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Biochemical Journal

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https://www.readbyqxmd.com/read/29321244/silencing-carboxylesterase-1-in-human-thp-1-macrophages-perturbs-genes-regulated-by-pparg-rxr-and-rar-rxr-downregulation-of-cyp27a1-lxr%C3%AE-signaling
#1
Lee C Mangum, Xiang Hou, Abdolsamad Borazjani, Jung Hwa Lee, Matthew K Ross, J Allen Crow
Macrophage foam cells store excess cholesterol as cholesteryl esters, which need to be hydrolyzed for cholesterol efflux. We recently reported that silencing expression of carboxylesterase 1 (CES1) in human THP-1 macrophages (CES1KD macrophages) reduced cholesterol uptake and decreased expression of CD36 and scavenger receptor-A in cells loaded with acetylated low-density lipoprotein (acLDL). Here, we report that CES1KD macrophages exhibit reduced transcription of cytochrome P450 27A1 ( CYP27A1 ) in non-loaded and acLDL-loaded cells...
January 10, 2018: Biochemical Journal
https://www.readbyqxmd.com/read/29321243/adipose-depot-specific-effects-of-ileal-interposition-surgery-in-ucd-t2d-rats-unexpected-implications-for-obesity-and-diabetes
#2
Connie Hung, Casey Bronec, Eleonora Napoli, James Graham, Kimber L Stanhope, Ilaria Marsilio, Maria Cecilia Giron, Peter J Havel, Cecilia Giulivi
Ileal interposition (IT) surgery delays the onset of diabetes in a rat model of type-2 diabetes (UCD-T2DM). Here, to gain a deeper understanding of the molecular events underlying the effects of IT surgery, we examined the changes in the proteome of 4 white adipose depots (retroperitoneal, mesenteric, inguinal, and epididymal), and plasma free fatty acid profile in pre-diabetic rats 1.5 months following IT or sham surgery. The IT-mediated changes were exerted mainly in mesenteric fat, and spanned from delayed adipocyte maturation to a neuroendocrine remodeling...
January 10, 2018: Biochemical Journal
https://www.readbyqxmd.com/read/29321242/adhesion-growth-regulatory-galectins-tested-in-combination-evidence-for-formation-of-hybrids-as-heterodimers
#3
Michelle C Miller, Anna-Kristen Ludwig, Kanin Wichapong, Herbert Kaltner, Jürgen Kopitz, Hans-Joachim Gabius, Kevin H Mayo
The delineation of the physiological significance of protein (lectin)-glycan recognition and the structural analysis of individual lectins have directed our attention to studying them in combination. In this report, we tested the hypothesis of hybrid formation by using binary mixtures of homodimeric galectins-1 and -7 as well as a proteolytically truncated version of chimera-type galectin-3. Initial supportive evidence is provided by affinity chromatography using resin-presented galectin-7. Intriguingly, extent of cell binding by cross-linking of surface counter-receptor increased significantly for monomeric galectin-3 form by presence of galectin-1 or -7...
January 10, 2018: Biochemical Journal
https://www.readbyqxmd.com/read/29301984/stromal-cell-derived-factor-1-cxcl12-activates-integrins-by-direct-binding-to-an-allosteric-ligand-binding-site-site-2-of-integrins-without-cxcr4
#4
Masaaki Fujita, Parastoo Davari, Yoko K Takada, Yoshikazu Takada
Leukocyte arrest on the endothelial cell surface during leukocyte extravasation is induced by rapid integrin activation by chemokines. We recently reported that fractalkine induces integrin activation without its receptor CX3CR1 through binding to the allosteric site (site 2) of integrins. Peptides from site 2 bound to fractalkine and suppressed integrin activation by fractalkine. We hypothesized that this is not limited to membrane-bound fractalkine. We studied ifstromal cell-derived factor 1(SDF1), another chemokine that plays a critical role in leukocyte arrest, activates integrins through binding to site 2...
January 4, 2018: Biochemical Journal
https://www.readbyqxmd.com/read/29301983/insights-into-the-effect-of-minor-groove-interactions-and-metal-cofactors-on-mutagenic-replication-by-human-dna-polymerase-%C3%AE
#5
Myong-Chul Koag, Seongmin Lee
DNA polymerases accommodate various base pair conformations in the event of incorrect insertions. In particular, Watson-Crick-like dG:dTTP base pair has been observed at the insertion site of human DNA polymerase β (pol β). A potential factor contributing to the diverse conformations of base pair mismatches is minor groove interactions. To gain insight into the effect of minor groove interactions on base pair conformations, we generated an Asn279Ala polβ mutant that cannot make minor groove contacts with incoming nucleotide...
January 4, 2018: Biochemical Journal
https://www.readbyqxmd.com/read/29301982/search-of-multiple-hot-spots-on-the-surface-of-peptidyl-trna-hydrolase-structural-binding-and-antibacterial-studies
#6
Sanket Kaushik, Naseer Iqbal, Nagendra Singh, Juhi Sikarwar, Prashant K Singh, Pradeep Sharma, Punit Kaur, Sujata Sharma, Mohammad Owais, Tej P Singh
Peptidyl-tRNA hydrolase (Pth) catalyzes the breakdown of peptidyl-tRNA into peptide and tRNA components. Pth from Acinetobacter baumannii ( Ab Pth) was cloned, expressed, purified and crystallized in native unbound ( Ab Pth-N) state and in bound state with phosphate ion and cytosine arabinoside (cytarabine) ( Ab Pth-C). Structures of Ab Pth-N and Ab Pth-C were determined at 1.36Å and 1.10Å resolutions respectively.  Structure of Ab Pth-N showed that the active site is filled with water molecules. In the structure of Ab Pth-C, a phosphate ion is present in the active site while cytarabine is bound in a cleft which is located away from the catalytic site...
January 4, 2018: Biochemical Journal
https://www.readbyqxmd.com/read/29301981/controlling-of-n-alkylpolyamine-analogue-metabolism-by-selective-deuteration
#7
Sebahat Ucal, Merja R Häkkinen, Aino-Liisa Alanne, Leena Alhonen, Jouko Vepsäläinen, Tuomo A Keinänen, Mervi T Hyvönen
Replacing protium with deuterium is an efficient method to modulate drug metabolism. N -alkylated polyamine analogues are polyamine antimetabolites with proven anticancer efficacy. We have characterized earlier the preferred metabolic routes of N1,N12 -diethylspermine (DESpm), N1 -benzyl- N12 -ethylspermine (BnEtSpm) and N1,N12 -dibenzylspermine (DBSpm) by human recombinant spermine oxidase (SMOX) and acetylpolyamine oxidase (APAO). Here we studied the above analogues, their variably deuterated counterparts and their metabolites as substrates and inhibitors of APAO, SMOX, semicarbazide-sensitive amine oxidase (SSAO), diamine oxidase (DAO) and monoamine oxidases...
January 4, 2018: Biochemical Journal
https://www.readbyqxmd.com/read/29295892/synergistic-drug-combination-gc7-dfmo-suppresses-hypusine-spermidine-dependent-eif5a-activation-and-induces-apoptotic-cell-death-in-neuroblastoma
#8
Chad R Schultz, Dirk Geerts, Marie Mooney, Raid El-Khawaja, Jan Koster, André S Bachmann
The eukaryotic initiation factor 5A (eIF5A), which contributes to several crucial processes during protein translation, is the only protein that requires activation by a unique post-translational hypusine modification. eIF5A hypusination controls cell proliferation, and has been linked to cancer. eIF5A hypusination requires the enzymes deoxyhypusine synthase (DHPS) and deoxyhypusine hydroxylase (DOHH) and uniquely depends on the polyamine (PA) spermidine as the sole substrate. Ornithine decarboxylase (ODC) is the rate-limiting enzyme in PA biosynthesis...
January 2, 2018: Biochemical Journal
https://www.readbyqxmd.com/read/29269396/mechanism-of-prostaglandin-e2-induced-transcriptional-upregulation-of-oncostatin-m-by-creb-and-sp1
#9
Srimoyee Mukherjee, Sumita Sengupta Bandyopadhyay
Oncostatin-M (OSM) is a pleotropic cytokine belonging to the Interleukin-6 family. Differential expression of OSM in response to varying stimuli and exhibiting repertoire of functions in different cells renders it challenging to study the mechanism of its expression. Prostaglandin E2 (PGE2) transcriptionally increased osm levels. In silico studies of about 1 kb upstream of osm promoter region yielded the presence of CRE (cAMP Response Element)-like sites at the distal end (CREosm). Deletion and point mutation of CREosm clearly indicated that this region imparted important role in PGE2-mediated transcription...
December 21, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/29259081/the-hydrophobic-region-of-the-leishmania-peroxin-14-requirements-for-association-with-a-glycosome-mimetic-membrane
#10
Normand Cyr, Terry K Smith, Élodie Boisselier, Louis-Philippe Leroux, Anwar H Kottarampatel, Amanda Davidsen, Christian Salesse, Armando Jardim
Protein import into the Leishmania glycosome requires docking of the cargo loaded peroxin 5(PEX5) receptor to the peroxin 14(PEX14) bound to the glycosome surface. To examine the LdPEX14-membrane interaction, we purified L.donovani promastigote glycosomes and determined the phospholipid and fatty acid composition. These membranes contained predominately phosphatidylethanolamine, phosphatidylcholine, and phosphatidylglycerol modified primarily with C18 and C22 unsaturated fatty acid. Using large unilamellar vesicles (LUVs) with a lipid composition mimicking the glycosomal membrane in combination with sucrose density centrifugation and fluorescence activated cell sorting technique we established that the LdPEX14 membrane binding activity was dependent on a predicted transmembrane helix found within residues 149-179...
December 19, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/29259080/identification-of-a-second-binding-site-on-the-trim25-b30-2-domain
#11
Akshay A D'Cruz, Nadia J Kershaw, Thomas J Hayman, Edmond M Linossi, Jessica J Chiang, May K Wang, Laura F Dagley, Tatiana B Kolesnik, Jian-Guo Zhang, Seth L Masters, Michael Dw Griffin, Michaela U Gack, James M Murphy, Nicos A Nicola, Jeffrey J Babon, Sandra E Nicholson
The retinoic acid-inducible gene-I (RIG-I) receptor recognizes short 5'-di and triphosphate base-paired viral RNA and is a critical mediator of the innate immune response against viruses such as influenza A, ebola, HIV and hepatitis C. This response is reported to require an orchestrated interaction with the tripartite motif 25 (TRIM25) B30.2 protein-interaction domain. Here we present a novel second RIG-I-binding interface on the TRIM25 B30.2 domain that interacts with CARD1 and CARD2 of RIG-I and is revealed by removal of an N-terminal alpha-helix that mimics dimerization of the full-length protein...
December 19, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/29259079/ezrin-anchored-pka-phosphorylates-serine-369-and-373-on-connexin-43-to-enhance-gap-junction-assembly-communication-and-cell-fusion
#12
Aleksandra R Dukic, Pascale Gerbaud, Jean Guibourdenche, Bernd Thiede, Kjetil Taskén, Guillaume Pidoux
A limited number of human cells can fuse to form multinucleated syncytia. In the differentiation of human placenta, mononuclear cytotrophoblasts fuse to form an endocrinologically active, non-proliferative, multinucleated syncytium. This syncytium covers the placenta and manages the exchange of nutrients and gases between maternal and fetal circulation. We recently reported protein kinase A (PKA) to be part of a macromolecular signaling complex with ezrin and gap junction protein connexin 43 (Cx43) that provides cAMP-mediated control of gap junction communication...
December 19, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/29247140/genetic-dissection-of-cyclic-pyranopterin-monophosphate-biosynthesis-in-plant-mitochondria
#13
Inga Kruse, Andrew Maclean, Lionel Hill, Janneke Balk
Mitochondria play a key role in the biosynthesis of two metal cofactors, iron-sulfur (FeS) clusters and molybdenum cofactor (Moco). The two pathways intersect at several points, but a scarcity of mutants has hindered studies to better understand these links. We screened a collection of sirtinol-resistant Arabidopsis thaliana mutants for lines with decreased activities of cytosolic FeS enzymes and Moco enzymes. We identified a new mutant allele of ATM3 , encoding the ATP-binding cassette Transporter of the Mitochondria 3 (systematic name ABCB25), confirming the previously reported role of ATM3 in both FeS cluster and Moco biosynthesis...
December 15, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/29229763/assaying-kinase-activity-of-the-tpl-2-nf-%C3%AE%C2%BAb1-p105-abin-2-complex-using-an-optimal-peptide-substrate
#14
Sandra Kümper, Thorsten Gantke, Chao-Sheng Chen, Yasmina Soneji, Michael J Pattison, Probir Chakravarty, Svend Kjær, Daniel Thomas, Carl Haslam, Bill J Leavens, David House, David J Powell, Steve C Ley
The MKK1/2 kinase TPL-2 is critical for the production of Tumour Necrosis Factor α (TNF) in innate immune responses and a potential anti-inflammatory drug target. Several earlier pharmaceutical company screens with the isolated TPL-2 kinase domain have identified small molecule inhibitors that specifically block TPL-2 signalling in cells but none of these have progressed to clinical development. We have previously shown that TPL-2 catalytic activity regulates TNF production by macrophages while associated with NF-κB1 p105 and ABIN-2, independently of MKK1/2 phosphorylation via an unknown downstream substrate...
December 11, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/29229762/multiple-substitutions-lead-to-increased-loop-flexibility-and-expanded-specificity-in-acinetobacter-baumannii-carbapenemase-oxa-239
#15
Thomas M Harper, Cynthia M June, Magdalena A Taracila, Robert A Bonomo, Rachel A Powers, David A Leonard
OXA-239 is a class D carbapenemase isolated from an Acinetobacter baumannii strain found in Mexico.  This enzyme is a variant of OXA-23 with three amino acid substitutions in or near the active site.  These substitutions cause OXA-239 to hydrolyze late-generation cephalosporins and the monobactam aztreonam with greater efficiency than OXA-23.  OXA-239 activity against the carbapenems doripenem and imipenem is reduced approximately 3-fold and 20-fold respectively.  Further analysis demonstrated that two of the substitutions (P225S and D222N) are largely responsible for the observed alteration of kinetic parameters, while the third (S109L) may serve to stabilize the protein...
December 11, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/29229761/an-unusual-diphosphatase-from-the-phnp-family-cleaves-reactive-fad-photoproducts
#16
Guillaume Aw Beaudoin, Qiang Li, Steven D Bruner, Andrew D Hanson
Flavins are notoriously photolabile, but while the photoproducts derived from the iso -alloxazine ring are well known the other photoproducts are not. In the case of FAD, typically the main cellular flavin, the other photoproducts are predicted to include four- and five-carbon sugars linked to ADP. These FAD photoproducts were shown to be potent glycating agents, more so than ADP-ribose. Such toxic compounds would require disposal via an ADP-sugar diphosphatase or other route. Comparative analysis of bacterial genomes uncovered a candidate disposal gene that is chromosomally clustered with genes for FAD synthesis or transport and is predicted to encode a protein of the PhnP cyclic phosphodiesterase family...
December 11, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/29229760/functional-characterization-of-the-ca2-atpase-sma1-from-schistosoma-mansoni
#17
Xavier Maréchal, Ricardo De Mendonça, Roger Miras, Jean Revilloud, Patrice Catty
Schistosoma mansoni is a parasite that causes bilharzia, a neglected tropical disease affecting hundreds of millions of people each year worldwide. In 2012, S. mansoni had been identified as the only invertebrate possessing two SERCA-type Ca2+-ATPases, SMA1 and SMA2. However, our analysis of recent genomic data shows that the presence of two SERCA pumps is rather frequent in parasitic flatworms. To understand the reasons of this redundancy in S. mansoni , we compared SMA1 and SMA2 at different levels. In terms of sequence and organization, the genes SMA1 and SMA2 are similar, suggesting that they might be the result of a duplication event...
December 11, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/29229759/jmjd6-induces-hotair-an-oncogenic-lincrna-by-physically-interacting-with-its-proximal-promoter
#18
Antara Biswas, Abhijith Shettar, Geetashree Mukherjee, Paturu Kondaiah, Kartiki V Desai
<span style="color: black;">Using microarray analysis we found that HOX transcript antisense intergenic RNA (HOTAIR) is upregulated by Jumonji domain containing-6 (JMJD6), a bifunctional lysyl hydroxylase and arginine demethylase. In breast cancer, JMJD6 and HOTAIR RNAs increase tumor growth and associate with poor prognosis but no molecular relationship between them is known. We show that overexpression of JMJD6 increased HOTAIR expression and JMJD6 siRNAs suppressed it in ER+ MCF-7, triple negative MDA-MB-231 and non-breast cancer HEK 293 cells...
December 11, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/29229758/the-stress-sigma-factor-of-rna-polymerase-rpos-%C3%AF-s-is-a-solvent-exposed-open-molecule-in-solution
#19
Paola Cavaliere, Sébastien Brier, Petr Filipenko, Christina Sizun, Bertrand Raynal, Françoise Bonneté, Fabienne Levi-Acobas, Jacques Bellalou, Patrick England, Julia Chamot-Rooke, Claudine Mayer, Françoise Norel
In bacteria, one primary and multiple alternative σ factors associate with the RNA polymerase core enzyme (E) to form holoenzymes (Eσ) with different promoter recognition specificities. The alternative σ factor RpoS/σS is produced in stationary phase and under stress conditions and reprograms global gene expression to promote bacterial survival. To date, the three-dimensional structure of a full-length free σ factor remains elusive. The current model suggests that extensive interdomain contacts in a free σ factor result in a compact conformation that masks the DNA-binding determinants of σ, explaining why a free σ factor does not bind double stranded promoter DNA efficiently...
December 11, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/29229757/structure-and-activity-of-chix-a-peptidoglycan-hydrolase-required-for-chitinase-secretion-by-serratia-marcescens
#20
Richard A Owen, Paul K Fyfe, Adam Lodge, Jacob Biboy, Waldemar Vollmer, William N Hunter, Frank Sargent
The Gram-negative bacterium Serratia marcescens secretes a number of proteins that are involved in extracellular chitin degradation. This so-called chitinolytic machinery includes three types of chitinase enzymes and a lytic polysaccharide monooxygenase. An operon has been identified in S. marcescens , chiWXYZ , that is thought to be involved in the secretion of the chitinolytic machinery. Genetic evidence points to the ChiX protein being a key player in the secretion mechanism, since deletion of the chiX gene in S...
December 11, 2017: Biochemical Journal
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