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Biochemical Journal

Fabian Giska, Gregory B Martin
Plant immune responses, including the production of reactive oxygen species (ROS), are triggered when pattern recognition receptors (PRR) become activated upon detection of microbe-associated molecular patterns (MAMPs). Receptor-like cytoplasmic kinases are key components of PRR-dependent signaling pathways. In tomato two such kinases, Pti1a and Pti1b, are important positive regulators of the plant immune response. However, it is unknown how these kinases control plant immunity at the molecular level, and how their activity is regulated...
May 16, 2019: Biochemical Journal
Palsa Kondaiah, Mohammad F Aslam, Purnachandra Mashurabad, Paul A Sharp, Raghu Pullakhandam
The absorption of dietary iron is influenced by numerous dietary and physiological factors. We have previously demonstrated that zinc treatment of intestinal cells increases iron absorption via induction of the apical membrane iron transporter divalent metal iron transporter-1 (DMT1). To better understand the mechanisms of zinc-induced iron absorption we have studied the effect of zinc on iron uptake, iron transporter and iron regulatory protein (IRP 1 and 2) expression and the impact of thePI3K pathway in differentiated Caco-2 cells, an intestinal cell culture model...
May 15, 2019: Biochemical Journal
Emma J Goldberg, Katherine A Buddo, Kelsey L McLaughlin, Regina F Fernandez, Andrea S Pereyra, Christine E Psaltis, Chien-Te Lin, James T Hagen, Ilya N Boykov, Tiffany K Nguyen, Kymberly M Gowdy, Jessica M Ellis, P Darrell Neufer, Joseph M McClung, Kelsey H Fisher-Wellman
Alterations to branched chain-keto acid (BCKA) oxidation have been implicated in a wide variety of human diseases, ranging from diabetes to cancer. Although global shifts in BCKA metabolism-evident by gene transcription, metabolite profiling, and in vivo flux analyses have been documented across various pathological conditions, the underlying biochemical mechanism(s) within the mitochondrion remain largely unknown. In vitro experiments using isolated mitochondria represent a powerful biochemical tool for elucidating the role of the mitochondrion in driving disease...
May 15, 2019: Biochemical Journal
Alyssa L Preiser, Nicholas Fisher, Aparajita Banerjee, Thomas D Sharkey
Glucose-6-phosphate dehydrogenase (G6PDH) can initiate the glucose 6-phosphate (G6P) shunt around the Calvin-Benson cycle. In order to understand the regulation of flux through this pathway, we have characterized the biochemical parameters and redox regulation of the three functional plastidic isoforms of Arabidopsis G6PDH. When purified, recombinant proteins were measured, all three exhibited significant substrate inhibition by G6P but not NADP+ , making the determination of enzyme kinetic parameters complex...
May 15, 2019: Biochemical Journal
Mengya Li, Yifeng Wei, Jinyu Yin, Lianyun Lin, Yan Zhou, Gaoqun Hua, Peng Cao, Ee Lui Ang, Huimin Zhao, Zhiguang Yuchi, Yan Zhang
Taurine aminotransferases catalyze the first step in taurine catabolism in many taurine-degrading bacteria, and play an important role in bacterial taurine metabolism in the mammalian gut. Here we report the biochemical and structural characterization of a new taurine:2-oxoglutarate aminotransferase from the human gut bacterium Bifidobacterium kashiwanohense ( Bk Toa). Biochemical assays revealed high specificity of Bk Toa for 2-oxoglutarate as the amine acceptor. The crystal structure of Bk Toa in complex with pyridoxal 5'-phosphate (PLP) and glutamate was determined at 2...
May 14, 2019: Biochemical Journal
Liziane Raquel Beckenkamp, Isabele Cristina Iser, Giovana Ravizzoni Onzi, Dieine Maira Fontoura, Ana Paula Santin Bertoni, Jean Sévigny, Guido Lenz, Marcia Rosângela Wink
Extracellular ATP (eATP) and its metabolites have emerged as key modulators of different diseases and comprise a complex pathway called purinergic signaling. An increased number of tools have been developed to study the role of nucleotides and nucleosides in cell proliferation and migration, influence on the immune system and tumor progression. These tools include receptors agonists/antagonists, engineered ectonucleotidases, interference RNAs and ectonucleotidases inhibitors that allow the control and quantification of nucleotide levels...
May 13, 2019: Biochemical Journal
Mam Y Mboge, Zhijuan Chen, Daniel Khokhar, Alyssa Wolff, Lingbao Ai, Coy D Heldermon, Murat Bozdag, Fabrizio Carta, Claudiu T Supuran, Kevin D Brown, Robert McKenna, Christopher J Frost, Susan C Frost
The most aggressive and invasive tumor cells often reside in hypoxic microenvironments and rely heavily on rapid anaerobic glycolysis for energy production.  This switch from oxidative phosphorylation to glycolysis, along with up-regulation of the glucose transport system, significantly increases the release of lactic acid from cells into the tumor microenvironment. Excess lactate and proton excretion exacerbate extracellular acidification to which cancer cells, but not normal cells, adapt.  We have hypothesized that carbonic anhydrases (CAs) play a role in stabilizing both intracellular and extracellular pH to favor cancer progression and metastasis...
May 9, 2019: Biochemical Journal
Edward D Sturrock, Lizelle Lubbe, Gyles E Cozier, Sylva L U Schwager, Afolake T Arowolo, Lauren B Arendse, Emma Ruth Belcher, K Ravi Acharya
Angiotensin-converting enzyme (ACE) is a zinc metalloprotease best known for its role in blood pressure regulation. ACE consists of two homologous catalytic domains, the N- and C-domain, that display distinct but overlapping catalytic functions in vivo owing to subtle differences in substrate specificity. While current generation ACE inhibitors target both ACE domains, domain-selective ACE inhibitors may be clinically advantageous, either reducing side-effects or having utility in new indications. Here, we used site-directed mutagenesis, an ACE chimera and X-ray crystallography to unveil the molecular basis for C-domain selective ACE inhibition by the bradykinin potentiating peptide b (BPPb), naturally present in Brazilian pit viper venom...
May 9, 2019: Biochemical Journal
Hua Wei, Suming Tang, Xuying Duan, Yifu Guan, Guojie Zhao
Nicking endonucleases (NEs) become increasingly attractive for their promising applications in isothermal amplifications. Unfortunately, in comparison with their applications, their catalytic mechanism studies have relatively lagged behind, due to a paucity of crystal structure information. Nt.BstNBI is one of those widely used NEs. However, many aspects of its catalytic mechanism still remained to be explored. Herein, we employed only rolling circle amplification (RCA) assay as a major analytic tool, and succeeded in identifying the potential binding positions and regions of the DNA substrate based on locked nucleic acid (LNA) modification, DNA duplex length of substrate, and substrate mismatch designs...
May 7, 2019: Biochemical Journal
Sayani Sarkar, Adaitya Prasad Behera, Prateeka Borar, Prerana Agarwal Banka, Ajit B Datta
Ubiquitin RING E3 ligases (E3s) catalyze ubiquitin (Ub) transfer to their substrates by engaging E2~Ub intermediates with the help of their RING domains. Various such E3s have been found to contain a conserved tryptophan residue in their RING that plays an essential role in E2 binding and, hence, enzymatic activity. Many active E3s, however, lack this specific residue. We mined through the existing data to observe that the conservation of the tryptophan and quaternary organization of the RING domains are remarkably correlated...
May 2, 2019: Biochemical Journal
Takuya Kojima, Yosuke Funato, Hiroaki Miki
Phosphatase of regenerating liver (PRL) is overexpressed in metastatic cancers and actively drives their malignant progression. A number of studies on cultured cancer cells have implied PRL overexpression as a stimulant for cellular signaling involved in cell proliferation. However, its role in the tightly adhered and polarized epithelial cells remains largely uncharacterized. In this study, we show that inducible expression of PRL in MDCK normal epithelial cells sensitized MET, the receptor for hepatocyte growth factor (HGF), to functional activation by HGF...
April 29, 2019: Biochemical Journal
Zhang Feng, Jiahai Zhang, Da Xu, Yong-Liang Jiang, Cong-Zhao Zhou, Yuxing Chen
The tubulin-like GTPase protein FtsZ, which forms a discontinuous cytokinetic ring at mid-cell, is a central player to recruit the division machinery to orchestrate cell division. To guarantee the production of two identical daughter cells, the assembly of FtsZ, namely Z-ring, and its precise positioning should be finely regulated. In Streptococcus pneumoniae , the positioning of Z-ring at the division site is mediated by a bitopic membrane protein MapZ through direct interactions between the intracellular domain (termed MapZ-N) and FtsZ...
April 29, 2019: Biochemical Journal
Yanli Xin, Yanliang Wang, Liang Zhong, Bingbo Shi, Hui Liang, Jianyong Han
Mitochondria play a central role in the maintenance of the naïve state of embryonic stem cells. Many details of the mechanism remain to be fully elucidate. Solute carrier family 25 member 36 ( Slc25a36 ) might regulate mitochondrial function through transporting pyrimidine nucleotides for mtDNA/RNA synthesis. Its physical role in this process remains unknown; however, Slc25a36 was recently found to be highly expressed in naïve mouse embryonic stem cells (mESCs). Here, the function of Slc25a36 was characterized as a maintenance factor of mESCs pluripotency...
April 29, 2019: Biochemical Journal
Jitendra Subhash Rane, Anuradha Kumari, Dulal Panda
In Alzheimer's disease, tau is predominantly acetylated at K174, K274, K280 and K281 residues. The acetylation of K274 tau is linked with memory loss and dementia. In this study, we have examined the molecular mechanism of the toxicity of acetylated K274 tau. We incorporated an acetylation mimicking mutation at K274 (K→Q) residue of tau. The mutation (K274Q) strongly reduced the ability of tau to bind to tubulin and also to polymerize tubulin while K274R mutation did not reduce the ability of tau either to bind or polymerize tubulin...
April 29, 2019: Biochemical Journal
Sheau-Chung Tang, Lee-Chun Tang, Chin-Hung Liu, Pei-Yun Liao, Ji-Ching Lai, Jen-Hung Yang
Ultraviolet-B exposure causes an inflammatory response, photoaged-skin, and degradation of extracellular matrix proteins including collagen and elastin. The regulation of these genes was suggested as an important mechanism to attenuate skin aging. Glycolic acid (GA) is commonly present in fruits and recently used to treat dermatological diseases. We had reported that GA slows down cell inflammation and aging caused by UVB. Little is known about GA retard the skin premature senescence or how to impede these events...
April 29, 2019: Biochemical Journal
Raghupathi Kummari, Shubhankar Dutta, Lalith K Chaganti, Kakoli Bose
High-temperature requirement protease A4 (HtrA4) is a secretary serine protease whose expression is up-regulated in pre-eclampsia (PE) and hence is a possible biomarker of PE. It has also been altered in cancers such as glioblastoma, breast carcinoma, and prostate cancer making it an emerging therapeutic target. Among the human HtrAs, HtrA4 is the least characterized protease pertaining to both structure as well as its functions. Although the members of human HtrA family share a significant structural and functional conservation, subtle structural changes have been associated with certain distinct functional requirements...
April 29, 2019: Biochemical Journal
Sam Wilson, Alexander V Ruban
Photoinhibition is the light-induced downregulation of photosynthetic efficiency, the primary target of which is photosystem II (PSII). Currently, there is no clear consensus on the exact mechanism of this process. However, it is clear that inhibition can occur through limitations on both the acceptor- and donor-side of PSII. The former mechanism is caused by electron transport limitations at the PSII acceptor side. Whilst, the latter mechanism relies on disruption of the oxygen-evolving complex (OEC). Both of these mechanisms damage the PSII reaction centre (RC)...
April 29, 2019: Biochemical Journal
Yanfang Zheng, Zhanru Chen, Zhuoyu Gu, Xiaoya Yang, Meisheng Yu, Chan Zhao, Jiawei Lin, Peisheng Xu, Linyan Zhu, Tim J C Jacob, Shuang Peng, Lixin Chen, Liwei Wang
Nutrient deficiency develops frequently in nasopharyngeal carcinoma cell (CNE-2Z) due to the characteristics of aggregation and uncontrolled proliferation. Therefore, starvation can induce autophagy in these cells. Chloride channel3 (ClC-3), a member of the chloride channel family, is involved in various biological processes. However, whether ClC-3 plays an important role in starvation-induced autophagy is unclear. In this study, Earle's Balanced Salt Solution (EBSS) was used to induce autophagy in CNE-2Z cells...
April 16, 2019: Biochemical Journal
David T Bloomer, Tanja Kitevska-Ilioski, Delara Pantaki-Eimany, Yanhao Ji, Mark A Miles, Begona Heras, Christine Hawkins
Poxviruses encode many proteins that enable them to evade host anti-viral defense mechanisms. Spi-2 proteins, including Cowpox virus CrmA, suppress anti-viral immune responses and contribute to poxviral pathogenesis and lethality. These proteins are "serpin" protease inhibitors, which function via a pseudosubstrate mechanism involving initial interactions between the protease and a cleavage site within the serpin. A conformational change within the serpin interrupts the cleavage reaction, deforming the protease active site and preventing dissociation...
April 16, 2019: Biochemical Journal
Ayan Adhikari, Saroj Biswas, Aditi Mukherjee, Sumit Das, Subrata Adak
Per-Arnt-Sim (PAS) domains are structurally conserved and present in numerous proteins throughout all branches of the phylogenetic tree. Although PAS domain containing proteins are major players for the adaptation to environmental stimuli in both prokaryotic and eukaryotic organisms, these types of proteins are still uncharacterized in the trypanosomatid parasites, Trypanosome and Leishmania In addition, PAS containing phosphoglycerate kinase protein is uncharacterized in the literature. Here, we report a PAS domain containing phosphoglycerate kinase (LmPAS-PGK) in the unicellular pathogen Leishmania The modeled structure of N-terminal of this protein exhibits four anti-parallel β sheets centrally flanked by α helices, which is similar to the characteristic signature of PAS domain...
April 15, 2019: Biochemical Journal
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