AMP-activated protein kinase regulates alternative pre-mRNA splicing by phosphorylation of SRSF1.
Abstract AMP-activated protein kinase (AMPK) regulates cellular energy homeostasis by inhibiting anabolic processes and activating catabolic processes. Recent studies have demonstrated that metformin, which is an AMPK activator, modifies alternative precursor mRNA (pre-mRNA)splicing. However, no direct substrate of AMPK for alternative pre-mRNA splicing has been reported. In the present study, we identified the splicing factor serine/arginine-rich splicing factor 1 (SRSF1) as a novel AMPK substrate. AMPK directly phosphorylated SRSF1 at Ser133 in an RNA recognition motif. Ser133 phosphorylation suppressed the inte...
Source: The Biochemical Journal - May 26, 2020 Category: Biochemistry Authors: Matsumoto E, Akiyama K, Saito T, Matsumoto Y, Kobayashi KI, Inoue J, Yamamoto Y, Suzuki T Tags: Biochem J Source Type: research

Bioinformatic and experimental evidence for suicidal and catalytic plant THI4s.
, Hanson AD Abstract Like fungi and some prokaryotes, plants use a thiazole synthase (THI4) to make the thiazole precursor of thiamin. Fungal THI4s are suicide enzymes that destroy an essential active-site Cys residue to obtain the sulfur atom needed for thiazole formation. In contrast, certain prokaryotic THI4s have no active-site Cys, use sulfide as sulfur donor, and are truly catalytic. The presence of a conserved active-site Cys in plant THI4s and other indirect evidence implies that they are suicidal. To confirm this, we complemented the Arabidopsis tz-1 mutant, which lacks THI4 activity, with a His-tagged Ar...
Source: The Biochemical Journal - May 22, 2020 Category: Biochemistry Authors: Joshi J, Beaudoin GAW, Patterson JA, García-García JD, Belisle CE, Chang LY, Li L, Duncan O, Millar AH, Hanson AD Tags: Biochem J Source Type: research

Methylation-mediated downregulation of microRNA-497-195 cluster confers osteogenic differentiation in ossification of the posterior longitudinal ligament of the spine via ADORA2A.
Abstract Aberrant expression of microRNAs (miRNAs) has been associated with spinal ossification of the posterior longitudinal ligament (OPLL). Our initial bioinformatic analysis identified differentially expressed ADORA2A in OPLL and its regulatory miRNAs miR-497 and miR-195. Hence, this study was conducted to clarify the functional relevance of miR-497-195 cluster in OPLL, which may implicate in Adenosine A2A (ADORA2A). PLL tissues were collected from OPLL and non-OPLL patients, followed by quantification of miR-497, miR-195 and ADORA2A expression. The expression of miR-497, miR-195 and/or ADORA2A was altered in ...
Source: The Biochemical Journal - May 20, 2020 Category: Biochemistry Authors: Jiang A, Wang N, Jiang Y, Yan X, Chen G, Chi H, Kong P, Ren H, Xia S, Ji Y, Yan J Tags: Biochem J Source Type: research

Rationally Designed Peptide-Based Inhibitor of A β42 Fibril Formation and Toxicity: A Potential Therapeutic Strategy for Alzheimer's Disease.
In this study, a hexapeptide containing a self-recognition component unique to Aβ42 was designed to mimic the β-strand hydrophobic core region of the Aβ peptide. The peptide is comprised exclusively of D-amino acids to enhance specificity towards Aβ42, in conjunction with a C-terminal disruption element to block the recruitment of Aβ42 monomers on to fibrils. The peptide was rationally designed to exploit the synergy between the recognition and disruption components, and incorporates features such as hydrophobicity, β-sheet propensity, and charge, that all play a critical role in the aggregati...
Source: The Biochemical Journal - May 19, 2020 Category: Biochemistry Authors: Horsley JR, Jovcevski B, Wegener KL, Yu J, Pukala TL, Abell A Tags: Biochem J Source Type: research

Starting at the beginning: endoplasmic reticulum proteostasis and systemic amyloid disease.
Abstract Systemic amyloid diseases are characterized by the deposition of an amyloidogenic protein as toxic oligomers and amyloid fibrils on tissues distal from the site of protein synthesis. Traditionally, these diseases have been viewed as disorders of peripheral target tissues where aggregates are deposited, and toxicity is observed. However, recent evidence highlights an important role for endoplasmic reticulum (ER) proteostasis pathways within tissues synthesizing and secreting amyloidogenic proteins, such as the liver, in the pathogenesis of these disorders. Here, we describe the pathologic implications of E...
Source: The Biochemical Journal - May 15, 2020 Category: Biochemistry Authors: Romine IC, Wiseman RL Tags: Biochem J Source Type: research

Development of novel anti-malarial from structurally diverse library of molecules, targeting plant-like CDPK1, a multistage growth regulator of P. falciparum.
Abstract Upon Plasmodium falciparum merozoites exposure to low [K+] environment in blood plasma, there is escalation of cytosolic [Ca2+] which activates Ca2+-Dependent Protein Kinase 1 (CDPK1), a signaling hub of intra-erythrocytic proliferative stages of parasite. Given its high abundance and multidimensional attributes in parasite life-cycle, this is a lucrative target for desiging antimalarials. Towards this, we have virtually screened MyriaScreenII diversity collection of 10,000 drug-like molecules, which resulted in 18 compounds complementing ATP-binding pocket of CDPK1. In vitro screening for toxicity in mam...
Source: The Biochemical Journal - May 13, 2020 Category: Biochemistry Authors: Jain R, Gupta S, Munde M, Pati S, Singh S Tags: Biochem J Source Type: research

Computationally Designed Synthetic Peptides for Transporter Proteins Imparts Allostericity in Miltefosine Resistant Leishmania major.
Abstract Emergence of drug resistance is major concern for combating against Cutaneous Leishmaniasis, a neglected tropical disease affecting 98 countries including India. Miltefosine is the only oral drug available for the disease and Miltefosine transporter proteins play pivotal role in the emergence of drug resistant Leishmania major. The cause of resistance is less accumulation of drug inside the parasite either by less uptake of drug due to decrease in the activity of P4ATPase-CDC50 complex or by increased efflux of the drug by P-glycoprotein (P-gp, an ABC transporter). In this paper, we are trying to alloster...
Source: The Biochemical Journal - May 11, 2020 Category: Biochemistry Authors: Kabra R, Ingale P, Singh S Tags: Biochem J Source Type: research

A Steady-State Approach for inhibition of Heterogeneous Enzyme reactions.
sth P Abstract Kinetic theory of enzymes that modify insoluble substrates is still underdeveloped, despite the prevalence of this type of reaction both in vivo and industrial applications. Here, we present a steady-state kinetic approach to investigate inhibition occurring at the solid-liquid interface. We propose to conduct experiments under enzyme excess (E0>>S0), i.e. the opposite limit compared to the conventional Michaelis-Menten framework. This inverse condition is practical for insoluble substrates and elucidates how the inhibitor reduces enzyme activity through binding to the substrate. We claim that...
Source: The Biochemical Journal - May 11, 2020 Category: Biochemistry Authors: Kari J, Schiano-di-Cola C, Hansen SF, Badino SF, Sørensen TH, Cavaleiro AM, Borch K, Westh P Tags: Biochem J Source Type: research

Translational regulation of Chk1 expression by eIF3a via interaction with the RNA-binding protein HuR.
In this study, we show that eIF3a up-regulates translation of Chk1 but not Chk2 mRNA by interacting with HuR, which binds directly to the 3'-UTR of Chk1 mRNA. The interaction between eIF3a and HuR occurs at the 10-amino-acid repeat domain of eIF3a and the RNA recognition motif domain of HuR. This interaction may effectively circularize Chk1 mRNA to form an end-to-end complex that has recently been suggested to accelerate mRNA translation. Together with previous findings, we conclude that eIF3a may regulate mRNA translation by directly binding to the 5'-UTR to suppress or interaction with RNA-binding proteins at 3'-UTRs to ...
Source: The Biochemical Journal - May 11, 2020 Category: Biochemistry Authors: Dong Z, Liu J, Zhang JT Tags: Biochem J Source Type: research

Runx1 up-regulates chondrocyte to osteoblast lineage commitment and promotes bone formation by enhancing both chondrogenesis and osteogenesis.
Abstract One of the fundamental questions in bone biology is where osteoblasts originate and how osteoblast differentiation is regulated. The mechanism underlying which factors regulate chondrocyte to osteoblast lineage commitment remains unknown. Our data showed that Runt-related transcription factor 1 (Runx1) is expressed at different stages of both chondrocyte and osteoblast differentiation. Runx1 chondrocyte-specific knockout (Runx1f/fCol2α1-cre) mice exhibited impaired cartilage formation, decreased bone density, and an osteoporotic phenotype. The expressions of chondrocyte differentiation regulati...
Source: The Biochemical Journal - May 11, 2020 Category: Biochemistry Authors: Tang C, Chen W, Luo Y, Wu J, Zhang Y, McVicar A, McConnell M, Liu Y, Zhou HD, Li YP Tags: Biochem J Source Type: research

Synergism between SLC6A14 blockade and gemcitabine in pancreactic cancer: A 1H-NMR-based metabolomic study in pancreatic cancer cells.
Abstract Gemcitabine is the first-line chemotherapy for pancreatic cancer. To overcome the often-acquired gemcitabine resistance, other drugs are used in combination with gemcitabine. It is well-known that cancer cells reprogram cellular metabolism, coupled with the upregulation of selective nutrient transporters to feed into the altered metabolic pathways. Our previous studies have demonstrated that the amino acid transporter SLC6A14 is markedly upregulated in pancreatic cancer and that it is a viable therapeutic target. α-Methyltryptophan (α-MT) is a blocker of SLC6A14 and is effective against pancre...
Source: The Biochemical Journal - May 7, 2020 Category: Biochemistry Authors: Cai A, Zheng H, Chen Z, Lin X, Li C, Yao Q, Bhutia YD, Ganapathy V, Chen R, Kou L Tags: Biochem J Source Type: research

Expanding our understanding of the role polyprotein conformation plays in the coronavirus life cycle.
Abstract Coronavirus are the causative agents in many globally concerning respiratory disease outbreaks such as severe acute respiratory syndrome (SARS), Middle East respiratory syndrome (MERS) and coronavirus disease-2019 (COVID-19). It is therefore important that we improve our understanding of how the molecular components of the virus facilitate the viral life cycle. These details will allow for the design of effective interventions. Krichel and coauthors in their article in the Biochemical Journal provide molecular details of how the viral polyprotein (nsp7-10) produced from the positive single stranded RNA ge...
Source: The Biochemical Journal - April 30, 2020 Category: Biochemistry Authors: Gildenhuys S Tags: Biochem J Source Type: research

O-glycan recognition and function in mice and human cancers.
Abstract Protein glycosylation represents a nearly ubiquitous post-translational modification, and altered glycosylation can result in clinically significant pathological consequences. Here we focus on O-glycosylation in tumor cells of mice and humans. O-glycans are those linked to serine and threonine (Ser/Thr) residues via N-acetylgalactosamine (GalNAc), which are oligosaccharides that occur widely in glycoproteins, such as those expressed on the surfaces and in secretions of all cell types. The structure and expression of O-glycans are dependent on the cell type and disease state of the cells. There is a great ...
Source: The Biochemical Journal - April 30, 2020 Category: Biochemistry Authors: Cervoni GE, Cheng JJ, Stackhouse KA, Heimburg-Molinaro J, Cummings RD Tags: Biochem J Source Type: research

Cell Atlas technologies and insights into tissue architecture.
Abstract Since Robert Hooke first described the existence of 'cells' in 1665, scientists have sought to identify and further characterise these fundamental units of life. While our understanding of cell location, morphology and function has expanded greatly; our understanding of cell types and states at the molecular level, and how these function within tissue architecture, is still limited. A greater understanding of our cells could revolutionise basic biology and medicine. Atlasing initiatives like the Human Cell Atlas aim to identify all cell types at the molecular level, including their physical locations, and...
Source: The Biochemical Journal - April 29, 2020 Category: Biochemistry Authors: Wilbrey-Clark A, Roberts K, Teichmann SA Tags: Biochem J Source Type: research

Cell-penetrating peptides: two faces of the same coin.
Abstract Cell-penetrating peptides (CPPs) are short peptides able to cross the cellular membranes without any interaction with specific receptors. Thanks to their ability to transport various cargo inside the cells are emerged as powerful therapeutic agents alternative to small molecules. In recent years, numerous preclinical studies provided promising results for the treatment of various human diseases. Several CPP-conjugated compounds are under clinical trials. PMID: 32322896 [PubMed - in process] (Source: The Biochemical Journal)
Source: The Biochemical Journal - April 25, 2020 Category: Biochemistry Authors: Pierantoni GM, Paladino S Tags: Biochem J Source Type: research

New structural insights into bacterial sulfoacetaldehyde and taurine metabolism.
Abstract In last year's issue 4 of Biochemical Journal, Zhou et al. (Biochem J. 476, 733-746) kinetically and structurally characterized the reductase IsfD from Klebsiella oxytoca that catalyzes the reversible reduction in sulfoacetaldehyde to the corresponding alcohol isethionate. This is a key step in detoxification of the carbonyl intermediate formed in bacterial nitrogen assimilation from the α-aminoalkanesulfonic acid taurine. In 2019, the work on sulfoacetaldehyde reductase IsfD was the exciting start to a quite remarkable series of articles dealing with structural elucidation of proteins involved in t...
Source: The Biochemical Journal - April 25, 2020 Category: Biochemistry Authors: Rohwerder T Tags: Biochem J Source Type: research

Ubiquitination-activating enzymes UBE1 and UBA6 regulate ubiquitination and expression of cardiac sodium channel Nav1.5.
Abstract Cardiac sodium channel Nav1.5 is associated with cardiac arrhythmias and heart failure. Protein ubiquitination is catalyzed by an E1-E2-E3 cascade of enzymes. However, the E1 enzyme catalyzing Nav1.5 ubiquitination is unknown. Here, we show that UBE1 and UBA6 are two E1 enzymes regulating Nav1.5 ubiquitination and expression. Western blot analysis and patch-clamping recordings showed that overexpression of UBE1 or UBA6 increased ubiquitination of Nav1.5 and significantly reduced Nav1.5 expression and sodium current density, and knockdown of UBE1 or UBA6 expression significantly increased Nav1.5 expression...
Source: The Biochemical Journal - April 21, 2020 Category: Biochemistry Authors: Hu Y, Bai X, Zhang C, Chakrabarti S, Tang B, Xiong H, Wang Z, Yu G, Xu C, Chen Q, Wang QK Tags: Biochem J Source Type: research

Trypanosoma cruzi synthesizes proline via a Δ1-pyrroline-5-carboxylate reductase whose activity is fine-tuned by NADPH cytosolic pools.
Trypanosoma cruzi synthesizes proline via a Δ1-pyrroline-5-carboxylate reductase whose activity is fine-tuned by NADPH cytosolic pools. Biochem J. 2020 Apr 21;: Authors: Marchese LM, Olavarria KM, Mantilla BS, Avila CC, Souza ROO, Damasceno FS, Elias MC, Silber AM Abstract In Trypanosoma cruzi, the etiological agent of Chagas disease, the amino acid proline participates in processes related to T. cruzi survival and infection, such as ATP production, cell differentiation, host-cell invasion, and in protection against osmotic, nutritional, and thermal stresses and oxidative imbalance. However, lit...
Source: The Biochemical Journal - April 21, 2020 Category: Biochemistry Authors: Marchese LM, Olavarria KM, Mantilla BS, Avila CC, Souza ROO, Damasceno FS, Elias MC, Silber AM Tags: Biochem J Source Type: research

Phosphatase-defective DevS sensor kinase mutants permit constitutive expression of DevR-regulated dormancy genes in Mycobacterium tuberculosis.
Abstract The DevR-DevS/DosR-DosS two-component system of Mycobacterium tuberculosis, that comprises of DevS sensor kinase and DevR response regulator, is essential for bacterial adaptation to hypoxia by inducing dormancy regulon expression. The dominant phosphatase activity of DevS under aerobic conditions enables tight negative control, whereas its kinase function activates DevR under hypoxia to induce the dormancy regulon. A net balance in these opposing kinase and phosphatase activities of DevS calibrates the response output of DevR. To gain mechanistic insights into the kinase-phosphatase balance of DevS, we g...
Source: The Biochemical Journal - April 20, 2020 Category: Biochemistry Authors: Kumari P, Kumar S, Kaur K, Gupta UD, Bhagyawant SS, Tyagi JS Tags: Biochem J Source Type: research

Thioproline formation as a driver of formaldehyde toxicity in Escherichia coli.
Abstract Formaldehyde (HCHO) is a reactive carbonyl compound that formylates and cross-links proteins, DNA, and small molecules. It is of specific concern as a toxic intermediate in the design of engineered pathways involving methanol oxidation or formate reduction. The interest in engineering these pathways is not, however, matched by engineering-relevant information on precisely why HCHO is toxic or on what damage-control mechanisms cells deploy to manage HCHO toxicity. The only well-defined mechanism for managing HCHO toxicity is formaldehyde dehydrogenase-mediated oxidation to formate, which is counterproducti...
Source: The Biochemical Journal - April 17, 2020 Category: Biochemistry Authors: Patterson JA, He H, Folz JS, Li Q, Wilson MA, Fiehn O, Bruner SD, Bar-Even A, Hanson AD Tags: Biochem J Source Type: research

Amyloid β chaperone - lipocalin-type prostaglandin D synthase acts as a peroxidase in the presence of heme.
Amyloid β chaperone - lipocalin-type prostaglandin D synthase acts as a peroxidase in the presence of heme. Biochem J. 2020 Apr 17;477(7):1227-1240 Authors: Phillips M, Kannaian B, Yang JNT, Kather R, Yuguang M, Harmer JR, Pervushin K Abstract The extracellular transporter, lipocalin-type prostaglandin D synthase (L-PGDS) binds to heme and heme metabolites with high affinity. It has been reported that L-PGDS protects neuronal cells against apoptosis induced by exposure to hydrogen peroxide. Our study demonstrates that when human WT L-PGDS is in complex with heme, it exhibits a strong peroxidase a...
Source: The Biochemical Journal - April 10, 2020 Category: Biochemistry Authors: Phillips M, Kannaian B, Yang JNT, Kather R, Yuguang M, Harmer JR, Pervushin K Tags: Biochem J Source Type: research

Reading the phosphorylation code: binding of the 14-3-3 protein to multivalent client phosphoproteins.
This study addresses a long-standing question in the 14-3-3 biology, unearthing a range of important details that are relevant for understanding binding mechanisms of other polyvalent proteins. PMID: 32271882 [PubMed - as supplied by publisher] (Source: The Biochemical Journal)
Source: The Biochemical Journal - April 10, 2020 Category: Biochemistry Authors: Sluchanko NN Tags: Biochem J Source Type: research

Functional characterization of human brown adipose tissue metabolism.
Abstract Brown adipose tissue (BAT) has long been described according to its histological features as a multilocular, lipid-containing tissue, light brown in color, that is also responsive to the cold and found especially in hibernating mammals and human infants. Its presence in both hibernators and human infants, combined with its function as a heat-generating organ, raised many questions about its role in humans. Early characterizations of the tissue in humans focused on its progressive atrophy with age and its apparent importance for cold-exposed workers. However, the use of positron emission tomography (PET) w...
Source: The Biochemical Journal - April 10, 2020 Category: Biochemistry Authors: Richard MA, Pallubinsky H, Blondin DP Tags: Biochem J Source Type: research

Inorganic polyphosphate is produced and hydrolysed in F0F1-ATP synthase of mammalian mitochondria.
Abstract Inorganic polyphosphate (polyP) is a polymer present in all living organisms. Although polyP is found to be involved in a variety of functions in cells of higher organisms, the enzyme responsible for polyP production and consumption has not yet been identified. Here we studied the effect of polyP on mitochondrial respiration, oxidative phosphorylation and activity of F0F1-ATPsynthase. We have found that polyP activates mitochondrial respiration which does not coupled with ATP production (V2) but inhibits ADP dependent respiration (V3). Moreover, PolyP can stimulate F0F1-ATPase activity in the presence of ...
Source: The Biochemical Journal - April 9, 2020 Category: Biochemistry Authors: Bayev AY, Angelova PR, Abramov AY Tags: Biochem J Source Type: research

Structure of a tRNA-specific deaminase with compromised deamination activity.
Abstract Nucleotide 34 in tRNA is extensively modified to ensure translational fidelity and efficacy in cells. The deamination of adenosine at this site catalyzed by the enzyme TadA gives rise to inosine (I), which serves as a typical example of the wobble hypothesis due to its diverse basepairing capability. However, recent studies have shown that tRNAArgACG in Mycoplasma capricolum contains unmodified adenosine, in order to decode the CGG codon. The structural basis behind the poorly performing enzyme M. capricolum TadA (named McTadA) is largely unclear. Here we present the structures of the WT and a mutant form...
Source: The Biochemical Journal - April 9, 2020 Category: Biochemistry Authors: Liu H, Wu S, Ran D, Xie W Tags: Biochem J Source Type: research

A local α-helix drives structural evolution of streptococcal M-protein affinity for host human plasminogen.
A local α-helix drives structural evolution of streptococcal M-protein affinity for host human plasminogen. Biochem J. 2020 Apr 09;: Authors: Qiu C, Yuan Y, Lee SW, Ploplis VA, Castellino FJ Abstract Plasminogen-binding group A streptococcal M-protein (PAM) is a signature surface virulence factor of specific strains of Group A Streptococcuspyogenes (GAS) and is an important tight binding protein for human plasminogen (hPg).  After activation of PAM-bound hPg to the protease, plasmin (hPm), GAS cells develop invasive surfaces that are critical for their pathogenicity.  PAMs are helical ...
Source: The Biochemical Journal - April 9, 2020 Category: Biochemistry Authors: Qiu C, Yuan Y, Lee SW, Ploplis VA, Castellino FJ Tags: Biochem J Source Type: research

PGR5 is required for efficient Q cycle in the cytochrome b6f complex during cyclic electron flow.
r M Abstract Proton Gradient Regulation 5 (PGR5) is involved in the control of photosynthetic electron transfer, but its mechanistic role is not yet clear. Several models have been proposed to explain phenotypes such as a diminished steady state proton motive force (pmf) and increased photodamage of photosystem I (PSI). Playing a regulatory role in cyclic electron flow (CEF) around PSI, PGR5 contributes indirectly to PSI protection by enhancing photosynthetic control, which is a pH-dependent downregulation of electron transfer at the cytochrome b6f complex (b6f). Here, we re-evaluated the role of PGR5 in the green...
Source: The Biochemical Journal - April 8, 2020 Category: Biochemistry Authors: Buchert F, Mosebach L, Gäbelein P, Hippler M Tags: Biochem J Source Type: research

Silencing of lncRNA 6030408B16RIK prevents ultrafiltration failure in peritoneal dialysis via microRNA-326-3p-mediated WISP2 downregulation.
Abstract Continuous exposure to peritoneal dialysis (PD) fluid results in peritoneal fibrosis and ultimately causes ultrafiltration failure. Noncoding RNAs, including long noncoding RNAs (lncRNAs) and microRNAs (miRNAs), have been reported to participate in ultrafiltration failure in PD. Therefore, our study aimed to investigate the mechanism of lncRNA 6030408B16RIK in association with miR-326-3p in ultrafiltration failure in PD. Peritoneal tissues were collected from uremic patients with or without PD. A uremic rat model with PD was first established by 5/6 nephrectomy. The relationship between lncRNA 6030408B16R...
Source: The Biochemical Journal - April 7, 2020 Category: Biochemistry Authors: Wang Z, Zhou Z, Ji W, Sun L, Man Y, Wang J, Zhang H Tags: Biochem J Source Type: research

Osmotic pressure effects identify dehydration upon cytochrome c - cytochrome c oxidase complex formation contributing to a specific electron pathway formation.
Abstract In the electron transfer (ET) reaction from cytochrome c (Cyt c) to cytochrome c oxidase (CcO), we determined the number and sites of the hydration water released from the protein surface upon formation of the ET complex by evaluating the osmotic pressure dependence of kinetics for the ET from Cyt c to CcO.  We identified that approximately 20 water molecules were dehydrated in complex formation under turnover conditions, and systematic Cyt c mutations in the interaction site for CcO revealed that nearly half of the released hydration water during the complexation were located around Ile81, one of th...
Source: The Biochemical Journal - April 6, 2020 Category: Biochemistry Authors: Sato W, Hitaoka S, Uchida T, Shinzawa-Itoh K, Yoshizawa K, Yoshikawa S, Ishimori K Tags: Biochem J Source Type: research

Glut1 expression is increased by p53 reduction to switch metabolism to glycolysis during osteoblast differentiation.
Abstract The glycolytic system is selected for ATP synthesis not only in tumor cells but also in differentiated cells. Differentiated osteoblasts also switch dominant metabolic pathway to aerobic glycolysis. We found that primary osteoblasts increased expressions of glycolysis-related enzymes such as Glut1, hexokinase 1 and 2, lactate dehydrogenase A and pyruvate kinase M2 during their differentiation. Osteoblast differentiation decreased expression of tumor suppressor p53, which negatively regulates Glut1 expression, and enhanced phosphorylation of AKT, which is regulated by phosphoinositol-3 kinase (PI3K). An in...
Source: The Biochemical Journal - April 3, 2020 Category: Biochemistry Authors: Ohnishi T, Kusuyama J, Bandow K, Matsuguchi T Tags: Biochem J Source Type: research

Differential Effects of "Resurrecting" Csp Pseudoproteases during Clostridioides difficile Spore Germination.
Differential Effects of "Resurrecting" Csp Pseudoproteases during Clostridioides difficile Spore Germination. Biochem J. 2020 Apr 03;: Authors: Donnelly ML, Forster ER, Rohlfing AE, Shen A Abstract Clostridioides difficileis a spore-forming bacterial pathogen that is the leading cause of hospital-acquired gastroenteritis. C. difficileinfections begin when its spore form germinates in the gut upon sensing bile acids. These germinants induce a proteolytic signaling cascade controlled by three members of the subtilisin-like serine protease family, CspA, CspB, and CspC. Notably, even though CspC...
Source: The Biochemical Journal - April 3, 2020 Category: Biochemistry Authors: Donnelly ML, Forster ER, Rohlfing AE, Shen A Tags: Biochem J Source Type: research

Nek7 conformational flexibility and inhibitor binding probed through protein engineering of the R-spine.
Abstract Nek7 is a serine/threonine protein kinase required for proper spindle formation and cytokinesis. Elevated Nek7 levels have been observed in several cancers, and inhibition of Nek7 might provide a route to the development of cancer therapeutics. To date no selective and potent Nek7 inhibitors have been identified. Nek7 crystal structures exhibit an improperly formed Regulatory-spine (R-spine), characteristic of an inactive kinase. We reasoned that the preference of Nek7 to crystallize in this inactive conformation might hinder attempts to capture Nek7 in complex with Type I inhibitors. Here we have introdu...
Source: The Biochemical Journal - April 3, 2020 Category: Biochemistry Authors: Byrne M, Nasir N, Basmadjian C, Bhatia C, Cunnison RF, Carr KH, Mas-Droux C, Yeoh S, Cano C, Bayliss R Tags: Biochem J Source Type: research

Interaction of the neutral amino acid transporter ASCT2 with basic amino acids.
Abstract Glutamine transport across cell membranes is performed by a variety of transporters, including the alanine serine cysteine transporter 2 (ASCT2). The substrate binding site of ASCT2 was proposed to be specific for small amino acids with neutral side chains, excluding basic substrates such as lysine. A series of competitive inhibitors of ASCT2 with low mM affinity were developed previously, on the basis of the 2,4-diaminobutyric acid (DAB) scaffold with a potential positive charge in the side chain. Therefore, we tested whether basic amino acids with side chains shorter than lysine can interact with the AS...
Source: The Biochemical Journal - April 3, 2020 Category: Biochemistry Authors: Ndaru E, Garibsingh RA, Zielewicz L, Schlessinger A, Grewer C Tags: Biochem J Source Type: research

Hereditary hemochromatosis disrupts uric acid homeostasis and causes hyperuricemia via altered expression/activity of xanthine oxidase and ABCG2.
Abstract Hereditary hemochromatosis (HH) is mostly caused by mutations in the iron-regulatory gene HFE. The disease is associated with iron overload, resulting in liver cirrhosis/cancer, cardiomegaly, kidney dysfunction, diabetes, and arthritis. Fe2+-induced oxidative damage is suspected in the etiology of these symptoms. Here we examined, using Hfe-/- mice, whether disruption of uric acid (UA) homeostasis plays any role in HH-associated arthritis. We detected elevated levels of UA in serum and intestine in Hfe-/-mice compared to controls. Though the expression of xanthine oxidase, which generates UA, was not diff...
Source: The Biochemical Journal - April 2, 2020 Category: Biochemistry Authors: Ristic B, Sivaprakasam S, Narayanan M, Ganapathy V Tags: Biochem J Source Type: research

A complex comprising C15ORF41 and Codanin-1- the products of two genes mutated in congenital dyserythropoietic anemia type I (CDA-I).
We present the characterization of the C15ORF41-Codanin-1 complex in humans in cells and in vitro, and demonstrate that Codanin-1 appears to sequester C15ORF41 in the cytoplasm as previously shown for ASF1. These findings in this study have major implications for the understanding of C15ORF41 and Codanin-1 function and CDA-I. PMID: 32239177 [PubMed - as supplied by publisher] (Source: The Biochemical Journal)
Source: The Biochemical Journal - April 2, 2020 Category: Biochemistry Authors: Shroff M, Knebel A, Toth R, Rouse J Tags: Biochem J Source Type: research

Unconventional biochemical regulation of the oxidative pentose phosphate pathway in the model cyanobacterium Synechocystis sp. PCC 6803.
Abstract Metabolite production from carbon dioxide using sugar catabolism in cyanobacteria has been in the spotlight recently. Synechocystis sp. PCC 6803 (Synechocystis 6803) is the most studied cyanobacterium for metabolite production. Previous in vivo analyses revealed that the oxidative pentose phosphate (OPP) pathway is at the core of sugar catabolism in Synechocystis 6803. However, the biochemical regulation of the OPP pathway enzymes in Synechocystis 6803 remains unknown. Therefore, we characterized a key enzyme of the OPP pathway, glucose-6-phosphate dehydrogenase (G6PDH), and related enzymes from Synechocy...
Source: The Biochemical Journal - March 30, 2020 Category: Biochemistry Authors: Ito S, Osanai T Tags: Biochem J Source Type: research

PINK1-dependent phosphorylation of Serine111 within the SF3 motif of Rab GTPases impairs effector interactions and LRRK2 mediated phosphorylation at Threonine72.
Abstract Loss of function mutations in the PINK1 kinase are causal for autosomal recessive Parkinson's disease (PD) whilst gain of function mutations in the LRRK2 kinase cause autosomal dominant PD. PINK1 indirectly regulates the phosphorylation of a subset of Rab GTPases at a conserved Serine111 (Ser111) residue within the SF3 motif. Using genetic code expansion technologies we have produced stoichiometric Ser111-phosphorylated Rab8A revealing impaired interactions with its cognate guanine nucleotide exchange factor (GEF) and GTPase activating protein (GAP). In a screen for Rab8A kinases we identify TAK1 and MST3...
Source: The Biochemical Journal - March 30, 2020 Category: Biochemistry Authors: Vieweg S, Mulholland K, Brauning B, Kacharia N, Lai YC, Toth R, Singh PK, Volpi I, Sattler M, Groll M, Itzen A, Muqit MMK Tags: Biochem J Source Type: research

SLC6A14, a Na+/Cl--coupled amino acid transporter, functions as a tumor promoter in colon and is a target for Wnt signaling.
Abstract SLC6A14 is a Na+/Cl--coupled transporter for neutral and cationic amino acids. It is expressed at basal levels in normal colon but is upregulated in colon cancer. However, the relevance of this upregulation to cancer progression and the mechanisms involved in the upregulation remain unknown. Here we show that SLC6A14 is essential for colon cancer and that its upregulation involves, at least partly, Wnt signaling. Upregulation of the transporter is evident in most human colon cancer cell lines and also in a majority of patient-derived xenografts. These findings are supported by publicly available TCGA (The...
Source: The Biochemical Journal - March 27, 2020 Category: Biochemistry Authors: Sikder MOF, Sivaprakasam S, Brown TP, Thangaraju M, Bhutia YD, Ganapathy V Tags: Biochem J Source Type: research

Epigenetic dynamics of the thermogenic gene program of adipocytes.
Abstract Brown adipose tissue (BAT) is a metabolically beneficial organ capable of burning fat by dissipating chemical energy into heat, thereby increasing energy expenditure. Moreover, subcutaneous white adipose tissue can undergo so-called browning/beiging. The recent recognition of the presence of brown or beige adipocytes in human adults has attracted much attention to elucidate the molecular mechanism underlying the thermogenic adipose program. Many key transcriptional regulators critical for the thermogenic gene program centering on activating the UCP1 promoter, have been discovered. Thermogenic gene express...
Source: The Biochemical Journal - March 27, 2020 Category: Biochemistry Authors: Yi D, Nguyen HP, Sul HS Tags: Biochem J Source Type: research

The NLRP3 inflammasome regulates adipose tissue metabolism.
r JD Abstract Adipose tissue regulates metabolic homeostasis by participating in endocrine and immune responses in addition to storing and releasing lipids from adipocytes. Obesity skews adipose tissue adipokine responses and degrades the coordination of adipocyte lipogenesis and lipolysis. These defects in adipose tissue metabolism can promote ectopic lipid deposition and inflammation in insulin-sensitive tissues such as skeletal muscle and liver. Sustained caloric excess can expand white adipose tissue to a point of maladaptation exacerbating both local and systemic inflammation. Multiple sources, instigators an...
Source: The Biochemical Journal - March 24, 2020 Category: Biochemistry Authors: Barra NG, Henriksbo BD, Anhê FF, Schertzer JD Tags: Biochem J Source Type: research

Molecular origins of folding rate differences in the thioredoxin family.
Abstract Thioredoxins are a family of conserved oxidoreductases responsible for maintaining redox balance within cells. They have also served as excellent model systems for protein design and engineering studies particularly through ancestral sequence reconstruction methods. The recent work by Gamiz-Arco et al. [Biochem J (2019) 476, 3631-3647] answers fundamental questions on how specific sequence differences can contribute to differences in folding rates between modern and ancient thioredoxins but also among a selected subset of modern thioredoxins. They surprisingly find that rapid unassisted folding, a feature...
Source: The Biochemical Journal - March 20, 2020 Category: Biochemistry Authors: Naganathan AN Tags: Biochem J Source Type: research

Biochemical adaptations in white adipose tissue following aerobic exercise: from mitochondrial biogenesis to browning.
Abstract Our understanding of white adipose tissue (WAT) biochemistry has evolved over the last few decades and it is now clear that WAT is not simply a site of energy storage, but rather a pliable endocrine organ demonstrating dynamic responsiveness to the effects of aerobic exercise. Similar to its established effects in skeletal muscle, aerobic exercise induces many biochemical adaptations in WAT including mitochondrial biogenesis and browning. While past research has focused on the regulation of these biochemical processes, there has been renewed interest as of late given the potential of harnessing WAT mitoch...
Source: The Biochemical Journal - March 20, 2020 Category: Biochemistry Authors: McKie GL, Wright DC Tags: Biochem J Source Type: research

Allosteric modulation of the GTPase activity of a bacterial LRRK2 homologue by conformation-specific Nanobodies.
;es W Abstract Mutations in the Parkinson's disease (PD)-associated protein leucine-rich repeat kinase 2 (LRRK2) commonly lead to a reduction of GTPase activity and increase in kinase activity. Therefore, strategies for drug development have mainly been focusing on the design of LRRK2 kinase inhibitors. We recently showed that the central RocCOR domains (Roc: Ras of complex proteins; COR: C-terminal of Roc) of a bacterial LRRK2 homologue cycle between a dimeric and monomeric form concomitant with GTP binding and hydrolysis. PD-associated mutations can slow down GTP hydrolysis by stabilizing the protein in its dime...
Source: The Biochemical Journal - March 13, 2020 Category: Biochemistry Authors: Leemans M, Galicia C, Deyaert E, Daems E, Krause L, Paesmans J, Pardon E, Steyaert J, Kortholt A, Sobott F, Klostermeier D, Versées W Tags: Biochem J Source Type: research

Adipocyte lipolysis: from molecular mechanisms of regulation to disease and therapeutics.
Abstract Fatty acids (FAs) are stored safely in the form of triacylglycerol (TAG) in lipid droplet (LD) organelles by professional storage cells called adipocytes. These lipids are mobilized during adipocyte lipolysis, the fundamental process of hydrolyzing TAG to FAs for internal or systemic energy use. Our understanding of adipocyte lipolysis has greatly increased over the past 50 years from a basic enzymatic process to a dynamic regulatory one, involving the assembly and disassembly of protein complexes on the surface of LDs. These dynamic interactions are regulated by hormonal signals such as catecholamines an...
Source: The Biochemical Journal - March 13, 2020 Category: Biochemistry Authors: Yang A, Mottillo EP Tags: Biochem J Source Type: research

Novel molecular aspects of the CRISPR backbone protein 'Cas7' from cyanobacteria.
Abstract The cyanobacterium Anabaena PCC 7120 shows the presence of Type I-D CRISPR system that can potentially confer adaptive immunity. The Cas7 protein (Alr1562), which forms the backbone of the type I-D surveillance complex, was characterized from Anabaena. Alr1562, showed the presence of the non-canonical RNA recognition motif and two intrinsically disordered regions (IDRs). When overexpressed in E. coli, the Alr1562 protein was soluble and could be purified by affinity chromatography, however, deletion of IDRs rendered Alr1562 completely insoluble. The purified Alr1562 was present in the dimeric or a RNA-ass...
Source: The Biochemical Journal - March 7, 2020 Category: Biochemistry Authors: Kalwani P, Rath D, Ballal A Tags: Biochem J Source Type: research

CBL-CIPK module-mediated phosphoregulation: facts and hypothesis.
We present here an overview of the phosphoregulation mechanism of the CBL-CIPK module. PMID: 32129820 [PubMed - in process] (Source: The Biochemical Journal)
Source: The Biochemical Journal - March 6, 2020 Category: Biochemistry Authors: Sanyal SK, Mahiwal S, Nambiar DM, Pandey GK Tags: Biochem J Source Type: research

Correction: The glutathione degrading enzyme, Chac1, is required for calcium signaling in developing zebrafish: redox as an upstream activator of calcium.
PMID: 32106303 [PubMed - in process] (Source: The Biochemical Journal)
Source: The Biochemical Journal - February 28, 2020 Category: Biochemistry Authors: Yadav S, Chawla B, Khursheed MA, Ramachandran R, Bachhawat AK Tags: Biochem J Source Type: research

Interaction of α-synuclein and Parkin in iron toxicity on SH-SY5Y cells: implications in the pathogenesis of Parkinson's disease.
This study has demonstrated that iron in varying concentrations (up to 400 µM) causes an increase in α-synuclein content in SH-SY5Y cells associated with mitochondrial depolarization, decreased cellular ATP content and loss of cell viability during incubation up to 96 h. Knocking-down α-synuclein expression prevents cytotoxic actions of iron, which can also be prevented by cyclosporine A (a blocker of mitochondrial permeability transition pore). These results indicate that iron cytotoxicity is mediated by α-synuclein acting on mitochondria. Likewise siRNA mediated knock-down of Parkin causes an ...
Source: The Biochemical Journal - February 28, 2020 Category: Biochemistry Authors: Ganguly U, Banerjee A, Chakrabarti SS, Kaur U, Sen O, Cappai R, Chakrabarti S Tags: Biochem J Source Type: research

Plant organellar DNA polymerases bypass Thymine Glycol using two conserved lysine residues.
ba LG Abstract Plant organelles cope with endogenous DNA damaging agents, byproducts of respiration and photosynthesis, and exogenous agents like ultraviolet light. Plant organellar DNA polymerases (DNAPs) are not phylogenetically related to yeast and metazoan DNAPs and they harbor three insertions not present in any other DNAPs. Plant organellar DNAPs from Arabidopsis thaliana (AtPolIA and AtPolIB) are translesion synthesis (TLS) DNAPs able to bypass abasic sites, a lesion that poses a strong block to replicative polymerases. Besides abasic sites, reactive oxidative species and ionizing radiation react with thymi...
Source: The Biochemical Journal - February 28, 2020 Category: Biochemistry Authors: Baruch-Torres N, Yamamoto J, Juárez-Quintero V, Iwai S, Brieba LG Tags: Biochem J Source Type: research

Transcriptional signature of prion-induced neurotoxicity in a Drosophila model of transmissible mammalian prion disease.
Abstract Prion diseases are fatal transmissible neurodegenerative conditions of humans and animals that arise through neurotoxicity induced by PrP misfolding. The cellular and molecular mechanisms of prion-induced neurotoxicity remain undefined. Understanding these processes will underpin therapeutic and control strategies for human and animal prion diseases, respectively. Prion diseases are difficult to study in their natural hosts and require the use of tractable animal models. Here we used RNA-Seq-based transcriptome analysis of prion-exposed Drosophila to probe the mechanism of prion-induced neurotoxicity. Adu...
Source: The Biochemical Journal - February 28, 2020 Category: Biochemistry Authors: Thackray AM, Lam B, Shahira Binti Ab Razak A, Yeo G, Bujdoso R Tags: Biochem J Source Type: research