A Biochemical Comparison of Fungal GH6 Cellobiohydrolases.
Abstract Cellobiohydrolases (CBHs) from Glycoside Hydrolase Family 6 (GH6) make up an important part of the secretome in many cellulolytic fungi. They are also of technical interest, particularly because they are part of the enzyme cocktails that are used for industrial breakdown of lignocellulosic biomass. Nevertheless, functional studies of GH6 CBHs are scarce and focused on a few model enzymes. To elucidate functional breadth among GH6 CBHs, we conducted a comparative biochemical study of seven GH6 CBHs originating from fungi living in different habitats, in addition to one enzyme variant. The enzyme sequences ...
Source: The Biochemical Journal - July 16, 2019 Category: Biochemistry Authors: Christensen SJ, Krogh KBRM, Spodsberg N, Borch K, Westh P Tags: Biochem J Source Type: research

The catalytic mechanism for NO production by the mitochondrial enzyme, sulfite oxidase.
Abstract Recently, Guenter Schwarz and colleagues published an elegant study in the Biochemical Journal (2019) 476, 1805-1815 which combines kinetic and spectroscopic studies with protein engineering to provide a mechanism for sulfite oxidase (SO)-catalyzed nitrite reduction that yields nitric oxide (NO). This work is noteworthy as it demonstrates that (i) for NO generation, both sulfite and nitrite must bind to the same molybdenum (Mo) center; (ii) upon sulfite reduction, Mo is reduced from +6 (MoVI) to +4 (MoIV) and MoIV reduces nitrite to NO yielding MoV; (iii) the heme moiety, linked to the Mo-center by an 11 ...
Source: The Biochemical Journal - July 15, 2019 Category: Biochemistry Authors: Mutus B Tags: Biochem J Source Type: research

Simple rules govern the diversity of bacterial nicotianamine-like metallophores.
Abstract In metal-scarce environments, some pathogenic bacteria produce opine-type metallophores mainly to face the host's nutritional immunity. This is the case of staphylopine, pseudopaline and yersinopine, identified in Staphylococcus aureus , Pseudomonas aeruginosa and Yersinia pestis respectively. Depending on the species, these metallophores are synthesized by two (CntLM) or three enzymes (CntKLM), CntM catalyzing the last step of biosynthesis using diverse substrates (pyruvate or α-ketoglutarate), pathway intermediates (xNA or yNA) and cofactors (NADH or NADPH). Here, we explored substrate specificity...
Source: The Biochemical Journal - July 12, 2019 Category: Biochemistry Authors: Laffont C, Brutesco C, Hajjar C, Cullia G, Fanelli R, Ouerdane L, Cavelier F, Arnoux P Tags: Biochem J Source Type: research

The role of PTB domain containing adaptor proteins on PICALM-mediated APP endocytosis and localization.
Abstract One hallmark of Alzheimer's disease (AD) is the presence of amyloid plaques, which mainly consist of the amyloid precursor protein (APP) cleavage product amyloid β (Aβ). For cleavage to occur, APP must be endocytosed from the cell surface. The phosphatidylinositol binding clathrin assembly protein (PICALM) is involved in clathrin-mediated endocytosis and polymorphisms in and near the gene locus were identified as genetic risk factors for AD. PICALM overexpression enhances APP internalization and Aβ production. Furthermore, PICALM shuttles into the nucleus, but its function within the nucleu...
Source: The Biochemical Journal - July 12, 2019 Category: Biochemistry Authors: Merthan L, Haller A, Thal DR, von Einem B, von Arnim CAF Tags: Biochem J Source Type: research

Structural insights into SUMO E1-E2 interactions in Arabidopsis uncovers a distinctive platform for securing SUMO conjugation specificity across evolution.
Abstract SUMOylation of proteins involves the concerted action of the E1-activating enzyme, E2-conjugating enzyme and E3-ligases. An essential discrimination step in the SUMOylation pathway corresponds to the initial interaction between E1 ubiquitin-fold domain (UFD) and E2 enzymes. Although E2 orthologs possess high sequence identity, the E2 binding region of the UFD domains have diverged across evolution. Moreover, in reciprocal in vitro conjugation reactions Arabidopsis E1 and E2 SCE1 fail to interact efficiently with cognate human E2 Ubc9 and E1 partners, respectively. To gain more insights into the properties...
Source: The Biochemical Journal - July 10, 2019 Category: Biochemistry Authors: Liu B, Lois LM, Reverter D Tags: Biochem J Source Type: research

Mechanisms of lipid droplet biogenesis.
Abstract Lipid droplets (LDs) are organelles that compartmentalize nonbilayer-forming lipids in the aqueous cytoplasm of cells. They are ubiquitous in most organisms, including in animals, protists, plants and microorganisms. In eukaryotes, LDs are believed to be derived by a budding and scission process from the surface of the endoplasmic reticulum, and this occurs concomitantly with the accumulation of neutral lipids, most often triacylglycerols and steryl esters. Overall, the mechanisms underlying LD biogenesis are difficult to generalize, in part because of the involvement of different sets of both evolutionar...
Source: The Biochemical Journal - July 9, 2019 Category: Biochemistry Authors: Chapman KD, Aziz M, Dyer JM, Mullen RT Tags: Biochem J Source Type: research

Sugar beet hemoglobins: reactions with nitric oxide and nitrite reveal differential roles for nitrogen metabolism.
w L Abstract In contrast to human hemoglobin (Hb) in red blood cells, plant Hbs do not transport oxygen, instead research points towards nitrogen metabolism. Using comprehensive and integrated biophysical methods we characterized three sugar beet Hbs: BvHb1.1, BvHb1.2 and BvHb2. Their affinities for oxygen, CO, and hexacoordination were determined. Their role in nitrogen metabolism was studied by assessing their ability to bind NO, to reduce nitrite (NiR, nitrite reductase), and to form nitrate (NOD, NO dioxygenase). Results show that BvHb1.2 has high NOD-like activity, in agreement with the high nitrate levels fo...
Source: The Biochemical Journal - July 8, 2019 Category: Biochemistry Authors: Leiva Eriksson N, Reeder BJ, Wilson MT, Bülow L Tags: Biochem J Source Type: research

Comprehensive analysis of yeast ESCRT-III composition in single ESCRT-III deletion mutants.
lling R Abstract The endosomal sorting complex required for transport (ESCRT)-III is associated with a multitude of cellular processes involving membrane remodeling and abscission. The exact composition of ESCRT-III and the contribution of individual ESCRT-III family members to these diverse functions is unclear. Most of the currently available information about ESCRT-III was obtained with tagged, largely non-functional proteins, which may not correctly reflect the in vivo situation. Here, we performed a comprehensive biochemical analysis of ESCRT-III localization and composition in yeast under purely native condi...
Source: The Biochemical Journal - July 4, 2019 Category: Biochemistry Authors: Heinzle C, Mücke L, Brune T, Kölling R Tags: Biochem J Source Type: research

Correction: Ezrin-anchored PKA phosphorylates serine 369 and 373 on connexin 43 to enhance gap junction assembly, communication, and cell fusion.
oux G PMID: 31266855 [PubMed - in process] (Source: The Biochemical Journal)
Source: The Biochemical Journal - July 2, 2019 Category: Biochemistry Authors: Dukic AR, Gerbaud P, Guibourdenche J, Thiede B, Taskén K, Pidoux G Tags: Biochem J Source Type: research

Gelatinase B/matrix metalloproteinase-9 and other neutrophil proteases switch off interleukin-2 activity.
Abstract Interleukin 2 (IL-2) is critical for T cell development and homeostasis, being a key regulator of adaptive immune responses in autoimmunity, hypersensitivity reactions and cancer. Therefore, its abundance in serum and peripheral tissues needs tight control. Here, we described a new mechanism contributing to the immunobiology of IL-2. We demonstrated, both in biochemical and cell-based assays, that IL-2 is subject to proteolytic processing by neutrophil matrix metalloproteinase-9 (MMP-9). IL-2 fragments produced after cleavage by MMP-9 remained linked by a disulfide bond and displayed reduced affinity for ...
Source: The Biochemical Journal - July 1, 2019 Category: Biochemistry Authors: Rybakin V, Stas M, Ugarte-Berzal E, Noppen S, Vandooren J, Van Aelst I, Liekens S, Proost P, Opdenakker G Tags: Biochem J Source Type: research

Structural basis for histone H3K4me3 recognition by the N-terminal domain of the PHD finger protein Spp1.
Abstract Saccharomyces cerevisiae Spp1, a plant homeodomain (PHD) finger containing protein, is a critical subunit of the histone H3K4 methyltransferase complex of proteins associated with Set1 (COMPASS). The chromatin binding affinity of the PHD finger of Spp1 has been proposed to modulate COMPASS activity. During meiosis, Spp1 plays another role in promoting programmed double-strand break (DSB) formation by binding H3K4me3 via its PHD finger and interacting with a DSB protein, Mer2. However, how the Spp1 PHD finger performs site-specific readout of H3K4me3 is still not fully understood. In the present study, we ...
Source: The Biochemical Journal - June 28, 2019 Category: Biochemistry Authors: He C, Liu N, Xie D, Liu Y, Xiao Y, Li F Tags: Biochem J Source Type: research

Biochemical features of primary cells from a pediatric patient with a gain-of-function ODC1 genetic mutation.
In conclusion, our patient and potentially other patients that carry a similar ODC1 gain-of-function mutation might benefit from treatment with DFMO, a drug with a good safety profile, to suppress the exceptionally high ODC activity and putrescine levels in the body. PMID: 31249027 [PubMed - as supplied by publisher] (Source: The Biochemical Journal)
Source: The Biochemical Journal - June 27, 2019 Category: Biochemistry Authors: Schultz CR, Bupp CP, Rajasekaran S, Bachmann AS Tags: Biochem J Source Type: research

Complementary substrate specificity and distinct quaternary assembly of the Escherichia coli aerobic and anaerobic beta-oxidation trifunctional enzyme complexes.
n R Abstract The trifunctional enzyme (TFE) catalyzes the last three steps of the fatty acid β-oxidation cycle. Two TFEs are present in Escherichia coli , EcTFE and anEcTFE. EcTFE is expressed only under aerobic conditions whereas anEcTFE is expressed also under anaerobic conditions, with nitrate or fumarate as the ultimate electron acceptor. The anEcTFE subunits have higher sequence identity with the human mitochondrial TFE (HsTFE) than with the soluble EcTFE. Like HsTFE, here it is found that anEcTFE is a membrane bound complex. Systematic enzyme kinetic studies show that anEcTFE has preference for medium a...
Source: The Biochemical Journal - June 25, 2019 Category: Biochemistry Authors: Sah-Teli SK, Hynönen MJ, Schmitz W, Geraets JA, Seitsonen J, Pedersen JS, Butcher SJ, Wierenga RK, Venkatesan R Tags: Biochem J Source Type: research

Allosteric, transcriptional and post-translational control of mitochondrial energy metabolism.
GD Abstract 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 c...
Source: The Biochemical Journal - June 19, 2019 Category: Biochemistry Authors: Karwi QG, Jörg AR, Lopaschuk GD Tags: Biochem J Source Type: research

Metabolic remodeling of cardiomyocyte identified in phosphoinositide-dependent kinase 1-deficient mice.
Abstract Metabolic remodeling plays an essential role in the pathophysiology of heart failure. Many studies have shown that disruption of phosphoinositide-dependent protein kinase-1 (PDK1) caused severe and lethal heart failure, however, the metabolic pattern of PDK1 deletion remain ambiguous. 1H NMR-based metabolomics was applied to explore the altered metabolic pattern in Pdk1 deficient mice. Principle components analysis (PCA) showed significant separation as early as 4 weeks-age, dysfunction of metabolism precedes morphological change in Pdk1 deficient mice. Time trajectory plot indicated that disturbed metabo...
Source: The Biochemical Journal - June 17, 2019 Category: Biochemistry Authors: Li C, Niu Y, Zheng H, Shan C, Chen Q, Yang Z, Zhao L, Yang C, Gao H Tags: Biochem J Source Type: research

Hsp70 molecular chaperones: multifunctional allosteric holding and unfolding machines.
Abstract 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 allostericall...
Source: The Biochemical Journal - June 14, 2019 Category: Biochemistry Authors: Clerico EM, Meng W, Pozhidaeva A, Bhasne K, Petridis C, Gierasch LM Tags: Biochem J Source Type: research

Nitration-Induced Ubiquitination and Degradation Control Quality of ERK1.
Abstract The mitogen-activated protein kinase ERK1/2 (ERKs) play important roles in a wide spectrum of cellular processes and have been implicated in a number of disease states. The spatiotemporal regulation of ERKs activity has been extensively studied. However, scarce information has been available regarding the quality control of the kinases to scavenge malfunctioning ERKs. Using site-specific mutagenesis and mass spectrometry (MS), we found that disruption of the conserved H-bond between Y210 and E237 of ERK1 through point mutation at or naturally-occurring nitration on Y210, initiates a quality control progra...
Source: The Biochemical Journal - June 13, 2019 Category: Biochemistry Authors: Zhang Y, Huang X, Wang J, Wang X, Liu X, Chen Y, Xu W, Wang Y Tags: Biochem J Source Type: research

DEK Terminates Diapause by Activation of Quiescent Cells in the Crustacean   Artemia.
DEK Terminates Diapause by Activation of Quiescent Cells in the Crustacean  Artemia. Biochem J. 2019 Jun 12;: Authors: Jia WH, Li AQ, Feng JY, Ding YF, Ye S, Yang JS, Yang WJ Abstract To cope with harsh environments the Artemia  shrimp produces gastrula embryos in diapause, a state of obligate dormancy, having cellular quiescence and suppressed metabolism. The mechanism behind these cellular events remains largely unknown. Here, we study the regulation of cell quiescence using diapause embryos of Artemia We found that Artemia  DEK ( Ar -DEK), a nuclear factor protein, was down-regulated...
Source: The Biochemical Journal - June 12, 2019 Category: Biochemistry Authors: Jia WH, Li AQ, Feng JY, Ding YF, Ye S, Yang JS, Yang WJ Tags: Biochem J Source Type: research

The glutathione degrading enzyme, Chac1, is required for calcium signaling in developing zebrafish: Redox as an upstream activator of calcium.
Abstract Calcium signaling is essential for embryonic development but the signals upstream of calcium are only partially understood. Here we investigate the role of the intracellular glutathione redox potential in calcium signaling using the Chac1 protein of zebrafish. A member of the Γ-glutamylcyclotransferase family of enzymes, the zebrafish Chac1 is a glutathione degrading enzyme that acts only on reduced glutathione.  The zebrafish chac1 expression was seen early in development, and in the latter stages, in the developing muscles, brain and heart. The chac1 knockdown was embryonic lethal, and the de...
Source: The Biochemical Journal - June 12, 2019 Category: Biochemistry Authors: Yadav S, Chawla B, Khursheed MA, Ramachandran R, Bachhawat AK Tags: Biochem J Source Type: research

AMP-activated protein kinase complexes containing the β2 regulatory subunit are upregulated during and contribute to adipogenesis.
This study therefore sought to determine the contribution of AMPKβ subunit isoforms to adipocyte biology, focussing on adipogenesis. AMPKβ2 was the principal AMPKβ isoform in 3T3-L1 adipocytes, isolated rodent adipocytes and human subcutaneous adipose tissue, as assessed by the contribution to total cellular AMPK activity. Downregulation of AMPKβ2 with siRNA inhibited lipid accumulation, cellular adiponectin levels and adiponectin secretion during 3T3-L1 adipogenesis, whereas downregulation of AMPKβ1 had no effect. Incubation of 3T3-L1 cells with MT47-100 selectively inhibited AMPK complexes contai...
Source: The Biochemical Journal - June 12, 2019 Category: Biochemistry Authors: Katwan OJ, Alghamdi F, Almabrouk TA, Mancini SJ, Kennedy S, Oakhill JS, Scott JW, Salt IP Tags: Biochem J Source Type: research

Chemical synthesis and characterization of a new quinazolinedione competitive antagonist for strigolactone receptors with an unexpected binding mode.
Abstract Strigolactones are multifunctional plant hormones regulating essential physiological processes affecting growth and development. In vascular plants, strigolactones are recognized by α/β hydrolase fold proteins from the D14/DAD2 family in the initial step of the signalling pathway. We have previously discovered that N -phenylanthranilic acid derivatives (e.g. tolfenamic acid) are potent antagonists of strigolactone receptors, prompting us to design quinazolinone and quinazolinedione derivatives (QADs and QADDs, respectively) as second-generation antagonists. Initial in silico docking studies sug...
Source: The Biochemical Journal - June 11, 2019 Category: Biochemistry Authors: Hamiaux C, Larsen L, Lee HW, Luo Z, Sharma P, Hawkins BC, Perry NB, Snowden KC Tags: Biochem J Source Type: research

Thioredoxin-like2/2-Cys peroxiredoxin redox cascade acts as oxidative activator of glucose-6-phosphate dehydrogenase in chloroplasts.
In this study, we report a novel protein-activation mechanism based on the TrxL2/2CP redox cascade. Glucose-6-phosphate dehydrogenase (G6PDH) catalyzes the first step of the oxidative pentose phosphate pathway (OPPP). Biochemical studies, including redox state determination and measurement of enzyme activity, suggested that the TrxL2/2CP pathway is involved in the oxidative activation of G6PDH. It is thus likely that the TrxL2/2CP redox cascade shifts chloroplast metabolism to night mode by playing a dual role, namely, downregulation of the Calvin-Benson cycle and upregulation of OPPP. G6PDH was also directly oxidized and ...
Source: The Biochemical Journal - June 6, 2019 Category: Biochemistry Authors: Yoshida K, Uchikoshi E, Hara S, Hisabori T Tags: Biochem J Source Type: research

Mechanism of nitrite-dependent NO synthesis by human sulfite oxidase.
Abstract In addition to nitric oxide (NO) synthases, molybdenum-dependent enzymes have been reported to reduce nitrite to produce NO. Here, we report the stoichiometric reduction of nitrite to NO by human sulfite oxidase, a mitochondrial intermembrane space enzyme primarily involved in cysteine catabolism. Kinetic and spectroscopic studies provide evidence for direct nitrite coordination at the molybdenum center followed by an inner shell electron transfer mechanism. In the presence of the physiological electron acceptor cytochrome c , we were able to close the catalytic cycle of sulfite-dependent nitrite reductio...
Source: The Biochemical Journal - June 5, 2019 Category: Biochemistry Authors: Bender D, Kaczmarek AT, Niks D, Hille R, Schwarz G Tags: Biochem J Source Type: research

The Histidine-rich Loop in the Extracellular Domain of ZIP4 Binds Zinc and Plays a Role in Zinc Transport.
Abstract The Zrt-/Irt-like protein (ZIP) family mediates zinc influx from extracellular space or intracellular vesicles/organelles, playing a central role in systemic and cellular zinc homeostasis. Out of the 14 family members encoded in human genome, ZIP4 is exclusively responsible for zinc uptake from dietary food and dysfunctional mutations of ZIP4 cause a lethal genetic disorder, Acrodermatitis Enteropathica (AE). About half of the missense AE-causing mutations occur within the large N-terminal extracellular domain (ECD), and our previous study has shown that ZIP4-ECD is crucial for optimal zinc uptake but the...
Source: The Biochemical Journal - June 4, 2019 Category: Biochemistry Authors: Zhang T, Kuliyev E, Sui D, Hu J Tags: Biochem J Source Type: research

The ChlD subunit links the motor and porphyrin binding subunits of magnesium chelatase.
Abstract Magnesium chelatase initiates chlorophyll biosynthesis, catalysing the MgATP2- dependent insertion of a Mg2+ ion into protoporphyin IX. The catalytic core of this large enzyme complex consists of three subunits: Bch/ChlI, Bch/ChlD and Bch/ChlH (in bacteriochlorophyll and chlorophyll producing species respectively). The D and I subunits are members of the AAA+ (ATPases associated with various cellular activities) superfamily of enzymes, and they form a complex that binds to H, the site of metal ion insertion. In order to investigate the physical coupling between ChlID and ChlH in vivo and in vitro , ChlD w...
Source: The Biochemical Journal - June 4, 2019 Category: Biochemistry Authors: Farmer DA, Brindley AA, Hitchcock A, Jackson PJ, Johnson B, Dickman MJ, Hunter CN, Reid JD, Adams NBP Tags: Biochem J Source Type: research

The β-hairpin region of cyanobacterial F1-ATPase γ subunit plays a regulatory role in the enzyme activity.
The β-hairpin region of cyanobacterial F1-ATPase γ subunit plays a regulatory role in the enzyme activity. Biochem J. 2019 Jun 04;: Authors: Akiyama K, Kondo K, Inabe K, Murakami S, Wakabayashi KI, Hisabori T Abstract The γ subunit of cyanobacterial and chloroplast ATP synthase, the rotary shaft of F1-ATPase, equips a specific insertion region that is only observed in photosynthetic organisms. This region plays a physiologically pivotal role in enzyme regulation, such as in ADP inhibition and redox response. Recently solved crystal structures of the γ subunit of F1-ATPase from p...
Source: The Biochemical Journal - June 4, 2019 Category: Biochemistry Authors: Akiyama K, Kondo K, Inabe K, Murakami S, Wakabayashi KI, Hisabori T Tags: Biochem J Source Type: research

The search for candidate genes associated with natural variation of grain Zn accumulation in barley.
s S Abstract Combating Hidden Hunger through molecular breeding of nutritionally enriched crops requires a better understanding of micronutrient accumulation. We studied natural variation in grain micronutrient accumulation in barley ( Hordeum vulgare L.) and searched for candidate genes by assessing marker trait associations (MTAs) and by analyzing transcriptional differences between low and high zinc (Zn) accumulating cultivars during grain filling. A collection of 180 barley lines was grown in three different environments. Our results show a pronounced variation in Zn accumulation, which was under strong genoty...
Source: The Biochemical Journal - June 4, 2019 Category: Biochemistry Authors: Detterbeck A, Nagel M, Rensch S, Weber M, Börner A, Persson DP, Schjoerring JK, Christov V, Clemens S Tags: Biochem J Source Type: research

Retraction: Bax channel triplet: co-operativity and voltage gating.
PMID: 31152072 [PubMed - in process] (Source: The Biochemical Journal)
Source: The Biochemical Journal - May 31, 2019 Category: Biochemistry Authors: Lin SH, Cherian N, Wu B, Phee H, Cho C, Colombini M Tags: Biochem J Source Type: research

Toxins for decoding interface selectivity in nicotinic acetylcholine receptors.
Abstract 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 ...
Source: The Biochemical Journal - May 28, 2019 Category: Biochemistry Authors: Kini RM Tags: Biochem J Source Type: research

Specific Keratinase Derived Designer Peptides Potently Inhibit A β Aggregation Resulting in Reduced Neuronal Toxicity and Apoptosis.
Specific Keratinase Derived Designer Peptides Potently Inhibit A β Aggregation Resulting in Reduced Neuronal Toxicity and Apoptosis. Biochem J. 2019 May 28;: Authors: Rajput R, G L B, Srivastava A, Wahi D, Shrivastava N, Kundu B, Grover A Abstract Compelling evidences implicate self-assembly of amyloid- β (A β 1-42) peptides into soluble oligomers and fibrils as a major underlying event in Alzheimer's disease (AD) pathogenesis. Herein, we employed amyloid-degrading keratinase (kerA) enzyme as a key A β 1-42-binding scaffold to identify five keratinase-guided peptides (KgPs) capable...
Source: The Biochemical Journal - May 28, 2019 Category: Biochemistry Authors: Rajput R, G L B, Srivastava A, Wahi D, Shrivastava N, Kundu B, Grover A Tags: Biochem J Source Type: research

Histone demethylase KDM6B regulates human podocyte differentiation in vitro.
In this study, we firstly examined the expression pattern of histone demethylase KDM6B at different times of cultured human podocytes in vitro. We found that the expressions of KDM6B and podocyte differentiation markers WT1 and Nephrin are increased in podocyte differentiation process. In cultured podocytes, KDM6B knockdown with siRNA impaired podocyte differentiation and led to expression down-regulation of WT1 and Nephrin. The treatment of podocytes with GSK-J4, a specific KDM6B inhibitor, can also obtain similar results. Overexpression of WT1  can rescue differentiated&n...
Source: The Biochemical Journal - May 28, 2019 Category: Biochemistry Authors: Guo Y, Xiong Z, Guo X Tags: Biochem J Source Type: research

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: The Biochemical Journal - May 28, 2019 Category: Biochemistry Authors: Manning JR, Thapa D, Zhang M, Stoner MW, Traba J, Corey C, Shiva S, Sack MN, Scott I Tags: Biochem J 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 ...
Source: The Biochemical Journal - May 22, 2019 Category: Biochemistry Authors: Chagot ME, Dos Santos Morais R, Dermouche S, Lefebvre D, Manival X, Chipot C, Dehez F, Quinternet M Tags: Biochem J Source Type: research

PP2C phosphatase Pic1 negatively regulates phosphorylation status of Pti1b kinase, a regulator of flagellin-triggered immunity in tomato.
Abstract 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. To investigate these issues, we used mass spectrometry to search for...
Source: The Biochemical Journal - May 16, 2019 Category: Biochemistry Authors: Giska F, Martin GB Tags: Biochem J Source Type: research

Plastidic glucose-6-phosphate dehydrogenase is regulated to maintain activity in the light.
Abstract 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. We found that the half saturation concentration of G6PDH isoform 1 is increased under reducing co...
Source: The Biochemical Journal - May 15, 2019 Category: Biochemistry Authors: Preiser AL, Fisher N, Banerjee A, Sharkey TD Tags: Biochem J Source Type: research

Tissue-Specific Characterization of Mitochondrial Branched-Chain Keto Acid Oxidation Using a Multiplexed Assay Platform.
Abstract 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 utiliz...
Source: The Biochemical Journal - May 15, 2019 Category: Biochemistry Authors: Goldberg EJ, Buddo KA, McLaughlin KL, Fernandez RF, Pereyra AS, Psaltis CE, Lin CT, Hagen JT, Boykov IN, Nguyen TK, Gowdy KM, Ellis JM, Neufer PD, McClung JM, Fisher-Wellman KH Tags: Biochem J Source Type: research

Zinc induces iron uptake and DMT1 expression in Caco-2 cells via a PI3K/IRP2 dependent mechanism.
Abstract 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. We found that zinc induces DMT1 prote...
Source: The Biochemical Journal - May 15, 2019 Category: Biochemistry Authors: Kondaiah P, Aslam MF, Mashurabad P, Sharp PA, Pullakhandam R Tags: Biochem J Source Type: research

Biochemical and structural investigation of taurine:2-oxoglutarate aminotransferase from Bifidobacterium kashiwanohense.
Abstract 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 2.7 Å resolution. The enzyme...
Source: The Biochemical Journal - May 14, 2019 Category: Biochemistry Authors: Li M, Wei Y, Yin J, Lin L, Zhou Y, Hua G, Cao P, Ang EL, Zhao H, Yuchi Z, Zhang Y Tags: Biochem J Source Type: research

Characterization of soluble CD39 (SolCD39/NTPDase1) from Piggy-Bac nonviral system as a tool to control the nucleotides level.
nk MR Abstract 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. NTPDase1 (also called apyrase, ecto-ATPase, CD39)is one of the...
Source: The Biochemical Journal - May 13, 2019 Category: Biochemistry Authors: Beckenkamp LR, Iser IC, Onzi GR, Fontoura DM, Bertoni APS, Sévigny J, Lenz G, Wink MR Tags: Biochem J Source Type: research

Tubulin heterogeneity regulates functions and dynamics of microtubules and plays a role in the development of drug resistance in cancer.
Abstract 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 curre...
Source: The Biochemical Journal - May 12, 2019 Category: Biochemistry Authors: Prassanawar SS, Panda D Tags: Biochem J 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 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, ...
Source: The Biochemical Journal - May 9, 2019 Category: Biochemistry Authors: Sturrock ED, Lubbe L, Cozier GE, Schwager SLU, Arowolo AT, Arendse LB, Belcher ER, Acharya KR Tags: Biochem J Source Type: research

A non-catalytic function of carbonic anhydrase IX contributes to the glycolytic phenotype and pH regulation in human breast cancer cells.
Abstract 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 ext...
Source: The Biochemical Journal - May 9, 2019 Category: Biochemistry Authors: Mboge MY, Chen Z, Khokhar D, Wolff A, Ai L, Heldermon CD, Bozdag M, Carta F, Supuran CT, Brown KD, McKenna R, Frost CJ, Frost SC Tags: Biochem J Source Type: research

Screening substrate binding positions by rolling circle amplification suggesting a binding model of Nt.BstNBI.
Abstract 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 lo...
Source: The Biochemical Journal - May 7, 2019 Category: Biochemistry Authors: Wei H, Tang S, Duan X, Guan Y, Zhao G Tags: Biochem J Source Type: research

Designing active RNF4 monomers by introducing a tryptophan: Avidity towards E2~Ub conjugates dictates the activity of ubiquitin RING E3 ligases.
Abstract 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. Monomeric RINGs possess the tryptophan while all well-characterized dimeric RIN...
Source: The Biochemical Journal - May 2, 2019 Category: Biochemistry Authors: Sarkar S, Behera AP, Borar P, Banka PA, Datta AB Tags: Biochem J 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 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 using ...
Source: The Biochemical Journal - April 29, 2019 Category: Biochemistry Authors: Wilson S, Ruban AV Tags: Biochem J Source Type: research

Discerning the Mechanism of Action of HtrA4: a Serine Protease Implicated in the Cell Death Pathway.
Abstract 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 functio...
Source: The Biochemical Journal - April 29, 2019 Category: Biochemistry Authors: Kummari R, Dutta S, Chaganti LK, Bose K Tags: Biochem J Source Type: research

Glycolic acid Attenuates UVB-induced Aquaporin-3, Matrix Metalloproteinase-9 Expression, and Collagen Degradation in Keratinocytes and Mouse Skin.
Abstract 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. To investigate the potential of GA to regulate the expression of MMPs and collagen, GA was t...
Source: The Biochemical Journal - April 29, 2019 Category: Biochemistry Authors: Tang SC, Tang LC, Liu CH, Liao PY, Lai JC, Yang JH Tags: Biochem J 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. Further, dynamic light scattering, atomic force microscopy, and ...
Source: The Biochemical Journal - April 29, 2019 Category: Biochemistry Authors: Rane JS, Kumari A, Panda D Tags: Biochem J 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 naïve pluripotency maintenance and stem cell fate decision. PMID: 31036718 [PubMed - as supplied by publisher] (Source: The Biochemical Journal)
Source: The Biochemical Journal - April 29, 2019 Category: Biochemistry Authors: Xin Y, Wang Y, Zhong L, Shi B, Liang H, Han J Tags: Biochem J Source Type: research

Multi-functional regulator MapZ controls both positioning and timing of FtsZ polymerization.
Abstract 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. Using nuclear magnetic resonance titration experiments, we clearly ...
Source: The Biochemical Journal - April 29, 2019 Category: Biochemistry Authors: Feng Z, Zhang J, Xu D, Jiang YL, Zhou CZ, Chen Y Tags: Biochem J Source Type: research