Potential role of a series of lysine-/leucine-rich antimicrobial peptide in inhibiting lipopolysaccharide-induced inflammation
In this study, the potent anti-inflammatory mechanism of L-K6 and its analogs in lipopolysaccharide (LPS)-stimulated human macrophage U937 cells were evaluated. We found that L-K6 suppressed the expression of inflammatory factors by two downstream signaling components in the MyD88-dependent pathway, including the mitogen-activated protein kinases (MAPKs) and the NF (nuclear factor)-B signaling pathway, but its analog L-K5, which had the same amino acid sequence as L-K6 but no Lys residue at the –COOH terminal, only inhibited the phosphorylation of I-B and NF-B. Importantly, L-K6 and L-K5 were actively taken up by U93...
Source: Biochemical Journal - November 30, 2018 Category: Biochemistry Authors: Dong, W., Zhu, X., Zhou, X., Yang, Y., Yan, X., Sun, L., Shang, D. Tags: Research Articles Source Type: research
Dimerization of the Trk receptors in the plasma membrane: effects of their cognate ligands
Receptor tyrosine kinases (RTKs) are cell surface receptors which control cell growth and differentiation, and play important roles in tumorigenesis. Despite decades of RTK research, the mechanism of RTK activation in response to their ligands is still under debate. Here, we investigate the interactions that control the activation of the tropomyosin receptor kinase (Trk) family of RTKs in the plasma membrane, using a FRET-based methodology. The Trk receptors are expressed in neuronal tissues, and guide the development of the central and peripheral nervous systems during development. We quantify the dimerization of human Tr...
Source: Biochemical Journal - November 30, 2018 Category: Biochemistry Authors: Ahmed, F., Hristova, K. Tags: Research Articles Source Type: research
Two active site arginines are critical determinants of substrate binding and catalysis in MenD: a thiamine-dependent enzyme in menaquinone biosynthesis
The bacterial enzyme MenD, or 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate (SEPHCHC) synthase, catalyzes an essential Stetter reaction in menaquinone (vitamin K2) biosynthesis via thiamine diphosphate (ThDP)-bound tetrahedral post-decarboxylation intermediates. The detailed mechanism of this intermediate chemistry, however, is still poorly understood, but of significant interest given that menaquinone is an essential electron transporter in many pathogenic bacteria. Here, we used site-directed mutagenesis, enzyme kinetic assays, and protein crystallography to reveal an active–inactive intermediate e...
Source: Biochemical Journal - November 30, 2018 Category: Biochemistry Authors: Qin, M., Song, H., Dai, X., Chen, Y., Guo, Z. Tags: Research Articles Source Type: research
Caffeine chelates calcium in the lumen of the endoplasmic reticulum
Cytosolic Ca2+ signals are often amplified by massive calcium release from the endoplasmic reticulum (ER). This calcium-induced calcium release (CICR) occurs by activation of an ER Ca2+ channel, the ryanodine receptor (RyR), which is facilitated by both cytosolic- and ER Ca2+ levels. Caffeine sensitizes RyR to Ca2+ and promotes ER Ca2+ release at basal cytosolic Ca2+ levels. This outcome is frequently used as a readout for the presence of CICR. By monitoring ER luminal Ca2+ with the low-affinity genetic Ca2+ probe erGAP3, we find here that application of 50 mM caffeine rapidly reduces the Ca2+ content of the ER in HeL...
Source: Biochemical Journal - November 28, 2018 Category: Biochemistry Authors: Rojo-Ruiz, J., Rodriguez-Prados, M., Delrio-Lorenzo, A., Alonso, M. T., Garcia-Sancho, J. Tags: Research Articles Source Type: research
Exosomal KLF3-AS1 from hMSCs promoted cartilage repair and chondrocyte proliferation in osteoarthritis
The present study was designed to explore whether exosomal lncRNA-KLF3-AS1 derived from human mesenchymal stem cells (hMSCs) can serve as a positive treatment for osteoarthritis (OA). hMSCs and MSC-derived exosomes (MSC-exo) were prepared for morphological observation and identification by transmission electron microscopy and flow cytometry. IL-1β-induced OA chondrocytes and collagenase-induced rat model of OA were established for the further experiments. Lentivirus-mediated siRNA targeting KLF3-AS1 was transfected into MSCs for silencing KLF3-AS1. The real-time quantitative PCR and western blotting analysis were perf...
Source: Biochemical Journal - November 28, 2018 Category: Biochemistry Authors: Liu, Y., Zou, R., Wang, Z., Wen, C., Zhang, F., Lin, F. Tags: Research Articles Source Type: research
The laterally acquired GH5 ZgEngAGH5_4 from the marine bacterium Zobellia galactanivorans is dedicated to hemicellulose hydrolysis
Cell walls of marine macroalgae are composed of diverse polysaccharides that provide abundant carbon sources for marine heterotrophic bacteria. Among them, Zobellia galactanivorans is considered as a model for studying algae–bacteria interactions. The degradation of typical algal polysaccharides, such as agars or alginate, has been intensively studied in this model bacterium, but the catabolism of plant-like polysaccharides is essentially uncharacterized. Here, we identify a polysaccharide utilization locus in the genome of Z. galactanivorans, induced by laminarin (β-1,3-glucans), and containing a putative GH5 s...
Source: Biochemical Journal - November 28, 2018 Category: Biochemistry Authors: Dorival, J., Ruppert, S., Gunnoo, M., Orłowski, A., Chapelais-Baron, M., Dabin, J., Labourel, A., Thompson, D., Michel, G., Czjzek, M., Genicot, S. Tags: Research Articles Source Type: research
DDX3 directly facilitates IKK{alpha} activation and regulates downstream signalling pathways
DDX3 is a DEAD-box RNA helicase that we and others have previously implicated in antiviral immune signalling pathways leading to type I interferon (IFN) induction. We previously demonstrated that it directly interacts with the kinase IKK (IB kinase ), enhances it activation, and then facilitates phosphorylation of the transcription factor IRF3 by IKK. However, the TLR7/9 (Toll-like receptor 7/9)-mediated pathway, one of the most physiologically relevant IFN induction pathways, proceeds independently of IKK or the related kinase TBK1 (TANK-binding kinase 1). This pathway induces type I IFN production via the kinases NIK (NF...
Source: Biochemical Journal - November 20, 2018 Category: Biochemistry Authors: Fullam, A., Gu, L., Höhn, Y., Schröder, M. Tags: Research Articles Source Type: research
The N-terminal domain of unknown function (DUF959) in collagen XVIII is intrinsically disordered and highly O-glycosylated
Collagen XVIII (ColXVIII) is a non-fibrillar collagen and proteoglycan that exists in three isoforms: short, medium and long. The medium and long isoforms contain a unique N-terminal domain of unknown function, DUF959, and our sequence-based secondary structure predictions indicated that DUF959 could be an intrinsically disordered domain. Recombinant DUF959 produced in mammalian cells consisted of ~50% glycans and had a molecular mass of 63 kDa. Circular dichroism spectroscopy confirmed the disordered character of DUF959, and static light scattering indicated a monomeric state for glycosylated DUF959 in solution. Smal...
Source: Biochemical Journal - November 20, 2018 Category: Biochemistry Authors: Kaur, I., Ruskamo, S., Koivunen, J., Heljasvaara, R., Lackman, J. J., Izzi, V., Petäjä-Repo, U. E., Kursula, P., Pihlajaniemi, T. Tags: Research Articles Source Type: research
Structural basis for the bi-functionality of human oxaloacetate decarboxylase FAHD1
We present crystallographic data of human FAHD1 that provide new insights into the structure of the catalytic center at high resolution, featuring a flexible ‘lid’-like helical region which folds into a helical structure upon binding of the ODx inhibitor oxalate. The oxalate-driven structural transition results in the generation of a potential catalytic triad consisting of E33, H30 and an associated water molecule. In silico docking studies indicate that the substrate is further stabilized by a complex hydrogen-bond network, involving amino acids Q109 and K123, identified herein as potential key residues for FA...
Source: Biochemical Journal - November 20, 2018 Category: Biochemistry Authors: Weiss, A. K. H., Naschberger, A., Loeffler, J. R., Gstach, H., Bowler, M. W., Holzknecht, M., Cappuccio, E., Pittl, A., Etemad, S., Dunzendorfer-Matt, T., Scheffzek, K., Liedl, K. R., Jansen-Dürr, P. Tags: Research Articles Source Type: research
Insights into leptin signaling and male reproductive health: the missing link between overweight and subfertility?
Obesity stands as one of the greatest healthcare challenges of the 21st century. Obesity in reproductive-age men is ever more frequent and is reaching upsetting levels. At the same time, fertility has taken an inverse direction and is decreasing, leading to an increased demand for fertility treatments. In half of infertile couples, there is a male factor alone or combined with a female factor. Furthermore, male fertility parameters such as sperm count and concentration went on a downward spiral during the last few decades and are now approaching the minimum levels established to achieve successful fertilization. Hence, the...
Source: Biochemical Journal - November 20, 2018 Category: Biochemistry Authors: Moreira, B. P., Monteiro, M. P., Sousa, M., Oliveira, P. F., Alves, M. G. Tags: Review Articles Source Type: research
Chemical biology probes of mammalian GLUT structure and function
The structure and function of glucose transporters of the mammalian GLUT family of proteins has been studied over many decades, and the proteins have fascinated numerous research groups over this time. This interest is related to the importance of the GLUTs as archetypical membrane transport facilitators, as key limiters of the supply of glucose to cell metabolism, as targets of cell insulin and exercise signalling and of regulated membrane traffic, and as potential drug targets to combat cancer and metabolic diseases such as type 2 diabetes and obesity. This review focusses on the use of chemical biology approaches and su...
Source: Biochemical Journal - November 20, 2018 Category: Biochemistry Authors: Holman, G. D. Tags: Review Articles Source Type: research
Structural insights into the interaction of helicase and primase in Mycobacterium tuberculosis
The helicase–primase interaction is an essential event in DNA replication and is mediated by the highly variable C-terminal domain of primase (DnaG) and N-terminal domain of helicase (DnaB). To understand the functional conservation despite the low sequence homology of the DnaB-binding domains of DnaGs of eubacteria, we determined the crystal structure of the helicase-binding domain of DnaG from Mycobacterium tuberculosis (MtDnaG-CTD) and did so to a resolution of 1.58 Å. We observed the overall structure of MtDnaG-CTD to consist of two subdomains, the N-terminal globular region (GR) and the C-terminal hel...
Source: Biochemical Journal - November 15, 2018 Category: Biochemistry Authors: Sharma, D. P., Vijayan, R., Rehman, S. A. A., Gourinath, S. Tags: Research Articles Source Type: research
Sab concentrations indicate chemotherapeutic susceptibility in ovarian cancer cell lines
We examined Sab expression in a panel of OC cell lines and found that the magnitude of Sab expression correlated to chemo-responsiveness; wherein, OC cells with low Sab levels were chemoresistant. The Sab levels were reflected by a corresponding amount of stress-induced c-Jun N-terminal kinase (JNK) on the MOM. BH3 profiling and examination of Bcl-2 and BH3-only protein concentrations revealed that cells with high Sab concentrations were primed for apoptosis, as determined by the decrease in pro-survival Bcl-2 proteins and an increase in pro-apoptotic BH3-only proteins on mitochondria. Furthermore, overexpression of Sab in...
Source: Biochemical Journal - November 15, 2018 Category: Biochemistry Authors: Paudel, I., Hernandez, S. M., Portalatin, G. M., Chambers, T. P., Chambers, J. W. Tags: Research Articles Source Type: research
The oxidation of dehydroascorbic acid and 2,3-diketogulonate by distinct reactive oxygen species
In conclusion, DHA and DKG yield different oxidation products when attacked by different ROS. DHA is more readily oxidised by H2O2 and superoxide; DKG more readily by 1O2. The diverse products are potential signals, enabling organisms to respond appropriately to diverse stresses. Also, the reaction-product ‘fingerprints’ are analytically useful, indicating which ROS are acting in vivo. (Source: Biochemical Journal)
Source: Biochemical Journal - November 9, 2018 Category: Biochemistry Authors: Dewhirst, R. A., Fry, S. C. Tags: Research Articles Source Type: research
The central region of CNOT1 and CNOT9 stimulates deadenylation by the Ccr4-Not nuclease module
Regulated degradation of cytoplasmic mRNA is important for the accurate execution of gene expression programmes in eukaryotic cells. A key step in this process is the shortening and removal of the mRNA poly(A) tail, which can be achieved by the recruitment of the multi-subunit Ccr4–Not nuclease complex via sequence-specific RNA-binding proteins or the microRNA machinery. The Ccr4–Not complex contains several modules that are attached to its large subunit CNOT1. Modules include the nuclease module, which associates with the MIF4G domain of CNOT1 and contains the catalytic subunits Caf1 and Ccr4, as well as the m...
Source: Biochemical Journal - November 9, 2018 Category: Biochemistry Authors: Pavanello, L., Hall, B., Airhihen, B., Winkler, G. S. Tags: Research Articles Source Type: research
