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Biochemical Journal

Ruifang Li, Ruiling Zhang, Yanhui Yang, Xueqin Wang, Yanjie Yi, Pei Fan, Zhengwei Liu, Chen Chen, Junpeng Chang
CGA-N12 is an antifungal peptide derived from human chromogranin A. In our previous investigation, CGA-N12 was found to have specific anti-candidal activity, though the mechanism of action remained unclear. Herein, we investigated the effects of CGA-N12 on mitochondria. We found that CGA-N12 induced an over-generation of intracellular reactive oxygen species and dissipation in mitochondrial membrane potential, in which the former plays key roles in the initiation of apoptosis and the latter is a sign of the cell apoptosis...
March 20, 2018: Biochemical Journal
Julián Esteban Sáez, Cristian Arredondo, Carlos Rivera, María Estela Andrés
CoREST family of transcriptional corepressors regulates gene expression and cell fate determination during development. CoREST corepressors recruit with different affinity the histone demethylase LSD1 (KDM1A) and the deacetylases HDAC1/2 to repress with variable strength the expression of target genes. CoREST protein levels are differentially regulated during cell fate decisions and in mature tissues. However, regulatory mechanisms of CoREST corepressors at the protein level have not been studied. Here, we report that CoREST (CoREST1, RCOR1) and its homologs CoREST2 (RCOR2) and CoREST3 (RCOR3) interact with PIASγ, a SUMO-E3 ligase...
March 19, 2018: Biochemical Journal
Hui-Jie Chen, Na Li, Ye Luo, Yong-Liang Jiang, Cong-Zhao Zhou, Yuxing Chen, Qiong Li
The second messenger c-di-GMP plays a key role in bacterial growth, survival and pathogenesis, thus its intracellular homeostasis should be finely maintained. Mycobacterium smegmatis encodes a GAF domain containing bifunctional enzyme DcpA that catalyzes the synthesis and hydrolysis of c-di-GMP . Here we found that M. smegmatis DcpA catalyzes the hydrolysis of c-di-GMP at a higher velocity, compared to the synthetic activity, resulting in a sum reaction from the ultimate substrate GTP to the final product pGpG...
March 19, 2018: Biochemical Journal
Stephen E Beaton, Rhiannon M Evans, Alexander J Finney, Ciaran M Lamont, Fraser A Armstrong, Frank Sargent, Stephen B Carr
Under anaerobic conditions Escherichia coli is able to metabolize molecular hydrogen via the action of several [NiFe]-hydrogenase enzymes. Hydrogenase-2, which is typically present in cells at low levels during anaerobic respiration, is a periplasmic-facing membrane-bound complex that functions as a proton pump to convert energy from H2 oxidation into a proton gradient; consequently, its structure is of great interest. Empirically, the complex consists of a tightly-bound core catalytic module, comprising large (HybC) and small (HybO) subunits, which is attached to an Fe-S protein (HybA) and an integral membrane protein, HybB...
March 19, 2018: Biochemical Journal
Benjamin M Fontaine, Kevin S Martin, Jennifer M Garcia-Rodriguez, Claire Jung, Laura Briggs, Jessica E Southwell, Xin Jia, Emily E Weinert
Regulation of nucleotide and nucleoside concentrations is critical for faithful DNA replication, transcription, and translation in all organisms, and has been linked to bacterial biofilm formation. Unusual 2',3'-cyclic nucleotide monophosphates (2',3'-cNMPs) recently were quantified in mammalian systems, and previous reports have linked these nucleotides to cellular stress and damage in eukaryotes, suggesting an intriguing connection with nucleotide/nucleoside pools and/or cyclic nucleotide signaling. This work reports the first quantification of 2',3'-cNMPs in Escherichia coli and demonstrates that 2',3'-cNMP levels in E...
March 19, 2018: Biochemical Journal
Palika Abayakoon, James P Lingford, Yi Jin, Christopher Bengt, Gideon J Davies, Shenggen Yao, Ethan D Goddard-Borger, Spencer J Williams
Bacterial sulfoglycolytic pathways catabolise sulfoquinovose (SQ), or glycosides thereof, to generate a three-carbon metabolite for primary cellular metabolism and a three-carbon sulfonate that is expelled from the cell. Sulfoglycolytic operons encoding an Embden-Meyerhof-Parnas (EMP)-like or Entner-Doudoroff (ED)-like pathway harbour an uncharacterized gene ( yihR in Escherichia coli ; PpSQ1_00415 in Pseudomonas putida ) that is upregulated in the presence of SQ and has been annotated as an aldose-1-epimerase and which may encode an SQ mutarotase...
March 13, 2018: Biochemical Journal
Itay Cohen, Si Naftaly, Efrat Ben-Zeev, Alexandra Hockla, Evette S Radisky, Niv Papo
High structural and sequence similarity within protein families can pose significant challenges to the development of selective inhibitors, especially towards proteolytic enzymes. Such enzymes usually belong to large families of closely similar proteases and may also hydrolyze, with different rates, protein or peptide-based inhibitors. To address this challenge, we employed a combinatorial yeast surface display library approach complemented with a novel pre-equilibrium, competitive screening strategy for facile assessment of the effects of multiple mutations on inhibitor association rates and binding specificity...
March 13, 2018: Biochemical Journal
Kristina K Durham, Kevin M Chathely, Bernardo L Trigatti
The cardioprotective lipoprotein HDL prevents myocardial infarction , and cardiomyocyte death due to ischemia/reperfusion injury .  The scavenger receptor class B, type 1 (SR-B1) is a high affinity HDL receptor and has been shown to mediate HDL dependent lipid transport as well as signaling in a variety of different cell types.  The contribution of SR-B1 in cardiomyocytes to the protective effects of HDL on cardiomyocyte survival following ischemia has not yet been studied.  Here we use a model of simulated ischemia (oxygen and glucose deprivation; OGD), to assess the mechanistic involvement of SR-B1, PI3K, and AKT in HDL mediated protection of cardiomyocytes from cell death...
March 9, 2018: Biochemical Journal
Yang Xu, Roman Holic, Darren Li, Xue Pan, Elzbieta Mietkiewska, Guanqun Chen, Jocelyn Ozga, Randall Weselake
Seed oil from flax ( Linum usitatissimum ) is enriched in α -linolenic acid (ALA; 18:3 Δ 9 cis ,12 cis ,15 cis ) but the biochemical processes underlying the enrichment of flax seed oil with this polyunsaturated fatty acid are not fully elucidated. Here, a potential process involving the catalytic actions of long-chain acyl-CoA synthetase (LACS) and diacylglycerol acyltransferase (DGAT) is proposed for ALA enrichment in triacylglycerol (TAG). LACS catalyzes the ATP-dependent activation of free fatty acid to form acyl-CoA, which in turn may serve as an acyl-donor in the DGAT-catalyzed reaction leading to TAG...
March 9, 2018: Biochemical Journal
Alexia F Kalogeropulou, Jing Zhao, Marc F Bolliger, Anna Memou, Shreya Narasimha, Tyler P Molitor, William H Wilson, Hardy J Rideout, R Jeremy Nichols
Autosomal dominant, missense mutations in the Leucine Rich Repeat protein Kinase 2 ( LRRK2 ) gene are the most common genetic predisposition to develop Parkinson's disease (PD). LRRK2 kinase activity is increased in several pathogenic mutations [N1437H, R1441C/G/H, Y1699C, G2019S], implicating hyperphosphorylation of a substrate in the pathogenesis of disease. Identification of the downstream targets of LRRK2 is a crucial endeavor in the field to understand LRRK2 pathway dysfunction in disease. We have identified the signaling adapter protein p62/SQSTM1 as a novel endogenous interacting partner and substrate of LRRK2...
March 8, 2018: Biochemical Journal
Erika Artukka, Heidi H Luoto, Alexander A Baykov, Reijo Lahti, Anssi M Malinen
Membrane-bound pyrophosphatases (mPPases), which couple pyrophosphate hydrolysis to transmembrane transport of H+ and/or Na+ ions, are divided into K+ ,Na+ -independent, Na+ -regulated, and K+ -dependent families. The first two families include H+ -transporting mPPases (H+ -PPases), whereas the last family comprises one Na+ -transporting, two Na+ -and H+ -transporting subfamilies (Na+ -PPases and Na+ ,H+ -PPases respectively), and three H+ -transporting subfamilies. Earlier studies of the few available model mPPases suggested that K+ binds to a site located adjacent to the pyrophosphate-binding site, but is substituted by the ε-amino group of an evolutionarily acquired lysine residue in the K+ -independent mPPases...
March 8, 2018: Biochemical Journal
Gourab Paul, Arunaditya Deshmukh, Bishwanath Kumar Chourasia, Md Kalamuddin, Ashutosh Panda, Susheel Kumar Singh, Puneet K Gupta, Asif Mohmmed, Virander S Chauhan, Michael Theisen, Pawan Malhotra
Plasmodium  falciparum Merozoite surface protein (MSP) 1 has been studied extensively as a vaccine candidate antigen. PfMSP-1 undergoes proteolytic processing into four major products; p83, p30, p38 and p42 that are associated in the form of non-covalent complex(s) with other merozoite surface proteins. To delineate MSP1 regions involved in the interaction with other MSPs, here we expressed recombinant proteins (PfMSP-165 ) encompassing part of p38 and p42 regions and PfMSP-119 PfMSP-165   interacted strongly with PfMSP-3, PfMSP-6, PfMSP-7, PfMSP-9, whereas PfMSP-119 did not interact with any of these proteins...
March 6, 2018: Biochemical Journal
Zongdong Li, Natasha M Nesbitt, Lisa E Malone, Dimitri V Gnatenko, Song Wu, Daifeng Wang, Wei Zhu, Geoffrey D Girnun, Wadie F Bahou
Bioenergetic requirements of hematopoietic stem cells (HSC) and pluripotent stem cells (PSC) vary with lineage fate, and cellular adaptations rely largely on substrate (glucose/glutamine) availability and mitochondrial function to balance TCA-derived anabolic and redox-regulated antioxidant functions.  Heme synthesis and degradation converge in a linear pathway that utilizes TCA cycle-derived carbon in cataplerotic reactions of tetrapyrrole biosynthesis, terminated by NAD(P)H-dependent biliverdin reductases (IXα, BLVRA and IXβ, BLVRB) that lead to bilirubin generation and cellular antioxidant functions...
March 2, 2018: Biochemical Journal
Kristen L Huber, Banyuhay P Serrano, Jeanne A Hardy
Caspase-9 is a critical factor in the initiation of apoptosis, and as a result is tightly regulated by a number of mechanisms. Caspase-9 contains a Caspase Activation and Recruitment Domain (CARD), which enables caspase-9 to form a tight interaction with the apoptosome, a heptameric activating platform. The caspase-9 CARD has been thought to be principally involved in recruitment to the apoptosome, but its roles outside this interaction have yet to be uncovered. In this work we show that the CARD is involved in physical interactions with the catalytic core of caspase-9 in the absence of the apoptosome; this interaction requires a properly formed caspase-9 active site...
March 2, 2018: Biochemical Journal
Tapan Kumar Mistri, Wibowo Arindrarto, Wei Ping Ng, Choayang Wang, Leng Hiong Lim, Lili Sun, Ian Chambers, Thorsten Wohland, Paul Robson
Oct4 and Sox2 regulate the expression of target genes such as Nanog, Fgf4 and Utf1 , by binding to their respective regulatory motifs. Their functional cooperation is reflected in their ability to heterodimerise on adjacent cis regulatory motifs, the composite Sox/Oct motif. Given that Oct4 and Sox2 regulate many developmental genes, a quantitative analysis of their synergistic action on different Sox/Oct motifs would yield valuable insights into the mechanisms of early embryonic development. In this study, we measured binding affinities of Oct4 and Sox2 to different Sox/Oct motifs using fluorescence correlation spectroscopy (FCS)...
February 27, 2018: Biochemical Journal
Atsushi Yoshida, Yosuke Funato, Hiroaki Miki
Phosphatase of regenerating liver (PRL) is highly expressed in malignant cancers and promotes cancer progression. Recent studies have suggested its functional relationship with Mg2+ , but the importance and molecular details of this relationship remain unknown. Here, we report that PRL expression is regulated by Mg2+ and PRL protects cells from apoptosis under Mg2+ -depleted conditions. When cultured cells were subjected to Mg2+ depletion, endogenous PRL protein levels increased significantly. siRNA-mediated knockdown of endogenous PRL did not significantly affect cell proliferation under normal culture conditions, but it increased cell death after Mg2+ depletion...
February 27, 2018: Biochemical Journal
Yang Qiu, Rachel J Perry, João-Paulo G Camporez, Xian-Man Zhang, Mario Kahn, Gary W Cline, Gerald I Shulman, Daniel F Vatner
Exposure to the toxins methylene cyclopropyl acetic acid (MCPA) and methylene cyclopropyl glycine (MCPG) of unripe ackee and litchi fruit can lead to hypoglycemia and death; however, the molecular mechanisms by which MCPA and MCPG cause hypoglycemia have not been established in vivo To determine the in vivo mechanisms of action of these toxins we infused them into conscious rodents and assessed rates of hepatic gluconeogenesis and ketogenesis, hepatic acyl-CoA and hepatic acetyl-CoA content, and hepatocellular energy charge...
February 26, 2018: Biochemical Journal
Andrew Michael Frey, Marianne J Satur, Chatchawal Phansopa, Jennifer Lee Parker, David Bradshaw, Jonathan Pratten, Graham Philip Stafford
Bacterial sialidases cleave terminal sialic acid from a variety of host glycoproteins, and contribute to survival and growth of many human-dwelling bacterial species, including various pathogens. Tannerella forsythia , an oral, Gram-negative, fastidious anaerobe, is a key organism in periodontal disease, and possesses a dedicated sialic acid utilisation and scavenging ( nan ) operon, including NanH sialidase. Here, we describe biochemical characterisation of recombinant NanH, including its action on host-relevant sialoglycans such as sialyl Lewis A and sialyl Lewis X (SLeA/X ), and on human cell-attached sialic acids directly, uncovering that it is a highly active broad specificity sialidase...
February 26, 2018: Biochemical Journal
Yuehui Tian, Shiqiang Gao, Shang Yang, Georg Nagel
It is since many years textbook knowledge that the concentration of the second messenger cGMP is regulated in animal rod and cone cells by type-II rhodopsins via a G protein signaling cascade. Microbial rhodopsins with enzymatic activity for regulation of cGMP concentration were only recently discovered: in 2014 light-activated guanylyl cyclase opsins in fungi and in 2017 a novel rhodopsin phosphodiesterase in the protist Salpingoeca rosetta ( Sr RhoPDE). The light-regulation of Sr RhoPDE however, seemed very weak or absent...
February 26, 2018: Biochemical Journal
Stanley M H Chan, Mark P Lowe, Ashton Bernard, Alyson A Miller, Terence P Herbert
Inositol Requiring Enzyme 1 alpha (IRE1α) is an ER-transmembrane endonuclease that is activated in response to ER stress as part of the unfolded protein response (UPR). Chronic activation of the UPR has been implicated in the pathogenesis of many common disease including diabetes, cancer and neurological pathologies such as Huntington's and Alzheimer's disease. 7-hydroxy-4-methyl-2-oxo-2H-chromene-8-carbaldehyde (4µ8C) is widely used as a specific inhibitor of IRE1α ribonuclease activity in mechanistic studies (IC50 of 6...
February 20, 2018: Biochemical Journal
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