Synthesis and degradation of cAMP in Giardia lamblia: possible role and characterization of a nucleotidyl cyclase with a single cyclase homology domain
Despite its importance in the regulation of growth and differentiation processes of a variety of organisms, the mechanism of synthesis and degradation of cAMP (cyclic AMP) has not yet been described in Giardia lamblia. In this work, we measured significant quantities of cAMP in trophozoites of G. lamblia incubated in vitro and later detected how it increases during the first hours of encystation, and how it then returns to basal levels at 24 h. Through an analysis of the genome of G. lamblia, we found sequences of three putative enzymes — one phosphodiesterase (gPDE) and two nucleotidyl cyclases (gNC1 and gNC2) ...
Source: Biochemical Journal - November 21, 2017 Category: Biochemistry Authors: Saraullo, V., Di Siervi, N., Jerez, B., Davio, C., Zurita, A. Tags: Research Articles Source Type: research

TSPO mutations in rats and a human polymorphism impair the rate of steroid synthesis
In this report, we show that TSPO deletion mutations in rat and its corresponding rs6971 polymorphism in humans alter adrenocorticotropic hormone-induced plasma corticosteroid concentrations. Rat tissues examined show increased cholesteryl ester accumulation, and neurosteroid formation was undetectable in homozygous rats. These results also support a role for TSPO ligands in diseases with steroid-dependent stress and anxiety elements. (Source: Biochemical Journal)
Source: Biochemical Journal - November 21, 2017 Category: Biochemistry Authors: Owen, D. R., Fan, J., Campioli, E., Venugopal, S., Midzak, A., Daly, E., Harlay, A., Issop, L., Libri, V., Kalogiannopoulou, D., Oliver, E., Gallego-Colon, E., Colasanti, A., Huson, L., Rabiner, E. A., Suppiah, P., Essagian, C., Matthews, P. M., Papadopou Tags: Research Articles Source Type: research

Dynamic multi-site phosphorylation by Fyn and Abl drives the interaction between CRKL and the novel scaffolding receptors DCBLD1 and DCBLD2
We report that Src family kinases (SFKs) and Abl differentially promote the interaction between the CRKL–SH2 domain and DCBLD1 and DCBLD2, and while SFKs and Abl each promote DCBLD1 and DCBLD2 binding to the CRKL–SH2 domain, the effect of Abl is more pronounced for DCBLD1. Using high-performance liquid chromatography coupled with tandem mass spectrometry, we quantified phosphorylation at several YxxP sites in DCBLD1 and DCBLD2, mapping site-specific preferences for SFKs and Abl. Together, these data provide a platform to decipher the signaling mechanisms by which these novel receptors drive their biological act...
Source: Biochemical Journal - November 21, 2017 Category: Biochemistry Authors: Schmoker, A. M., Weinert, J. L., Kellett, K. J., Johnson, H. E., Joy, R. M., Weir, M. E., Ebert, A. M., Ballif, B. A. Tags: Research Articles Source Type: research

BamA {beta}16C strand and periplasmic turns are critical for outer membrane protein insertion and assembly
Outer membrane (OM) β-barrel proteins play important roles in importing nutrients, exporting wastes and conducting signals in Gram-negative bacteria, mitochondria and chloroplasts. The outer membrane proteins (OMPs) are inserted and assembled into the OM by OMP85 family proteins. In Escherichia coli, the β-barrel assembly machinery (BAM) contains four lipoproteins such as BamB, BamC, BamD and BamE, and one OMP BamA, forming a ‘top hat’-like structure. Structural and functional studies of the E. coli BAM machinery have revealed that the rotation of periplasmic ring may trigger the barrel β1C&ndash...
Source: Biochemical Journal - November 21, 2017 Category: Biochemistry Authors: Gu, Y., Zeng, Y., Wang, Z., Dong, C. Tags: Research Articles Source Type: research

Holistic bioengineering: rewiring central metabolism for enhanced bioproduction
What does it take to convert a living organism into a truly productive biofactory? Apart from optimizing biosynthesis pathways as standalone units, a successful bioengineering approach must bend the endogenous metabolic network of the host, and especially its central metabolism, to support the bioproduction process. In practice, this usually involves three complementary strategies which include tuning-down or abolishing competing metabolic pathways, increasing the availability of precursors of the desired biosynthesis pathway, and ensuring high availability of energetic resources such as ATP and NADPH. In this review, we e...
Source: Biochemical Journal - November 16, 2017 Category: Biochemistry Authors: Aslan, S., Noor, E., Bar-Even, A. Tags: Review Articles Source Type: research

Recombinant human islet amyloid polypeptide forms shorter fibrils and mediates {beta}-cell apoptosis via generation of oxidative stress
Protein misfolding and aggregation play an important role in many human diseases including Alzheimer's, Parkinson's and type 2 diabetes mellitus (T2DM). The human islet amyloid polypeptide (hIAPP) forms amyloid plaques in the pancreas of T2DM subjects (>95%) that are involved in deteriorating islet function and in mediating β-cell apoptosis. However, the detailed mechanism of action, structure and nature of toxic hIAPP species responsible for this effect remains elusive to date mainly due to the high cost associated with the chemical synthesis of pure peptide required for these studies. In the present work, we atte...
Source: Biochemical Journal - November 16, 2017 Category: Biochemistry Authors: Dubey, R., Minj, P., Malik, N., Sardesai, D. M., Kulkarni, S. H., Acharya, J. D., Bhavesh, N. S., Sharma, S., Kumar, A. Tags: Research Articles Source Type: research

Rac1-stimulated macropinocytosis enhances G{beta}{gamma} activation of PI3K{beta}
Phosphoinositide 3-kinases (PI 3-kinases) are regulated by a diverse range of upstream activators, including receptor tyrosine kinases (RTKs), G-protein-coupled receptors (GPCRs), and small GTPases from the Ras, Rho and Rab families. For the Class IA PI 3-kinase PI3Kβ, two mechanisms for GPCR-mediated regulation have been described: direct binding of Gβ subunits to the C2-helical domain linker of p110β, and Dock180/Elmo1-mediated activation of Rac1, which binds to the Ras-Binding Domain of p110β. We now show that the integration of these dual pathways is unexpectedly complex. In breast cancer cells, exp...
Source: Biochemical Journal - November 16, 2017 Category: Biochemistry Authors: Erami, Z., Khalil, B. D., Salloum, G., Yao, Y., LoPiccolo, J., Shymanets, A., Nürnberg, B., Bresnick, A. R., Backer, J. M. Tags: Research Articles Source Type: research

Lipid-based DNA/siRNA transfection agents disrupt neuronal bioenergetics and mitophagy
A multitude of natural and artificial compounds have been recognized to modulate autophagy, providing direct or, through associated pathways, indirect entry points to activation and inhibition. While these pharmacological tools are extremely useful in the study of autophagy, their abundance also suggests the potential presence of unidentified autophagic modulators that may interfere with experimental designs if applied unknowingly. Here, we report unanticipated effects on autophagy and bioenergetics in neuronal progenitor cells (NPCs) incubated with the widely used lipid-based transfection reagent lipofectamine (LF), which...
Source: Biochemical Journal - November 10, 2017 Category: Biochemistry Authors: Napoli, E., Liu, S., Marsilio, I., Zarbalis, K., Giulivi, C. Tags: Research Articles Source Type: research

OleA Glu117 is key to condensation of two fatty-acyl coenzyme A substrates in long-chain olefin biosynthesis
In this report, the mechanistic role of Xanthomonas campestris OleA Glu117 is investigated through mutant enzymes. Crystal structures were determined for each mutant as well as their complex with the inhibitor cerulenin. Complemented by substrate modeling, these structures suggest that Glu117 aids in substrate positioning for productive carbon–carbon bond formation. Analysis of acyl-CoA substrate hydrolysis shows diminished activity in all mutants. When the active site lacks an acidic residue in the 117 position, OleA cannot form condensed product, demonstrating that Glu117 has a critical role upstream of the essenti...
Source: Biochemical Journal - November 10, 2017 Category: Biochemistry Authors: Jensen, M. R., Goblirsch, B. R., Christenson, J. K., Esler, M. A., Mohamed, F. A., Wackett, L. P., Wilmot, C. M. Tags: Research Articles Source Type: research

Correction: HIV-1 Tat potently stabilises Mdm2 and enhances viral replication
(Source: Biochemical Journal)
Source: Biochemical Journal - November 9, 2017 Category: Biochemistry Authors: Raja, R., Ronsard, L., Lata, S., Trivedi, S., Banerjea, A. C. Tags: Corrections Source Type: research

Macromolecular assemblies of complex polysaccharides with galectin-3 and their synergistic effects on function
Although pectin-derived polysaccharides can antagonize galectin function in various pathological disorders, the nature of their binding interactions needs to be better defined for developing them as drugs. Moreover, given their relatively large size and complexity, pectin-derived polysaccharides are also useful as model systems to assess inter-polysaccharide and protein–polysaccharide interactions. Here, we investigated interactions between galectin-3 (Gal-3) and pectin-derived polysaccharides: a rhamnogalacturonan (RG) and two homogalacturonans (HGs). BioLayer Interferometry and fluorescence-linked immunosorbent ass...
Source: Biochemical Journal - November 9, 2017 Category: Biochemistry Authors: Zhang, T., Miller, M. C., Zheng, Y., Zhang, Z., Xue, H., Zhao, D., Su, J., Mayo, K. H., Zhou, Y., Tai, G. Tags: Research Articles Source Type: research

Sequencing of chondroitin sulfate oligosaccharides using a novel exolyase from a marine bacterium that degrades hyaluronan and chondroitin sulfate/dermatan sulfate
Glycosaminoglycans (GAGs) are a family of chemically heterogeneous polysaccharides that play important roles in physiological and pathological processes. Owing to the structural complexity of GAGs, their sophisticated chemical structures and biological functions have not been extensively studied. Lyases that cleave GAGs are important tools for structural analysis. Although various GAG lyases have been identified, exolytic lyases with unique enzymatic property are urgently needed for GAG sequencing. In the present study, a putative exolytic GAG lyase from a marine bacterium was recombinantly expressed and characterized in d...
Source: Biochemical Journal - November 9, 2017 Category: Biochemistry Authors: Wang, W., Cai, X., Han, N., Han, W., Sugahara, K., Li, F. Tags: Research Articles Source Type: research

Recognition of hyperacetylated N-terminus of H2AZ by TbBDF2 from Trypanosoma brucei
Histone modification plays an important role in various biological processes, including gene expression regulation. Bromodomain, as one of histone readers, recognizes specifically the -N-lysine acetylation (KAc) of histone. Although the bromodomains and histone acetylation sites of Trypanosoma brucei (T. brucei), a lethal parasite responsible for sleeping sickness in human and nagana in cattle, have been identified, how acetylated histones are recognized by bromodomains is still unknown. Here, the bromodomain factor 2 (TbBDF2) from T. brucei was identified to be located in the nucleolus and bind to the hyperacetylated N-te...
Source: Biochemical Journal - November 9, 2017 Category: Biochemistry Authors: Yang, X., Wu, X., Zhang, J., Zhang, X., Xu, C., Liao, S., Tu, X. Tags: Research Articles Source Type: research

Reduction potentials of protein disulfides and catalysis of glutathionylation and deglutathionylation by glutaredoxin enzymes
Glutaredoxins (Grxs) are a class of GSH (glutathione)-dependent thiol–disulfide oxidoreductase enzymes. They use the cellular redox buffer GSSG (glutathione disulfide)/GSH directly to catalyze these exchange reactions. Grxs feature dithiol active sites and can shuttle rapidly between three oxidation states, namely dithiol Grx(SH)2, mixed disulfide Grx(SH)(SSG) and oxidized disulfide Grx(SS). Each is characterized by a distinct standard reduction potential (Eo'). The EP(SS)o' values for the redox couple Grx(SS)/Grx(SH)2 are available, but a recent estimate differs by over 100 mV from the literature values. No est...
Source: Biochemical Journal - November 9, 2017 Category: Biochemistry Authors: Ukuwela, A. A., Bush, A. I., Wedd, A. G., Xiao, Z. Tags: Research Articles Source Type: research

A conserved mammalian mitochondrial isoform of acetyl-CoA carboxylase ACC1 provides the malonyl-CoA essential for mitochondrial biogenesis in tandem with ACSF3
We report the identification of a conserved vertebrate mitochondrial isoform of ACC1 expressed from an ACACA transcript splicing variant. A specific knockdown (KD) of the corresponding transcript in mouse cells, or CRISPR/Cas9-mediated inactivation of the putative mitochondrial targeting sequence in human cells, leads to decreased lipoylation and mitochondrial fragmentation. Simultaneous KD of ACSF3, encoding a mitochondrial malonyl-CoA synthetase previously implicated in the mtFAS process, resulted in almost complete ablation of protein lipoylation, indicating that these enzymes have a redundant function in mtFAS. The dis...
Source: Biochemical Journal - November 6, 2017 Category: Biochemistry Authors: Monteuuis, G., Suomi, F., Kerätär, J. M., Masud, A. J., Kastaniotis, A. J. Tags: Research Articles Source Type: research

Onconase dimerization through 3D domain swapping: structural investigations and increase in the apoptotic effect in cancer cells
Onconase® (ONC), a protein extracted from the oocytes of the Rana pipiens frog, is a monomeric member of the secretory ‘pancreatic-type’ RNase superfamily. Interestingly, ONC is the only monomeric ribonuclease endowed with a high cytotoxic activity. In contrast with other monomeric RNases, ONC displays a high cytotoxic activity. In this work, we found that ONC spontaneously forms dimeric traces and that the dimer amount increases about four times after lyophilization from acetic acid solutions. Differently from RNase A (bovine pancreatic ribonuclease) and the bovine seminal ribonuclease, which produce N- an...
Source: Biochemical Journal - November 6, 2017 Category: Biochemistry Authors: Fagagnini, A., Pica, A., Fasoli, S., Montioli, R., Donadelli, M., Cordani, M., Butturini, E., Acquasaliente, L., Picone, D., Gotte, G. Tags: Research Articles Source Type: research

Carbidopa: a selective Ah receptor modulator (SAhRM)
The aryl hydrocarbon receptor (AhR) was discovered as the intracellular receptor that bound with high affinity to the environmental toxicant 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), and the AhR is required for mediating the toxicity induced by TCDD. Subsequent studies show that the AhR binds structurally diverse chemicals including plant-derived compounds that promote health and several AhR-active pharmaceuticals that exhibit anticancer activity. In this issue, there is a report that carbidopa, a drug used for treating Parkinson's disease, is also an AhR ligand, and this compound inhibits pancreatic cancer cell and tumo...
Source: Biochemical Journal - November 6, 2017 Category: Biochemistry Authors: Safe, S. Tags: Commentaries Source Type: research

Structural complexity in the KCTD family of Cullin3-dependent E3 ubiquitin ligases
Members of the potassium channel tetramerization domain (KCTD) family are soluble non-channel proteins that commonly function as Cullin3 (Cul3)-dependent E3 ligases. Solution studies of the N-terminal BTB domain have suggested that some KCTD family members may tetramerize similarly to the homologous tetramerization domain (T1) of the voltage-gated potassium (Kv) channels. However, available structures of KCTD1, KCTD5 and KCTD9 have demonstrated instead pentameric assemblies. To explore other phylogenetic clades within the KCTD family, we determined the crystal structures of the BTB domains of a further five human KCTD prot...
Source: Biochemical Journal - November 1, 2017 Category: Biochemistry Authors: Pinkas, D. M., Sanvitale, C. E., Bufton, J. C., Sorrell, F. J., Solcan, N., Chalk, R., Doutch, J., Bullock, A. N. Tags: Research Articles Source Type: research

Depletion of MUC5B mucin in gastrointestinal cancer cells alters their tumorigenic properties: implication of the Wnt/{beta}-catenin pathway
Secreted mucins are large O-glycosylated proteins that participate in the protection/defence of underlying mucosae in normal adults. Alteration of their expression is a hallmark of numerous epithelial cancers and has often been correlated to bad prognosis of the tumour. The secreted mucin MUC5B is overexpressed in certain subtypes of gastric and intestinal cancers, but the consequences of this altered expression on the cancer cell behaviour are not known. To investigate the role of MUC5B in carcinogenesis, its expression was knocked-down in the human gastric cancer cell line KATO-III and in the colonic cancer cell line LS1...
Source: Biochemical Journal - November 1, 2017 Category: Biochemistry Authors: Lahdaoui, F., Messager, M., Vincent, A., Hec, F., Gandon, A., Warlaumont, M., Renaud, F., Leteurtre, E., Piessen, G., Jonckheere, N., Mariette, C., Van Seuningen, I. Tags: Research Articles Source Type: research

Processing of syndecan-2 by matrix metalloproteinase-14 and effect of its cleavage on VEGF-induced tube formation of HUVECs
Syndecans (SDCs) are transmembrane proteoglycans that are involved in cell adhesion and cell communication. Specifically, SDC2 plays a key role in tumorigenesis, metastasis, and angiogenesis. Previously, we found that rat SDC2 is shed by matrix metalloproteinase-7 (MMP-7) in colon cancer cells. Here, we analyzed the susceptibility of rat SDC2 to various MMPs. We found that the rat SDC2 ectodomain (ECD) fused to the C-terminal Fc region, which was expressed in mammalian cells, was cleaved more efficiently by MMP-14 than MMP-7. Likewise, when anchored on the surface of HeLa cells, rat SDC2 was cleaved more efficiently by the...
Source: Biochemical Journal - November 1, 2017 Category: Biochemistry Authors: Lee, Y. H., Park, J. H., Cheon, D. H., Kim, T., Park, Y. E., Oh, E.-S., Lee, J. E., Lee, S.-T. Tags: Research Articles Source Type: research

Evolution of allosteric regulation in chorismate mutases from early plants
Plants, fungi, and bacteria synthesize the aromatic amino acids: l-phenylalanine, l-tyrosine, and l-tryptophan. Chorismate mutase catalyzes the branch point reaction of phenylalanine and tyrosine biosynthesis to generate prephenate. In Arabidopsis thaliana, there are two plastid-localized chorismate mutases that are allosterically regulated (AtCM1 and AtCM3) and one cytosolic isoform (AtCM2) that is unregulated. Previous analysis of plant chorismate mutases suggested that the enzymes from early plants (i.e. bryophytes/moss, lycophytes, and basal angiosperms) formed a clade distinct from the isoforms found in flowering plan...
Source: Biochemical Journal - November 1, 2017 Category: Biochemistry Authors: Kroll, K., Holland, C. K., Starks, C. M., Jez, J. M. Tags: Research Articles Source Type: research

The spliceosomal proteins PPIH and PRPF4 exhibit bi-partite binding
Pre-mRNA splicing is a dynamic, multistep process that is catalyzed by the RNA (ribonucleic acid)–protein complex called the spliceosome. The spliceosome contains a core set of RNAs and proteins that are conserved in all organisms that perform splicing. In higher organisms, peptidyl-prolyl isomerase H (PPIH) directly interacts with the core protein pre-mRNA processing factor 4 (PRPF4) and both integrate into the pre-catalytic spliceosome as part of the tri-snRNP (small nuclear RNA–protein complex) subcomplex. As a first step to understand the protein interactions that dictate PPIH and PRPF4 function, we express...
Source: Biochemical Journal - October 25, 2017 Category: Biochemistry Authors: Rajiv, C., Jackson, S. R., Cocklin, S., Eisenmesser, E. Z., Davis, T. L. Tags: Research Articles Source Type: research

AtSPX1 affects the AtPHR1-DNA-binding equilibrium by binding monomeric AtPHR1 in solution
Phosphorus is an essential macronutrient for plant growth and is deficient in ~50% of agricultural soils. The transcription factor phosphate starvation response 1 (PHR1) plays a central role in regulating the expression of a subset of phosphate starvation-induced (PSI) genes through binding to a cis-acting DNA element termed P1BS (PHR1-binding sequences). In Arabidopsis and rice, activity of AtPHR1/OsPHR2 is regulated in part by their downstream target SPX (Syg1, Pho81, Xpr1) proteins through protein–protein interaction. Here, we provide kinetic and affinity data for interaction between AtPHR1 and P1BS sites. Using s...
Source: Biochemical Journal - October 23, 2017 Category: Biochemistry Authors: Qi, W., Manfield, I. W., Muench, S. P., Baker, A. Tags: Research Articles Source Type: research

The role and mechanism of action of sperm PLC-zeta in mammalian fertilisation
At mammalian fertilisation, the fundamental stimulus that triggers oocyte (egg) activation and initiation of early embryonic development is an acute rise of the intracellular-free calcium (Ca2+) concentration inside the egg cytoplasm. This essential Ca2+ increase comprises a characteristic series of repetitive Ca2+ oscillations, starting soon after sperm–egg fusion. Over the last 15 years, accumulating scientific and clinical evidence supports the notion that the physiological stimulus that precedes the cytosolic Ca2+ oscillations is a novel, testis-specific phospholipase C (PLC) isoform, known as PLC-zeta (PLC). Spe...
Source: Biochemical Journal - October 23, 2017 Category: Biochemistry Authors: Nomikos, M., Kashir, J., Lai, F. A. Tags: Review Articles Source Type: research

Therapeutics targeting Bcl-2 in hematological malignancies
Members of the B-cell lymphoma 2 (BCL-2) gene family are attractive targets for cancer therapy as they play a key role in promoting cell survival, a long-since established hallmark of cancer. Clinical utility for selective inhibition of specific anti-apoptotic Bcl-2 family proteins has recently been realized with the Food and Drug Administration (FDA) approval of venetoclax (formerly ABT-199/GDC-0199) in relapsed chronic lymphocytic leukemia (CLL) with 17p deletion. Despite the impressive monotherapy activity in CLL, such responses have rarely been observed in other B-cell malignancies, and preclinical data suggest that co...
Source: Biochemical Journal - October 23, 2017 Category: Biochemistry Authors: Ruefli-Brasse, A., Reed, J. C. Tags: Review Articles Source Type: research

Suppression of store-operated Ca2+ entry by activation of GPER: contribution to a clamping effect on endothelial Ca2+ signaling
The G protein-coupled estrogen receptor 1 (GPER, formerly also known as GPR30) modulates many Ca2+-dependent activities in endothelial cells. However, the underlying mechanisms are poorly understood. We recently reported that GPER acts to prolong cytoplasmic Ca2+ signals by interacting with and promoting inhibitory phosphorylation of the plasma membrane Ca2+-ATPase. In the present study, we examined the role of GPER activation in modulating store-operated Ca2+ entry (SOCE) via effects on the stromal interaction molecule 1 (STIM1). GPER activation by agonist G-1 reduces the peak but prolongs the plateau of bradykinin-induce...
Source: Biochemical Journal - October 23, 2017 Category: Biochemistry Authors: Terry, L. E., VerMeer, M., Giles, J., Tran, Q.-K. Tags: Research Articles Source Type: research

VPS18 recruits VPS41 to the human HOPS complex via a RING-RING interaction
Eukaryotic cells use conserved multisubunit membrane tethering complexes, including CORVET (class C core vacuole/endosome tethering) and HOPS (homotypic fusion and vacuole protein sorting), to control the fusion of endomembranes. These complexes have been extensively studied in yeast, but to date there have been far fewer studies of metazoan CORVET and HOPS. Both of these complexes comprise six subunits: a common four-subunit core and two unique subunits. Once assembled, these complexes function to recognise specific endosomal membrane markers and facilitate SNARE-mediated membrane fusion. CORVET promotes the homotypic fus...
Source: Biochemical Journal - October 23, 2017 Category: Biochemistry Authors: Hunter, M. R., Scourfield, E. J., Emmott, E., Graham, S. C. Tags: Research Articles Source Type: research

Trz1, the long form RNase Z from yeast, forms a stable heterohexamer with endonuclease Nuc1 and mutarotase
Proteomic studies have established that Trz1, Nuc1 and mutarotase form a complex in yeast. Trz1 is a β-lactamase-type RNase composed of two β-lactamase-type domains connected by a long linker that is responsible for the endonucleolytic cleavage at the 3'-end of tRNAs during the maturation process (RNase Z activity); Nuc1 is a dimeric mitochondrial nuclease involved in apoptosis, while mutarotase (encoded by YMR099C) catalyzes the conversion between the α- and β-configuration of glucose-6-phosphate. Using gel filtration, small angle X-ray scattering and electron microscopy, we demonstrated that Trz1, Nu...
Source: Biochemical Journal - October 18, 2017 Category: Biochemistry Authors: Ma, M., Li de la Sierra-Gallay, I., Lazar, N., Pellegrini, O., Lepault, J., Condon, C., Durand, D., van Tilbeurgh, H. Tags: Research Articles Source Type: research

Escherichia coli and Neisseria gonorrhoeae UvrD helicase unwinds G4 DNA structures
G-quadruplex (G4) secondary structures have been implicated in various biological processes, including gene expression, DNA replication and telomere maintenance. However, unresolved G4 structures impede replication progression which can lead to the generation of DNA double-strand breaks and genome instability. Helicases have been shown to resolve G4 structures to facilitate faithful duplication of the genome. Escherichia coli UvrD (EcUvrD) helicase plays a crucial role in nucleotide excision repair, mismatch repair and in the regulation of homologous recombination. Here, we demonstrate a novel role of E. coli and Neisseria...
Source: Biochemical Journal - October 18, 2017 Category: Biochemistry Authors: Shukla, K., Thakur, R. S., Ganguli, D., Rao, D. N., Nagaraju, G. Tags: Research Articles Source Type: research

Kinetochore-microtubule interactions in chromosome segregation: lessons from yeast and mammalian cells
Chromosome congression and segregation require robust yet dynamic attachment of the kinetochore with the spindle microtubules. Force generated at the kinetochore–microtubule interface plays a vital role to drive the attachment, as it is required to move chromosomes and to provide signal to sense correct attachments. To understand the mechanisms underlying these processes, it is critical to describe how the force is generated and how the molecules at the kinetochore–microtubule interface are organized and assembled to withstand the force and respond to it. Research in the past few years or so has revealed intere...
Source: Biochemical Journal - October 18, 2017 Category: Biochemistry Authors: Thomas, G. E., Renjith, M. R., Manna, T. K. Tags: Review Articles Source Type: research

Post-translational modification of the interferon-gamma receptor alters its stability and signaling
The IFN gamma receptor 1 (IFNGR1) binds IFN- and activates gene transcription pathways crucial for controlling bacterial and viral infections. Although decreases in IFNGR1 surface levels have been demonstrated to inhibit IFN- signaling, little is known regarding the molecular mechanisms controlling receptor stability. Here, we show in epithelial and monocytic cell lines that IFNGR1 displays K48 polyubiquitination, is proteasomally degraded, and harbors three ubiquitin acceptor sites at K277, K279, and K285. Inhibition of glycogen synthase kinase 3 beta (GSK3β) destabilized IFNGR1 while overexpression of GSK3β inc...
Source: Biochemical Journal - October 10, 2017 Category: Biochemistry Authors: Londino, J. D., Gulick, D. L., Lear, T. B., Suber, T. L., Weathington, N. M., Masa, L. S., Chen, B. B., Mallampalli, R. K. Tags: Research Articles Source Type: research

Toward a systems approach to the human cytochrome P450 ensemble: interactions between CYP2D6 and CYP2E1 and their functional consequences
Functional cross-talk among human drug-metabolizing cytochrome P450 through their association is a topic of emerging importance. Here, we studied the interactions of human CYP2D6, a major metabolizer of psychoactive drugs, with one of the most prevalent human P450 enzymes, ethanol-inducible CYP2E1. Detection of P450–P450 interactions was accomplished through luminescence resonance energy transfer between labeled proteins incorporated into human liver microsomes and the microsomes of insect cells containing NADPH-cytochrome P450 reductase. The potential of CYP2D6 to form oligomers in the microsomal membrane is among t...
Source: Biochemical Journal - October 10, 2017 Category: Biochemistry Authors: Davydov, D. R., Davydova, N. Y., Rodgers, J. T., Rushmore, T. H., Jones, J. P. Tags: Research Articles Source Type: research

The coproporphyrin ferrochelatase of Staphylococcus aureus: mechanistic insights into a regulatory iron-binding site
The majority of characterised ferrochelatase enzymes catalyse the final step of classical haem synthesis, inserting ferrous iron into protoporphyrin IX. However, for the recently discovered coproporphyrin-dependent pathway, ferrochelatase catalyses the penultimate reaction where ferrous iron is inserted into coproporphyrin III. Ferrochelatase enzymes from the bacterial phyla Firmicutes and Actinobacteria have previously been shown to insert iron into coproporphyrin, and those from Bacillus subtilis and Staphylococcus aureus are known to be inhibited by elevated iron concentrations. The work herein reports a Km (coproporphy...
Source: Biochemical Journal - October 10, 2017 Category: Biochemistry Authors: Hobbs, C., Reid, J. D., Shepherd, M. Tags: Research Articles Source Type: research

Novel endogenous retrovirus-derived transcript expressed in the bovine placenta is regulated by WNT signaling
Endogenous retroviruses (ERVs) are involved in placentation; perhaps, the most well-known ERVs are the syncytins, actively transcribed env genes involved in cell–cell fusion and possible morphological variations. However, ERVs other than syncytins that play an important role in placental development have not been well characterized. To identify ERV genes expressed during the onset of placentation in the bovine species, we characterized the expression profiles of bovine conceptus transcripts during the peri-attachment period using RNA-seq analysis, and confirming some candidates through real-time PCR. Using in silico ...
Source: Biochemical Journal - October 10, 2017 Category: Biochemistry Authors: Sakurai, T., Nakagawa, S., Bai, H., Bai, R., Kusama, K., Ideta, A., Aoyagi, Y., Kaneko, K., Iga, K., Yasuda, J., Miyazawa, T., Imakawa, K. Tags: Research Articles Source Type: research

Bindings of NO, CO, and O2 to multifunctional globin type dehaloperoxidase follow the 'sliding scale rule
Dehaloperoxidase–hemoglobin (DHP), a multifunctional globin protein, not only functions as an oxygen carrier as typical globins such as myoglobin and hemoglobin, but also as a peroxidase, a mono- and dioxygenase, peroxygenase, and an oxidase. Kinetics of DHP binding to NO, CO, and O2 were characterized for wild-type DHP A and B and the H55D and H55V DHP A mutants using stopped-flow methods. All three gaseous ligands bind to DHP significantly more weakly than sperm whale myoglobin (SWMb). Both CO and NO bind to DHP in a one-step process to form a stable six-coordinate complex. Multiple-step NO binding is not observed ...
Source: Biochemical Journal - October 5, 2017 Category: Biochemistry Authors: Wu, G., Zhao, J., Franzen, S., Tsai, A.-L. Tags: Research Articles Source Type: research

Expression of an RNA glycosidase inhibits HIV-1 transactivation of transcription
HIV-1 (human immunodeficiency virus) transcription is primarily controlled by the virally encoded Tat (transactivator of transcription) protein and its interaction with the viral TAR (transcription response element) RNA element. Specifically, binding of a Tat-containing complex to TAR recruits cellular factors that promote elongation of the host RNA polymerase engaging the viral DNA template. Disruption of this interaction halts viral RNA transcription. In the present study, we investigated the effect of pokeweed antiviral protein (PAP), an RNA glycosidase (EC#: 3.2.2.22) synthesized by the pokeweed plant (Phytolacca ameri...
Source: Biochemical Journal - October 5, 2017 Category: Biochemistry Authors: Kutky, M., Hudak, K. A. Tags: Research Articles Source Type: research

The chromatin remodeling Isw1a complex is regulated by SUMOylation
The ISWI class of proteins consists of a family of chromatin remodeling ATPases that is ubiquitous in eukaryotes and predominantly functions to slide nucleosomes laterally. The yeast Saccharomyces cerevisiae Isw1 partners with several non-essential alternative subunits — Ioc2, Ioc3, or Ioc4 — to form two distinct complexes Isw1a and Isw1b. Besides its ATPase domain, Isw1 presents a C-terminal region formed by HAND, SANT, and SLIDE domains responsible for interaction with the Ioc proteins and optimal association of Isw1 to chromatin. Despite diverse studies on the functions of the Isw1-containing complexes, mole...
Source: Biochemical Journal - October 5, 2017 Category: Biochemistry Authors: Shen, Q., Beyrouthy, N., Matabishi-Bibi, L., Dargemont, C. Tags: Research Articles Source Type: research

Human TorsinA can function in the yeast cytosol as a molecular chaperone
TorsinA (TorA) is an AAA+ (ATPases associated with diverse cellular activities) ATPase linked to dystonia type 1 (DYT1), a neurological disorder that leads to uncontrollable muscular movements. Although DYT1 is linked to a 3 bp deletion in the C-terminus of TorA, the biological function of TorA remains to be established. Here, we use the yeast Saccharomyces cerevisiae as a tractable in vivo model to explore TorA function. We demonstrate that TorA can protect yeast cells against different forms of environmental stress and show that in the absence of the molecular disaggregase Hsp104, TorA can refold heat-denatured luci...
Source: Biochemical Journal - October 5, 2017 Category: Biochemistry Authors: Adam, I., Josse, L., Tuite, M. F. Tags: Research Articles Source Type: research

Constitutive activation of p46JNK2 is indispensable for C/EBP{delta} induction in the initial stage of adipogenic differentiation
Adipogenic differentiation plays a vital role in energy homeostasis and endocrine system. Several transcription factors, including peroxisome proliferator-activated receptor gamma 2 and CCAAT–enhancer-binding protein (C/EBP) α, β, and , are important for the process, whereas the stage-specific intracellular signal transduction regulating the onset of adipogenesis remains enigmatic. Here, we explored the functional role of c-jun N-terminal kinases (JNKs) in adipogenic differentiation using in vitro differentiation models of 3T3-L1 cells and primary adipo-progenitor cells. JNK inactivation with either a phar...
Source: Biochemical Journal - October 5, 2017 Category: Biochemistry Authors: Kusuyama, J., Ohnishi, T., Bandow, K., Amir, M. S., Shima, K., Semba, I., Matsuguchi, T. Tags: Research Articles Source Type: research

A novel image-based high-throughput screening assay discovers therapeutic candidates for adult polyglucosan body disease
Glycogen storage disorders (GSDs) are caused by excessive accumulation of glycogen. Some GSDs [adult polyglucosan (PG) body disease (APBD), and Tarui and Lafora diseases] are caused by intracellular accumulation of insoluble inclusions, called PG bodies (PBs), which are chiefly composed of malconstructed glycogen. We developed an APBD patient skin fibroblast cell-based assay for PB identification, where the bodies are identified as amylase-resistant periodic acid–Schiff's-stained structures, and quantified. We screened the DIVERSet CL 10 084 compound library using this assay in high-throughput format and discovered 1...
Source: Biochemical Journal - September 28, 2017 Category: Biochemistry Authors: Solmesky, L. J., Khazanov, N., Senderowitz, H., Wang, P., Minassian, B. A., Ferreira, I. M., Yue, W. W., Lossos, A., Weil, M., Kakhlon, O. Tags: Research Articles Source Type: research

Carbidopa is an activator of aryl hydrocarbon receptor with potential for cancer therapy
Carbidopa is used with l-DOPA (l-3,4-dihydroxyphenylalanine) to treat Parkinson's disease (PD). PD patients exhibit lower incidence of most cancers including pancreatic cancer, but with the notable exception of melanoma. The decreased cancer incidence is not due to l-DOPA; however, the relevance of Carbidopa to this phenomenon has not been investigated. Here, we tested the hypothesis that Carbidopa, independent of l-DOPA, might elicit an anticancer effect. Carbidopa inhibited pancreatic cancer cell proliferation both in vitro and in vivo. Based on structural similarity with phenylhydrazine, an inhibitor of indoleamine-2,3-...
Source: Biochemical Journal - September 28, 2017 Category: Biochemistry Authors: Ogura, J., Miyauchi, S., Shimono, K., Yang, S., Gonchigar, S., Ganapathy, V., Bhutia, Y. D. Tags: Research Articles Source Type: research

Structural insights into the substrate specificity of a glycoside hydrolase family 5 lichenase from Caldicellulosiruptor sp. F32
Glycoside hydrolase (GH) family 5 is one of the largest GH families with various GH activities including lichenase, but the structural basis of the GH5 lichenase activity is still unknown. A novel thermostable lichenase F32EG5 belonging to GH5 was identified from an extremely thermophilic bacterium Caldicellulosiruptor sp. F32. F32EG5 is a bi-functional cellulose and a lichenan-degrading enzyme, and exhibited a high activity on β-1,3-1,4-glucan but side activity on cellulose. Thin-layer chromatography and NMR analyses indicated that F32EG5 cleaved the β-1,4 linkage or the β-1,3 linkage while a 4-O-substitued...
Source: Biochemical Journal - September 26, 2017 Category: Biochemistry Authors: Meng, D.-D., Liu, X., Dong, S., Wang, Y.-F., Ma, X.-Q., Zhou, H., Wang, X., Yao, L.-S., Feng, Y., Li, F.-L. Tags: Research Articles Source Type: research

Regulating protein breakdown through proteasome phosphorylation
The ubiquitin proteasome system degrades the great majority of proteins in mammalian cells. Countless studies have described how ubiquitination promotes the selective degradation of different cell proteins. However, there is a small but the growing literature that protein half-lives can also be regulated by post-translational modifications of the 26S proteasome. The present study reviews the ability of several kinases to alter proteasome function through subunit phosphorylation. For example, PKA (protein kinase A) and DYRK2 (dual-specificity tyrosine-regulated kinase 2) stimulate the proteasome's ability to degrade ubiquit...
Source: Biochemical Journal - September 24, 2017 Category: Biochemistry Authors: VerPlank, J. J. S., Goldberg, A. L. Tags: Review Articles Source Type: research

Munc18a clusters SNARE-bearing liposomes prior to trans-SNARE zippering
Sec1–Munc18 (SM) proteins co-operate with SNAREs {SNAP [soluble NSF (N-ethylmaleimide-sensitive factor) attachment protein] receptors} to mediate membrane fusion in eukaryotic cells. Studies of Munc18a/Munc18-1/Stxbp1 in neurotransmission suggest that SM proteins accelerate fusion kinetics primarily by activating the partially zippered trans-SNARE complex. However, accumulating evidence has argued for additional roles for SM proteins in earlier steps in the fusion cascade. Here, we investigate the function of Munc18a in reconstituted exocytic reactions mediated by neuronal and non-neuronal SNAREs. We show that Munc18...
Source: Biochemical Journal - September 24, 2017 Category: Biochemistry Authors: Arnold, M. G., Adhikari, P., Kang, B., Xu (徐昊), H. Tags: Research Articles Source Type: research

Identification of drivers for the metamorphic transition of HIV-1 reverse transcriptase
Recent structural characterizations of the p51 and p66 monomers have established an important starting point for understanding the maturation pathway of the human immunodeficiency virus (HIV)-1 reverse transcriptase p66/p51 heterodimer. This process requires a metamorphic transition of the polymerase domain leading to formation of a p66/p66' homodimer that exists as a structural heterodimer. To better understand the drivers for this metamorphic transition, we have performed NMR studies of 15N-labeled RT216 — a construct that includes the fingers and most of the palm domains. These studies are consistent with the conc...
Source: Biochemical Journal - September 24, 2017 Category: Biochemistry Authors: Zheng, X., Mueller, G. A., Kim, K., Perera, L., DeRose, E. F., London, R. E. Tags: Research Articles Source Type: research

Structural evidence of a phosphoinositide-binding site in the Rgd1-RhoGAP domain
We report here the X-ray structure of the Rgd1p–RhoGAP domain, identify by NMR spectroscopy and confirm by docking simulations, a new but cryptic phosphoinositide-binding site, comprising contiguous A1, A1' and B helices. The addition of helix A1', unusual among RhoGAP domains, seems to be crucial for lipid interactions. Such a site was totally unexpected inside a RhoGAP domain, as it was not predicted from either the protein sequence or its three-dimensional structure. Phosphoinositide-binding sites in RhoGAP domains have been reported to correspond to polybasic regions, which are located at the unstructured flexibl...
Source: Biochemical Journal - September 20, 2017 Category: Biochemistry Authors: Martinez, D., Langlois d'Estaintot, B., Granier, T., Tolchard, J., Courreges, C., Prouzet-Mauleon, V., Hugues, M., Gallois, B., Doignon, F., Odaert, B. Tags: Research Articles Source Type: research

Targeting epithelial-mesenchymal plasticity in cancer: clinical and preclinical advances in therapy and monitoring
The concept of epithelial–mesenchymal plasticity (EMP), which describes the dynamic flux within the spectrum of phenotypic states that invasive carcinoma cells may reside, is being increasingly recognised for its role in cancer progression and therapy resistance. The myriad of events that are able to induce EMP, as well as the more recently characterised control loops, results in dynamic transitions of cancerous epithelial cells to more mesenchymal-like phenotypes through an epithelial–mesenchymal transition (EMT), as well as the reverse transition from mesenchymal phenotypes to an epithelial one. The significa...
Source: Biochemical Journal - September 20, 2017 Category: Biochemistry Authors: Bhatia, S., Monkman, J., Toh, A. K. L., Nagaraj, S. H., Thompson, E. W. Tags: Review Articles Source Type: research

Genetic human prion disease modelled in PrP transgenic Drosophila
Inherited human prion diseases, such as fatal familial insomnia (FFI) and familial Creutzfeldt–Jakob disease (fCJD), are associated with autosomal dominant mutations in the human prion protein gene PRNP and accumulation of PrPSc, an abnormal isomer of the normal host protein PrPC, in the brain of affected individuals. PrPSc is the principal component of the transmissible neurotoxic prion agent. It is important to identify molecular pathways and cellular processes that regulate prion formation and prion-induced neurotoxicity. This will allow identification of possible therapeutic interventions for individuals with, or...
Source: Biochemical Journal - September 20, 2017 Category: Biochemistry Authors: Thackray, A. M., Cardova, A., Wolf, H., Pradl, L., Vorberg, I., Jackson, W. S., Bujdoso, R. Tags: Research Articles Source Type: research

Nitric oxide stimulates cellular degradation of human CYP51A1, the highly conserved lanosterol 14{alpha}-demethylase
Nitric oxide (NO) is known to down-regulate drug-metabolizing cytochrome P450 enzymes in an enzyme-selective manner. Ubiquitin–proteasome-dependent and -independent pathways have been reported. Here, we studied the regulation of expression of human CYP51A1, the lanosterol 14α-demethylase required for synthesis of cholesterol and other sterols in mammals, which is found in every kingdom of life. In Huh7 human hepatoma cells, treatment with NO donors caused rapid post-translational down-regulation of CYP51A1 protein. Human NO synthase (NOS)-dependent down-regulation was also observed in cultured human hepatocytes...
Source: Biochemical Journal - September 14, 2017 Category: Biochemistry Authors: Park, J. W., Byrd, A., Lee, C.-m., Morgan, E. T. Tags: Research Articles Source Type: research

Activation of tissue plasminogen activator by metastasis-inducing S100P protein
S100P protein in human breast cancer cells is associated with reduced patient survival and, in a model system of metastasis, it confers a metastatic phenotype upon benign mammary tumour cells. S100P protein possesses a C-terminal lysine residue. Using a multiwell in vitro assay, S100P is now shown for the first time to exhibit a strong, C-terminal lysine-dependent activation of tissue plasminogen activator (tPA), but not of urokinase-catalysed plasminogen activation. The presence of 10 μM calcium ions stimulates tPA activation of plasminogen 2-fold in an S100P-dependent manner. S100P physically interacts with both ...
Source: Biochemical Journal - September 12, 2017 Category: Biochemistry Authors: Clarke, C. J., Gross, S. R., Ismail, T. M., Rudland, P. S., Al-Medhtiy, M., Santangeli, M., Barraclough, R. Tags: Research Articles Source Type: research