Loss of GCN5L1 in cardiac cells disrupts glucose metabolism and promotes cell death via reduced Akt/mTORC2 signaling
In this study, we sought to determine the mechanism by which GCN5L1 impacts energy substrate utilization and mitochondrial health. We find that hypoxia and reoxygenation (H/R) leads to a reduction in cell viability and Akt phosphorylation in GCN5L1 knockdown AC16 cardiomyocytes, in parallel with elevated glucose utilization and impaired fatty acid use. We demonstrate that glycolysis is uncoupled from glucose oxidation under normoxic conditions in GCN5L1-depleted cells. We show that GCN5L1 directly binds to the Akt-activating mTORC2 component Rictor, and that loss of Rictor acetylation is evident in GCN5L1 knockdown cells. ...
Source: Biochemical Journal - June 19, 2019 Category: Biochemistry Authors: Manning, J. R., Thapa, D., Zhang, M., Stoner, M. W., Traba, J., Corey, C., Shiva, S., Sack, M. N., Scott, I. Tags: Research Articles Source Type: research

Allosteric, transcriptional and post-translational control of mitochondrial energy metabolism
The heart is the organ with highest energy turnover rate (per unit weight) in our body. The heart relies on its flexible and powerful catabolic capacity to continuously generate large amounts of ATP utilizing many energy substrates including fatty acids, carbohydrates (glucose and lactate), ketones and amino acids. The normal health mainly utilizes fatty acids (40–60%) and glucose (20–40%) for ATP production while ketones and amino acids have a minor contribution (10–15% and 1–2%, respectively). Mitochondrial oxidative phosphorylation is the major contributor to cardiac energy production (95%) while...
Source: Biochemical Journal - June 19, 2019 Category: Biochemistry Authors: Karwi, Q. G., Jörg, A. R., Lopaschuk, G. D. Tags: Review Articles Source Type: research

Binding properties of the quaternary assembly protein SPAG1
In this study, we have investigated the role of TPR domains of SPAG1 in the recruitment of HSP chaperones by combining biochemical assays, ITC, NMR spectroscopy and molecular dynamics (MD) simulations. First, we propose that only two, out of the three TPR domains, are able to recruit the protein chaperones HSP70 and HSP90. We then focused on one of these TPR domains and elucidated its 3D structure using NMR spectroscopy. Relying on an NMR-driven docking approach and MD simulations, we deciphered its binding interface with the C-terminal tails of both HSP70 and HSP90. Finally, we addressed the biological function of SPAG1 a...
Source: Biochemical Journal - June 14, 2019 Category: Biochemistry Authors: Chagot, M.-E., Dos Santos Morais, R., Dermouche, S., Lefebvre, D., Manival, X., Chipot, C., Dehez, F., Quinternet, M. Tags: Research Articles Source Type: research

Hsp70 molecular chaperones: multifunctional allosteric holding and unfolding machines
The Hsp70 family of chaperones works with its co-chaperones, the nucleotide exchange factors and J-domain proteins, to facilitate a multitude of cellular functions. Central players in protein homeostasis, these jacks-of-many-trades are utilized in a variety of ways because of their ability to bind with selective promiscuity to regions of their client proteins that are exposed when the client is unfolded, either fully or partially, or visits a conformational state that exposes the binding region in a regulated manner. The key to Hsp70 functions is that their substrate binding is transient and allosterically cycles in a nucl...
Source: Biochemical Journal - June 14, 2019 Category: Biochemistry Authors: Clerico, E. M., Meng, W., Pozhidaeva, A., Bhasne, K., Petridis, C., Gierasch, L. M. Tags: Review Articles Source Type: research

Characterization of soluble CD39 (SolCD39/NTPDase1) from PiggyBac nonviral system as a tool to control the nucleotides level
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 receptor agonists/antagonists, engineered ectonucleotidases, interference RNAs and ectonucleotidase inhibitors that allow the control and quantification of nucleotide levels. NTPDase1 (also called apyrase, ecto-ATPase and CD39) is one of the main enzymes responsi...
Source: Biochemical Journal - June 11, 2019 Category: Biochemistry Authors: Beckenkamp, L. R., Iser, I. C., Onzi, G. R., Fontoura, D. M. S. d., Bertoni, A. P. S., Sevigny, J., Lenz, G., Wink, M. R. Tags: Research Articles Source Type: research

PP2C phosphatase Pic1 negatively regulates the phosphorylation status of Pti1b kinase, a regulator of flagellin-triggered immunity in tomato
Plant immune responses, including the production of reactive oxygen species (ROS), are triggered when pattern recognition receptors (PRRs) 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. To investigate these issues, we used mass spectrometry to search for interactors of P...
Source: Biochemical Journal - June 11, 2019 Category: Biochemistry Authors: Giska, F., Martin, G. B. Tags: Research Articles Source Type: research

Biochemical and structural investigation of taurine:2-oxoglutarate aminotransferase from Bifidobacterium kashiwanohense
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 (BkToa). Biochemical assays revealed high specificity of BkToa for 2-oxoglutarate as the amine acceptor. The crystal structure of BkToa in complex with pyridoxal 5'-phosphate (PLP) and glutamate was determined at 2.7 Å resolution. The enzyme forms a homodime...
Source: Biochemical Journal - June 11, 2019 Category: Biochemistry Authors: Li, M., Wei, Y., Yin, J., Lin, L., Zhou, Y., Hua, G., Cao, P., Ang, E. L., Zhao, H., Yuchi, Z., Zhang, Y. Tags: Research Articles Source Type: research

Slc25a36 modulates pluripotency of mouse embryonic stem cells by regulating mitochondrial function and glutathione level
This study improves the understanding of the function of Slc25a36, as well as the relationship of mitochondrial function with naive pluripotency maintenance and stem cell fate decision. (Source: Biochemical Journal)
Source: Biochemical Journal - June 11, 2019 Category: Biochemistry Authors: Xin, Y., Wang, Y., Zhong, L., Shi, B., Liang, H., Han, J. Tags: Research Articles Source Type: research

Zinc induces iron uptake and DMT1 expression in Caco-2 cells via a PI3K/IRP2 dependent mechanism
The absorption of 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 ion 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 the PI3K pathway in differentiated Caco-2 cells, an intestinal cell culture model. We found that zinc induces DMT1 protein and mRNA expression. Z...
Source: Biochemical Journal - June 11, 2019 Category: Biochemistry Authors: Kondaiah, P., Aslam, M. F., Mashurabad, P. C., Sharp, P. A., Pullakhandam, R. Tags: Research Articles Source Type: research

Retraction: Bax channel triplet: co-operativity and voltage gating
(Source: Biochemical Journal)
Source: Biochemical Journal - May 31, 2019 Category: Biochemistry Authors: Lin, S. H., Cherian, N., Wu, B., Phee, H., Cho, C., Colombini, M. Tags: Retractions Source Type: research

Structural basis for the C-domain-selective angiotensin-converting enzyme inhibition by bradykinin-potentiating peptide b (BPPb)
We present the BPPb N-domain structure in comparison with the previously reported BPPb C-domain structure and highlight key differences in peptide interactions with the S4 to S9 subsites. This suggests the involvement of these subsites in conferring C-domain-selective BPPb binding, in agreement with the mutagenesis results where unique residues governing differences in active site exposure, lid structure and dynamics between the two domains were the major drivers for C-domain-selective BPPb binding. Mere disruption of BPPb interactions with unique S2 and S4 subsite residues, which synergistically assist in BPPb binding, wa...
Source: Biochemical Journal - May 31, 2019 Category: Biochemistry Authors: Sturrock, E. D., Lubbe, L., Cozier, G. E., Schwager, S. L. U., Arowolo, A. T., Arendse, L. B., Belcher, E., Acharya, K. R. Tags: Research Articles Source Type: research

Plastidic glucose-6-phosphate dehydrogenases are regulated to maintain activity in the light
Glucose-6-phosphate dehydrogenase (G6PDH) can initiate the glucose-6-phosphate (G6P) shunt around the Calvin–Benson cycle. 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. We found that the half-saturation concentration of G6PDH isoform 1 is increased under reducing conditions. The other t...
Source: Biochemical Journal - May 31, 2019 Category: Biochemistry Authors: Preiser, A. L., Fisher, N., Banerjee, A., Sharkey, T. D. Tags: Research Articles Source Type: research

Tissue-specific characterization of mitochondrial branched-chain keto acid oxidation using a multiplexed assay platform
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. Such analyses have routinely been utilized across di...
Source: Biochemical Journal - May 31, 2019 Category: Biochemistry Authors: Goldberg, E. J., Buddo, K. A., McLaughlin, K. L., Fernandez, R. F., Pereyra, A. S., Psaltis, C. E., Lin, C.-T., Hagen, J. T., Boykov, I. N., Nguyen, T. K., Gowdy, K. M., Ellis, J. M., Neufer, P. D., McClung, J. M., Fisher-Wellman, K. H. Tags: Research Articles Source Type: research

Toxins for decoding interface selectivity in nicotinic acetylcholine receptors
Nicotinic acetylcholine receptors (nAChRs) are pentameric ligand-gated ion channels that play crucial roles in neurotransmission and regulate complex processes in brain functions, including anxiety, learning and memory, food intake, drug addiction, cognition and nociception. To perform these and other functions, a diverse array of nAChR subtypes are generated by homomeric or heteromeric assembly of 17 homologous nAChR subunits. Agonists, acetylcholine and nicotine, bind to the interface formed between two α subunits and between α and non-α subunits to activate the nAChR and allow cation influx. The divers...
Source: Biochemical Journal - May 28, 2019 Category: Biochemistry Authors: Kini, R. M. Tags: Commentaries Source Type: research

A non-catalytic function of carbonic anhydrase IX contributes to the glycolytic phenotype and pH regulation in human breast cancer cells
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 ...
Source: Biochemical Journal - May 28, 2019 Category: Biochemistry Authors: Mboge, M. Y., Chen, Z., Khokhar, D., Wolff, A., Ai, L., Heldermon, C. D., Bozdag, M., Carta, F., Supuran, C. T., Brown, K. D., McKenna, R., Frost, C. J., Frost, S. C. Tags: Research Articles Source Type: research

Screening substrate-binding positions by rolling circle amplification suggesting a binding model of Nt.BstNBI
Nicking endonucleases (NEs) become increasingly attractive for their promising applications in isothermal amplification. 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 mod...
Source: Biochemical Journal - May 28, 2019 Category: Biochemistry Authors: Wei, H., Tang, S., Duan, X., Guan, Y., Zhao, G. Tags: Research Articles Source Type: research

Designing active RNF4 monomers by introducing a tryptophan: avidity towards E2~Ub conjugates dictates the activity of ubiquitin RING E3 ligases
Ubiquitin RING E3 ligases (E3s) catalyze ubiquitin (Ub) transfer to their substrates by engaging E2~Ub intermediates with the help of their RING domains. Different 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. Monomeric RINGs possess the tryptophan while all well-characterized dimeric RINGs, except RNF8, cont...
Source: Biochemical Journal - May 28, 2019 Category: Biochemistry Authors: Sarkar, S., Behera, A. P., Borar, P., Banka, P. A., Datta, A. B. Tags: Research Articles Source Type: research

Discerning the mechanism of action of HtrA4: a serine protease implicated in the cell death pathway
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 and 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. Therefo...
Source: Biochemical Journal - May 21, 2019 Category: Biochemistry Authors: Kummari, R., Dutta, S., Chaganti, L. K., Bose, K. Tags: Research Articles Source Type: research

Multi-functional regulator MapZ controls both positioning and timing of FtsZ polymerization
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 (mid-cell-anchored protein Z) through direct interactions between the intracellular domain (termed MapZ-N (the intracellular domain of MapZ)) and FtsZ. Using nuclear magneti...
Source: Biochemical Journal - May 21, 2019 Category: Biochemistry Authors: Feng, Z., Zhang, J., Xu, D., Jiang, Y.-L., Zhou, C.-Z., Chen, Y. Tags: Research Articles Source Type: research

Phosphatase of regenerating liver sensitizes MET to functional activation by hepatocyte growth factor
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. We found that PRL expression amplified tyrosine phosphorylation levels of various proteins, among which MET was identified to be the most abundant. This phosphorylation occurred selectively at Y1234/1235 in the activation loop of MET, whereas phosphorylation of Y1349 in the effector-binding site, which is directly involved in downstream signaling, was almost undetectable. Consistently, PRL overexpression by itself did not cause observable a...
Source: Biochemical Journal - May 21, 2019 Category: Biochemistry Authors: Kojima, T., Funato, Y., Miki, H. Tags: Research Articles Source Type: research

An acetylation mimicking mutation, K274Q, in tau imparts neurotoxicity by enhancing tau aggregation and inhibiting tubulin polymerization
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. In addition, K274Q-tau displayed a higher aggregation propensity than wild-type tau as evident from thioflavin S fluorescence, tryptophan fluorescence, and electron microscopic images. Furthermore, dynamic light scattering, atomic force microscopy, a...
Source: Biochemical Journal - May 21, 2019 Category: Biochemistry Authors: Rane, J. S., Kumari, A., Panda, D. Tags: Research Articles Source Type: research

Glycolic acid attenuates UVB-induced aquaporin-3, matrix metalloproteinase-9 expression, and collagen degradation in keratinocytes and mouse skin
We reported that GA slows down cell inflammation and aging caused by UVB. Little is known about GA retarding the skin premature senescence or how to impede these events. To investigate the potential of GA to regulate the expression of MMPs and collagen, GA was topically applied onto human keratinocytes and the C57BL/6J mice dorsal skin. In the present study, we demonstrated that GA reduced UVB-induced type-I procollagen expression and secretory collagen levels. GA reverted and dose-dependently increased the level of aquaporin-3 (AQP3), the expression of which was down-regulated by UVB. The UV-induced MMP-9 level and activi...
Source: Biochemical Journal - May 21, 2019 Category: Biochemistry Authors: Tang, S.-C., Tang, L.-C., Liu, C.-H., Liao, P.-Y., Lai, J.-C., Yang, J.-H. Tags: Research Articles Source Type: research

Quantitative assessment of the high-light tolerance in plants with an impaired photosystem II donor side
This study shows that through the use of PSII donor-side inhibitors, such as UV-B and Cd2+, there is a steeper gradient of photoinactivation in the systems with a weakened donor side, independent of the level of NPQ attained. This is coupled with a concomitant decline in the light tolerance of PSII. The native light tolerance is partially restored upon the use of 1,5-diphenylcarbazide (DPC), a PSII electron donor, allowing for the balance between the inhibitory pathways to be sensitively quantified. Thus, this study confirms that the impact of donor-side inhibition can be detected alongside acceptor-side photoinhibition us...
Source: Biochemical Journal - May 15, 2019 Category: Biochemistry Authors: Wilson, S., Ruban, A. V. Tags: Research Articles Source Type: research

Tubulin heterogeneity regulates functions and dynamics of microtubules and plays a role in the development of drug resistance in cancer
Microtubules, composed of αβ-tubulin heterodimers, exhibit diverse structural and functional properties in different cell types. The diversity in the microtubule structure originates from tubulin heterogeneities, namely tubulin isotypes and their post-translational modifications (PTMs). These heterogeneities confer differential stability to microtubules and provide spatial cues for the functioning of the cell. Furthermore, the altered expressions of tubulin isotypes and PTMs are prominent factors for the development of resistance against some cancer drugs. In this review, we summarize our current knowledge of th...
Source: Biochemical Journal - May 12, 2019 Category: Biochemistry Authors: Prassanawar, S. S., Panda, D. Tags: Review Articles Source Type: research

CrmA orthologs from diverse poxviruses potently inhibit caspases-1 and -8, yet cleavage site mutagenesis frequently produces caspase-1-specific variants
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. Spi-2 proteins like CrmA potently inhibit caspases-1, -4 and...
Source: Biochemical Journal - May 7, 2019 Category: Biochemistry Authors: Bloomer, D. T., Kitevska-Ilioski, T., Pantaki-Eimany, D., Ji, Y., Miles, M. A., Heras, B., Hawkins, C. J. Tags: Research Articles Source Type: research

Starvation-induced autophagy is up-regulated via ROS-mediated ClC-3 chloride channel activation in the nasopharyngeal carcinoma cell line CNE-2Z
In this study, Earle's balanced salt solution (EBSS) was used to induce autophagy in CNE-2Z cells. We found that autophagy and the chloride current induced by EBSS were inhibited by chloride channel blockers. ClC-3 knockdown inhibited the degradation of LC3-II and P62. Furthermore, when reactive oxygen species (ROS) generation was suppressed by antioxidant N-acetyl-l-cysteine (L-NAC) pretreatment, EBSS-induced autophagy was inhibited, and the chloride current was unable to be activated. Nevertheless, ClC-3 knockdown had little effect on ROS levels, indicating that ROS acted upstream of ClC-3 and that both ROS and ClC-3 par...
Source: Biochemical Journal - May 7, 2019 Category: Biochemistry Authors: Zheng, Y., Chen, Z., Gu, Z., Yang, X., Yu, M., Zhao, C., Lin, J., Xu, P., Zhu, L., Jacob, T. J. C., Peng, S., Chen, L., Wang, L. Tags: Research Articles Source Type: research

PAS domain-containing phosphoglycerate kinase deficiency in Leishmania major results in increased autophagosome formation and cell death
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 (PGK) protein is uncharacterized in the literature. Here, we report a PAS domain-containing PGK (LmPAS-PGK) in the unicellular pathogen Leishmania. The modeled structure of N-termina...
Source: Biochemical Journal - April 30, 2019 Category: Biochemistry Authors: Adhikari, A., Biswas, S., Mukherjee, A., Das, S., Adak, S. Tags: Research Articles Source Type: research

Novel long-chain neurotoxins from Bungarus candidus distinguish the two binding sites in muscle-type nicotinic acetylcholine receptors
α-Bungarotoxins, a novel group of long-chain α-neurotoxins, manifest different affinity to two agonist/competitive antagonist binding sites of muscle-type nicotinic acetylcholine receptors (nAChRs), being more active at the interface of α– subunits. Three isoforms (α-BgTx-1–3) were identified in Malayan Krait (Bungarus candidus) from Thailand by genomic DNA analysis; two of them (α-BgTx-1 and 2) were isolated from its venom. The toxins comprise 73 amino acid residues and 5 disulfide bridges, being homologous to α-bungarotoxin (α-BgTx), a classical blocker of muscle-type...
Source: Biochemical Journal - April 26, 2019 Category: Biochemistry Authors: Utkin, Y. N., Kuch, U., Kasheverov, I. E., Lebedev, D. S., Cederlund, E., Molles, B. E., Polyak, I., Ivanov, I. A., Prokopev, N. A., Ziganshin, R. H., Jornvall, H., Alvelius, G., Chanhome, L., Warrell, D. A., Mebs, D., Bergman, T., Tsetlin, V. I. Tags: Research Articles Source Type: research

Periplanetasin-4, a novel antimicrobial peptide from the cockroach, inhibits communications between mitochondria and vacuoles
In this study, we found a couple of cell death features, membrane damage, and apoptosis using antimicrobial peptide from American Cockroach. Periplanetasin-4 (LRHKVYGYCVLGP-NH2) is a 13-mer peptide derived from Periplaneta americana and exhibits phosphatidylserine exposure and caspase activation without DNA fragmentation. Apoptotic features without DNA damage provide evidence that this peptide did not interact with DNA directly and exhibited dysfunction of mitochondria and vacuoles. Superoxide radicals were generated from mitochondria and converted to hydrogen peroxide. Despite the enhancement of catalase and total glutath...
Source: Biochemical Journal - April 26, 2019 Category: Biochemistry Authors: Lee, H., Hwang, J. S., Lee, D. G. Tags: Research Articles Source Type: research

Regulation of differential proton-coupled folate transporter gene expression in human tumors: transactivation by KLF15 with NRF-1 and the role of Sp1
Tumors can be therapeutically targeted with novel antifolates (e.g. AGF94) that are selectively transported by the human proton-coupled folate transporter (hPCFT). Studies were performed to determine the transcription regulation of hPCFT in tumors and identify possible mechanisms that contribute to the highly disparate levels of hPCFT in HepG2 versus HT1080 tumor cells. Transfection of hPCFT-null HT1080 cells with hPCFT restored transport and sensitivity to AGF94. Progressive deletions of the hPCFT promoter construct (–2005 to +96) and reporter gene assays in HepG2 and HT1080 cells confirmed differences in hPCFT tran...
Source: Biochemical Journal - April 26, 2019 Category: Biochemistry Authors: Hou, Z., O'Connor, C., Frühauf, J., Orr, S., Kim, S., Gangjee, A., Matherly, L. H. Tags: Research Articles Source Type: research

The chemical diversity of RNA modifications
Nucleic acid modifications in DNA and RNA ubiquitously exist among all the three kingdoms of life. This trait significantly broadens the genome diversity and works as an important means of gene transcription regulation. Although mammalian systems have limited types of DNA modifications, over 150 different RNA modification types have been identified, with a wide variety of chemical diversities. Most modifications occur on transfer RNA and ribosomal RNA, however many of the modifications also occur on other types of RNA species including mammalian mRNA and small nuclear RNA, where they are essential for many biological roles...
Source: Biochemical Journal - April 26, 2019 Category: Biochemistry Authors: Ontiveros, R. J., Stoute, J., Liu, K. F. Tags: Review Articles Source Type: research

Correction: Phosphorylation of CK1{delta}: identification of Ser370 as the major phosphorylation site targeted by PKA in vitro and in vivo
(Source: Biochemical Journal)
Source: Biochemical Journal - April 18, 2019 Category: Biochemistry Authors: Giamas, G., Hirner, H., Shoshiashvili, L., Grothey, A., Gessert, S., Kühl, M., Henne-Bruns, D., Vorgias, C. E., Knippschild, U. Tags: Correction Source Type: research

Diacylglycerol kinase control of protein kinase C
The diacylglycerol kinases (DGK) are lipid kinases that transform diacylglycerol (DAG) into phosphatidic acid (PA) in a reaction that terminates DAG-based signals. DGK provide negative regulation to conventional and novel protein kinase C (PKC) enzymes, limiting local DAG availability in a tissue- and subcellular-restricted manner. Defects in the expression/activity of certain DGK isoforms contribute substantially to cognitive impairment and mental disorders. Abnormal DGK overexpression in tumors facilitates invasion and resistance to chemotherapy preventing tumor immune destruction by tumor-infiltrating lymphocytes. Effec...
Source: Biochemical Journal - April 18, 2019 Category: Biochemistry Authors: Merida, I., Arranz-Nicolas, J., Rodriguez-Rodriguez, C., Avila-Flores, A. Tags: Review Articles Source Type: research

Plant glutathione biosynthesis revisited: redox-mediated activation of glutamylcysteine ligase does not require homo-dimerization
Plant -glutamylcysteine ligase (GCL), catalyzing the first and tightly regulated step of glutathione (GSH) biosynthesis, is redox-activated via formation of an intramolecular disulfide bond. In vitro, redox-activation of recombinant GCL protein causes formation of homo-dimers. Here, we have investigated whether dimerization occurs in vivo and if so whether it contributes to redox-activation. FPLC analysis indicated that recombinant redox-activated WT (wild type) AtGCL dissociates into monomers at concentrations below 10–6 M, i.e. below the endogenous AtGCL concentration in plastids, which was estimated to be in ...
Source: Biochemical Journal - April 15, 2019 Category: Biochemistry Authors: Yang, Y., Lenherr, E. D., Gromes, R., Wang, S., Wirtz, M., Hell, R., Peskan-Berghöfer, T., Scheffzek, K., Rausch, T. Tags: Research Articles Source Type: research

Molecular dynamics of C99-bound {gamma}-secretase reveal two binding modes with distinct compactness, stability, and active-site retention: implications for A{beta} production
We report here an essentially complete atomic model of C99 within wild-type -secretase that respects all the experimental constraints and additionally describes loop, helix, and C99 substrate dynamics in a realistic all-atom membrane. Our model represents the matured auto-cleaved state required for catalysis. From two independent 500-ns molecular dynamic simulations, we identify two conformation states of C99 in equilibrium, a compact and a loose state. Our simulations provide a basis for C99 processing and Aβ formation and explain the production of longer and shorter Aβ, as the compact state retains C99 for long...
Source: Biochemical Journal - April 15, 2019 Category: Biochemistry Authors: Dehury, B., Tang, N., Kepp, K. P. Tags: Research Articles Source Type: research

Chloroplast thioredoxin systems dynamically regulate photosynthesis in plants
Photosynthesis is a highly regulated process in photoautotrophic cells. The main goal of the regulation is to keep the basic photosynthetic reactions, i.e. capturing light energy, conversion into chemical energy and production of carbohydrates, in balance. The rationale behind the evolution of strong regulation mechanisms is to keep photosynthesis functional under all conditions encountered by sessile plants during their lifetimes. The regulatory mechanisms may, however, also impair photosynthetic efficiency by overriding the photosynthetic reactions in controlled environments like crop fields or bioreactors, where light e...
Source: Biochemical Journal - April 15, 2019 Category: Biochemistry Authors: Nikkanen, L., Rintamäki, E. Tags: Review Articles Source Type: research

Stem cell models as an in vitro model for predictive toxicology
Adverse drug reactions (ADRs) are the unintended side effects of drugs. They are categorised as either predictable or unpredictable drug-induced injury and may be exhibited after a single or prolonged exposure to one or multiple compounds. Historically, toxicology studies rely heavily on animal models to understand and characterise the toxicity of novel compounds. However, animal models are imperfect proxies for human toxicity and there have been several high-profile cases of failure of animal models to predict human toxicity e.g. fialuridine, TGN1412 which highlight the need for improved predictive models of human toxicit...
Source: Biochemical Journal - April 15, 2019 Category: Biochemistry Authors: Lynch, S., Pridgeon, C. S., Duckworth, C. A., Sharma, P., Park, B. K., Goldring, C. E. P. Tags: Review Articles Source Type: research

Calcium-calmodulin gating of a pH-insensitive isoform of connexin43 gap junctions
Intracellular protons and calcium ions are two major chemical factors that regulate connexin43 (Cx43) gap junction communication and the synergism or antagonism between pH and Ca2+ has been questioned for decades. To assess the ability of Ca2+ ions to modulate Cx43 junctional conductance (gj) in the absence of pH-sensitivity, patch clamp experiments were performed on Neuroblastoma-2a (N2a) cells or neonatal mouse ventricular myocytes (NMVMs) expressing either full-length Cx43 or the Cx43-M257 (Cx43K258stop) mutant protein, a carboxyl-terminus (CT) truncated version of Cx43 lacking pH-sensitivity. The addition of 1 &mu...
Source: Biochemical Journal - April 10, 2019 Category: Biochemistry Authors: Wei, S., Cassara, C., Lin, X., Veenstra, R. D. Tags: Research Articles Source Type: research

Preferential adsorption to air-water interfaces: a novel cryoprotective mechanism for LEA proteins
Late embryogenesis abundant (LEA) proteins comprise a diverse family whose members play a key role in abiotic stress tolerance. As intrinsically disordered proteins, LEA proteins are highly hydrophilic and inherently stress tolerant. They have been shown to stabilise multiple client proteins under a variety of stresses, but current hypotheses do not fully explain how such broad range stabilisation is achieved. Here, using neutron reflection and surface tension experiments, we examine in detail the mechanism by which model LEA proteins, AavLEA1 and ERD10, protect the enzyme citrate synthase (CS) from aggregation during free...
Source: Biochemical Journal - April 10, 2019 Category: Biochemistry Authors: Yuen, F., Watson, M., Barker, R., Grillo, I., Heenan, R. K., Tunnacliffe, A., Routh, A. F. Tags: Research Articles Source Type: research

Investigating the active site of human trimethyllysine hydroxylase
The biologically important carnitine biosynthesis pathway in humans proceeds via four enzymatic steps. The first step in carnitine biosynthesis is catalyzed by trimethyllysine hydroxylase (TMLH), a non-heme Fe(II) and 2-oxoglutarate (2OG)-dependent oxygenase, which catalyzes the stereospecific hydroxylation of (2S)-N-trimethyllysine to (2S,3S)-3-hydroxy-N-trimethyllysine. Here, we report biocatalytic studies on human TMLH and its 19 variants introduced through site-directed mutagenesis. Amino acid substitutions at the sites involved in binding of the Fe(II) cofactor, 2OG cosubstrate and (2S)-N-trimethyllysine substrate pro...
Source: Biochemical Journal - April 10, 2019 Category: Biochemistry Authors: Wang, Y., Reddy, Y. V., Al Temimi, A. H. K., Venselaar, H., Nelissen, F. H. T., Lenstra, D. C., Mecinovic, J. Tags: Research Articles Source Type: research

Plant nitrilase: a new job for an old enzyme
Nitrilases are versatile enzymes that hydrolyze nitriles to carboxylic acids and ammonia, but many members of this family lack defined biological functions. In plants, nitrilases have been associated with detoxification of cyanide-containing compounds and auxin biosynthesis; however, recent work suggests that the chemical versatility of these proteins contributes to metabolite repair. In this issue of the Biochemical Journal, Niehaus et al. demonstrate that the Nit1 nitrilase from Arabidopsis thaliana functions as a metabolite repair enzyme that removes deaminated glutathione from the cytoplasm and plastids. (Source: Biochemical Journal)
Source: Biochemical Journal - April 10, 2019 Category: Biochemistry Authors: Jez, J. M. Tags: Commentaries Source Type: research

lncRedibly versatile: biochemical and biological functions of long noncoding RNAs
Long noncoding RNAs (lncRNAs) are transcripts that do not code for proteins, but nevertheless exert regulatory effects on various biochemical pathways, in part via interactions with proteins, DNA, and other RNAs. LncRNAs are thought to regulate transcription and other biological processes by acting, for example, as guides that target proteins to chromatin, scaffolds that facilitate protein–protein interactions and complex formation, and orchestrators of phase-separated compartments. The study of lncRNAs has reached an exciting time, as recent advances in experimental and computational methods allow for genome-wide in...
Source: Biochemical Journal - April 10, 2019 Category: Biochemistry Authors: Shields, E. J., Petracovici, A. F., Bonasio, R. Tags: Review Articles Source Type: research

Glycolytic flux in Saccharomyces cerevisiae is dependent on RNA polymerase III and its negative regulator Maf1
Protein biosynthesis is energetically costly, is tightly regulated and is coupled to stress conditions including glucose deprivation. RNA polymerase III (RNAP III)-driven transcription of tDNA genes for production of tRNAs is a key element in efficient protein biosynthesis. Here we present an analysis of the effects of altered RNAP III activity on the Saccharomyces cerevisiae proteome and metabolism under glucose-rich conditions. We show for the first time that RNAP III is tightly coupled to the glycolytic system at the molecular systems level. Decreased RNAP III activity or the absence of the RNAP III negative regulator, ...
Source: Biochemical Journal - April 4, 2019 Category: Biochemistry Authors: Szatkowska, R., Garcia-Albornoz, M., Roszkowska, K., Holman, S. W., Furmanek, E., Hubbard, S. J., Beynon, R. J., Adamczyk, M. Tags: Research Articles Source Type: research

Solution structures and biophysical analysis of full-length group A PAKs reveal they are monomeric and auto-inhibited in cis
The group A p21-activated kinases (PAKs) exist in an auto-inhibited form until activated by GTPase binding and auto-phosphorylation. In the auto-inhibited form, a regulatory domain binds to the kinase domain (KD) blocking the binding of substrates, and CDC42 or Rac binding to the regulatory domain relieves this auto-inhibition allowing auto-phosphorylation on the KD activation loop. We have determined the crystal structure of the PAK3 catalytic domain and by small angle X-ray scattering, the solution-phase structures of full-length inactive PAK1 and PAK3. The structures reveal a compact but elongated molecular shape that d...
Source: Biochemical Journal - April 4, 2019 Category: Biochemistry Authors: Sorrell, F. J., Kilian, L. M., Elkins, J. M. Tags: Research Articles Source Type: research

ADS-J1 disaggregates semen-derived amyloid fibrils
Semen-derived amyloid fibrils, comprising SEVI (semen-derived enhancer of viral infection) fibrils and SEM1 fibrils, could remarkably enhance HIV-1 sexual transmission and thus are potential targets for the development of an effective microbicide. Previously, we found that ADS-J1, apart from being an HIV-1 entry inhibitor, could also potently inhibit seminal amyloid fibrillization and block fibril-mediated enhancement of viral infection. However, the remodeling effects of ADS-J1 on mature seminal fibrils were unexplored. Herein, we investigated the capacity of ADS-J1 to disassemble seminal fibrils and the potential mode of...
Source: Biochemical Journal - March 29, 2019 Category: Biochemistry Authors: Li, J., Yang, Z., Liu, H., Qiu, M., Zhang, T., Li, W., Li, Z., Qi, T., Qiu, Y., Li, L., Zhou, X., Liu, S., Tan, S. Tags: Research Articles Source Type: research

Crystal structure of dimeric Synechococcus spermidine synthase with bound polyamine substrate and product
Spermidine is a ubiquitous polyamine synthesized by spermidine synthase (SPDS) from the substrates, putrescine and decarboxylated S-adenosylmethionine (dcAdoMet). SPDS is generally active as homodimer, but higher oligomerization states have been reported in SPDS from thermophiles, which are less specific to putrescine as the aminoacceptor substrate. Several crystal structures of SPDS have been solved with and without bound substrates and/or products as well as inhibitors. Here, we determined the crystal structure of SPDS from the cyanobacterium Synechococcus (SySPDS) that is a homodimer, which we also observed in solution....
Source: Biochemical Journal - March 29, 2019 Category: Biochemistry Authors: Guedez, G., Pothipongsa, A., Siren, S., Liljeblad, A., Jantaro, S., Incharoensakdi, A., Salminen, T. A. Tags: Research Articles Source Type: research

Unraveling the role of the MOV10 RNA helicase during influenza A virus infection
Moloney leukemia virus 10 (MOV10) is an interferon-inducible RNA helicase that has been implicated in a broad range of cellular functions, including modulating the replication of a diverse range of viruses. However, the mechanisms by which MOV10 promotes or inhibits the replication of particular viruses have not been well defined. A recent paper published in the Biochemical Journal by Li et al. [Biochem. J. (2019) 476, 467–481] provides insight regarding the mechanisms by which MOV10 restricts influenza A virus (IAV) infection in host cells. First, the authors confirm that MOV10 binds to the viral nucleoprotein (NP) ...
Source: Biochemical Journal - March 27, 2019 Category: Biochemistry Authors: Villalon-Letelier, F., Reading, P. C. Tags: Commentaries Source Type: research

Discovery of natural product ovalicin sensitive type 1 methionine aminopeptidases: molecular and structural basis
In this study, we have discovered two Type 1 wild-type MetAPs (Streptococcus pneumoniae and Enterococcus faecalis) that are inhibited at low micromolar to nanomolar concentrations and established the molecular mechanism. F309 in the active site of Type 1 human MetAP (HsMetAP1b) seems to be the key to the resistance, while newly identified ovalicin sensitive Type 1 MetAPs have a methionine or isoleucine at this position. Type 2 human MetAP (HsMetAP2) also has isoleucine (I338) in the analogous position. Ovalicin inhibited F309M and F309I mutants of human MetAP1b at low micromolar concentration. Molecular dynamics simulation...
Source: Biochemical Journal - March 22, 2019 Category: Biochemistry Authors: Pillalamarri, V., Arya, T., Haque, N., Bala, S. C., Marapaka, A. K., Addlagatta, A. Tags: Research Articles Source Type: research

Conservation of the structural and functional architecture of encapsulated ferritins in bacteria and archaea
Ferritins are a large family of intracellular proteins that protect the cell from oxidative stress by catalytically converting Fe(II) into less toxic Fe(III) and storing iron minerals within their core. Encapsulated ferritins (EncFtn) are a sub-family of ferritin-like proteins, which are widely distributed in all bacterial and archaeal phyla. The recently characterized Rhodospirillum rubrum EncFtn displays an unusual structure when compared with classical ferritins, with an open decameric structure that is enzymatically active, but unable to store iron. This EncFtn must be associated with an encapsulin nanocage in order to...
Source: Biochemical Journal - March 22, 2019 Category: Biochemistry Authors: He, D., Piergentili, C., Ross, J., Tarrant, E., Tuck, L. R., Mackay, C. L., McIver, Z., Waldron, K. J., Clarke, D. J., Marles-Wright, J. Tags: Research Articles Source Type: research

Abscisic acid-determined seed vigour differences do not influence redox regulation during ageing
In conclusion, both ABA signalling and seed ageing impact seed vigour but not necessarily through the same biochemical mechanisms. (Source: Biochemical Journal)
Source: Biochemical Journal - March 22, 2019 Category: Biochemistry Authors: Schausberger, C., Roach, T., Stöggl, W., Arc, E., Finch-Savage, W. E., Kranner, I. Tags: Research Articles Source Type: research