8, 2019 Category: Biochemistry Authors: Antoine L, Wolff P, Westhof E, Romby P, Marzi S Tags: Biochimie Source Type: research

Relationship between acyl-lipid and sterol metabolisms in diatoms.
tte J Abstract 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-calle...
Source: Biochimie - July 7, 2019 Category: Biochemistry Authors: Maréchal E, Lupette J Tags: Biochimie Source Type: research

Characterization of all the lipolytic activities in pancreatin and comparison with porcine and human pancreatic juices.
In conclusion, PPE do not provide a full substitution of the lipolytic enzymes present in HPJ. PMID: 31288050 [PubMed - as supplied by publisher] (Source: Biochimie)
Source: Biochimie - July 6, 2019 Category: Biochemistry Authors: Salhi A, Amara S, Mansuelle P, Puppo R, Lebrun R, Gontero B, Aloulou A, Carrière F Tags: Biochimie Source Type: research

An approach to recombinantly produce mature grape polyphenol oxidase.
Abstract 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 ...
Source: Biochimie - July 5, 2019 Category: Biochemistry Authors: Li Y, McLarin MA, Middleditch MJ, Morrow SJ, Kilmartin PA, Leung IKH Tags: Biochimie Source Type: research

MMP-14 degrades tropoelastin and elastin.
This study focuses on investigating the elastinolytic capability of membrane-type 1 matrix metalloproteinase, also known as matrix metalloproteinase-14. We digested recombinant human tropoelastin and human skin elastin with matrix metalloproteinase-14 and analyzed the peptide mixtures using complementary mass spectrometric techniques and bioinformatics tools. The results and additional molecular docking studies show that matrix metalloproteinase-14 cleaves tropoelastin as well as elastin. While tropoelastin was well degraded, fewer cleavages occurred in the highly cross-linked mature elastin. The study also provides insigh...
Source: Biochimie - July 3, 2019 Category: Biochemistry Authors: Miekus N, Luise C, Sippl W, Baczek T, Schmelzer CEH, Heinz A Tags: Biochimie Source Type: research

Upregulation of JHDM1D-AS1 protects PDLSCs from H2O2-induced apoptosis by decreasing DNAJC10 via phosphorylation of eIF2 α.
Upregulation of JHDM1D-AS1 protects PDLSCs from H2O2-induced apoptosis by decreasing DNAJC10 via phosphorylation of eIF2α. Biochimie. 2019 Jul 02;: Authors: Shi B, Shao B, Yang C, Guo Y, Fu X, Gan N Abstract 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 underly...
Source: Biochimie - July 2, 2019 Category: Biochemistry Authors: Shi B, Shao B, Yang C, Guo Y, Fu X, Gan N Tags: Biochimie Source Type: research

Implication of Homocysteine in protein quality control processes.
Abstract 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, i...
Source: Biochimie - June 30, 2019 Category: Biochemistry Authors: Reddy VS, Trinath J, Reddy GB Tags: Biochimie Source Type: research

How are circRNAs translated by non-canonical initiation mechanisms?
Abstract Circular RNAs (circRNAs) are covalently closed RNA loops produced by a very large number of expressed eukaryotic genes. Initially considered as splicing background and/or splicing side products, recent studies have shown that they are evolutionary conserved and abundant in cells. Yet, their functions remain largely unknown. Because of their circular shape, they were initially categorized as non-coding RNAs. However, recent studies based on mass spectrometry analysis indicate that some cytoplasmic circRNAs are effectively translated into detectable peptides. This raises the interesting question of which me...
Source: Biochimie - June 29, 2019 Category: Biochemistry Authors: Diallo LH, Tatin F, Florian D, Godet AC, Zamora A, Prats AC, Garmy-Susini B, Lacazette E Tags: Biochimie Source Type: research

Targeting TOR signaling for enhanced lipid productivity in algae.
ero B Abstract 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 ...
Source: Biochimie - June 29, 2019 Category: Biochemistry Authors: Prioretti L, Carriere F, Field B, Avilan L, Montané MH, Menand B, Gontero B Tags: Biochimie Source Type: research

Increasing evidence of pathogenic role of the Mediator (MED) complex in the development of cardiovascular diseases.
Abstract 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...
Source: Biochimie - June 27, 2019 Category: Biochemistry Authors: Napoli C, Schiano C, Soricelli A Tags: Biochimie Source Type: research

Disturbances in H+ dynamics during environmental carcinogenesis.
Huc L Abstract 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 benz...
Source: Biochimie - June 19, 2019 Category: Biochemistry Authors: Lagadic-Gossmann D, Hardonnière K, Mograbi B, Sergent O, Huc L Tags: Biochimie Source Type: research

LncRNA THOR promotes tongue squamous cell carcinomas by stabilizing IGF2BP1 downstream targets.
Abstract 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, xenog...
Source: Biochimie - June 17, 2019 Category: Biochemistry Authors: Yang H, Fu G, Liu F, Hu C, Lin J, Tan Z, Fu Y, Ji F, Cao M Tags: Biochimie Source Type: research

Diversity of circular RNAs and RNA ligases in archaeal cells.
Abstract 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...
Source: Biochimie - June 15, 2019 Category: Biochemistry Authors: Becker HF, L'Hermitte-Stead C, Myllykallio H Tags: Biochimie Source Type: research

Interplay between Primary cilia, Ubiquitin-Proteasome system and Autophagy.
ont N Abstract 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 ...
Source: Biochimie - June 15, 2019 Category: Biochemistry Authors: Boukhalfa A, Miceli C, Ávalos Y, Morel E, Dupont N Tags: Biochimie Source Type: research

Proteolytic processing and activation of gingipain zymogens secreted by T9SS of Porphyromonas gingivalis.
mpa J Abstract 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 strai...
Source: Biochimie - June 15, 2019 Category: Biochemistry Authors: Veillard F, Sztukowska M, Nowakowska Z, Mizgalska D, Thøgersen IB, Enghild JJ, Bogyo M, Potempa B, Nguyen KA, Potempa J Tags: Biochimie Source Type: research

Overexpression of CKIP-1 alleviates hypoxia-induced cardiomyocyte injury by up-regulating Nrf2 antioxidant signaling via Keap1 inhibition.
This study aimed to explore the potential role of CKIP-1 in regulating hypoxia-induced cardiomyocyte injury and reveal the underlying mechanism. The results demonstrated that hypoxia-exposed cardiomyocytes showed lower CKIP-1 expression. CKIP-1 restoration by transfecting a CKIP-1 expression vector significantly improved viability and reduced apoptosis in hypoxia-treated cardiomyocytes. Moreover, CKIP-1 overexpression suppressed hypoxia-induced oxidative stress in cardiomyocytes. Mechanism research revealed that CKIP-1 overexpression reduced the expression of kelch-like ECH-associated protein 1 (Keap1) and increased the nu...
Source: Biochimie - June 12, 2019 Category: Biochemistry Authors: Ren J, Li J, Hu J, Yu H, Yang Q, Mu J Tags: Biochimie Source Type: research

Gangliosidome of human anencephaly: a high resolution multistage mass spectrometry study.
Abstract 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 b...
Source: Biochimie - June 12, 2019 Category: Biochemistry Authors: Sarbu M, Ica R, Petrut A, Vukelic Z, Munteanu CVA, Petrescu AJ, Zamfir AD Tags: Biochimie Source Type: research

Induction of endothelial dysfunction by oxidized low-density lipoproteins via downregulation of Erk-5/Mef2c/Klf2 signaling: Amelioration by fisetin.
Abstract Extra-cellular signal regulated kinase-5 (Erk-5), a transcriptional activator and regulator of endothelial cells (ECs) homeostasis, has been implicated in shear stress-induced endothelial dysfunction (ED), however its role in oxidized low-density lipoprotein (oxLDL)- induced ED during metabolic stress is not known. Herein, regulation and function of Erk-5 in oxLDL-induced EC death, inflammation and dysfunction has been investigated. Primary Human Umbilical Vein Endothelial Cells (pHUVECs) were stimulated with oxLDL. MTT and Trypan blue exclusion assays to assess cell viability, RT-qPCR and Western blottin...
Source: Biochimie - June 11, 2019 Category: Biochemistry Authors: Patel R, Varghese JF, Singh RP, Yadav UCS Tags: Biochimie Source Type: research

Phospho-peptide binding domains in S. cerevisiae model organism.
Abstract 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 class...
Source: Biochimie - June 10, 2019 Category: Biochemistry Authors: Panni S Tags: Biochimie Source Type: research

Recombinant cystatins in plants.
Abstract 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 stru...
Source: Biochimie - June 10, 2019 Category: Biochemistry Authors: Tremblay J, Goulet MC, Michaud D Tags: Biochimie Source Type: research