Withdrawal: Exercise increases mitochondrial PGC-1{alpha} content and promotes nuclear-mitochondrial cross-talk to coordinate mitochondrial biogenesis. [Withdrawals/Retractions]
This article has been withdrawn by the authors. In Fig. 6B the top two panels, corresponding to TOMM22 and Bcl-2, with trypsin treatment samples presented background issues. In Fig. 5, the H2B and VDAC immunoblot panels were duplicated and flipped vertically. The immunoblots for VDAC in Fig. 7A and the VDAC panels in Fig. 8B were duplicated and represented different experimental conditions. The immunoblots for Tfam (IP: PGC-1a) in Fig. 7A and the nuclear PGC-1a in Fig. 5 were flipped vertically. The immunoblots for PGC-1a (IP: Tfam) in Fig. 7B and PGC-1a (Input: D-Loop) in Fig. 8 were flipped horizontally and duplicated. D...
Source: Journal of Biological Chemistry - December 18, 2020 Category: Chemistry Authors: Adeel Safdar, Jonathan P. Little, Andrew J. Stokl, Bart P. Hettinga, Mahmood Akhtar, Mark A. Tarnopolsky Tags: Withdrawals/Retractions Source Type: research

Withdrawal: ETS-1 protein regulates vascular endothelial growth factor-induced matrix metalloproteinase-9 and matrix metalloproteinase-13 expression in human ovarian carcinoma cell line SKOV-3. [Withdrawals/Retractions]
VOLUME 287 (2012) PAGES 15001–15015The article has been withdrawn by the authors. The authors were made aware that the panel corresponding to lanes 3 and 4 of the total Akt immunoblot in Fig. 3A was reused as a GAPDH panel in Fig. 6B. In addition, the panel corresponding to the GAPDH immunoblot in Fig. 3A was inappropriately manipulated to reduce background noise. The authors responded that all the experiments were executed appropriately, and the data obtained at that time or by subsequent experiments support the original conclusion of the paper. Furthermore, the authors state that these issues do not affect the accu...
Source: Journal of Biological Chemistry - December 18, 2020 Category: Chemistry Authors: Sonali Ghosh, Moitri Basu, Sib Sankar Roy Tags: Withdrawals/Retractions Source Type: research

Genetic diseases of the Kennedy pathways for membrane synthesis [Molecular Bases of Disease]
The two branches of the Kennedy pathways (CDP-choline and CDP-ethanolamine) are the predominant pathways responsible for the synthesis of the most abundant phospholipids, phosphatidylcholine and phosphatidylethanolamine, respectively, in mammalian membranes. Recently, hereditary diseases associated with single gene mutations in the Kennedy pathways have been identified. Interestingly, genetic diseases within the same pathway vary greatly, ranging from muscular dystrophy to spastic paraplegia to a childhood blinding disorder to bone deformations. Indeed, different point mutations in the same gene (PCYT1; CCTα) result ...
Source: Journal of Biological Chemistry - December 18, 2020 Category: Chemistry Authors: Mahtab Tavasoli, Sarah Lahire, Taryn Reid, Maren Brodovsky, Christopher R. McMaster Tags: JBC Reviews Source Type: research

Antibiotic binding releases autoinhibition of the TipA multidrug-resistance transcriptional regulator [Gene Regulation]
Investigations of bacterial resistance strategies can aid in the development of new antimicrobial drugs as a countermeasure to the increasing worldwide prevalence of bacterial antibiotic resistance. One such strategy involves the TipA class of transcription factors, which constitute minimal autoregulated multidrug resistance (MDR) systems against diverse antibiotics. However, we have insufficient information regarding how antibiotic binding induces transcriptional activation to design molecules that could interfere with this process. To learn more, we determined the crystal structure of SkgA from Caulobacter crescentus as ...
Source: Journal of Biological Chemistry - December 18, 2020 Category: Chemistry Authors: Xuguang Jiang, Linjuan Zhang, Maikun Teng, Xu Li Tags: Protein Structure and Folding Source Type: research

Identification and biochemical characterization of Asp t 36, a new fungal allergen from Aspergillus terreus [Protein Structure and Folding]
Aspergillus terreus is an allergenic fungus, in addition to causing infections in both humans and plants. However, the allergens in this fungus are still unknown, limiting the development of diagnostic and therapeutic strategies. We used a proteomic approach to search for allergens, identifying 16 allergens based on two-dimensional immunoblotting with A. terreus susceptible patient sera. We further characterized triose-phosphate isomerase (Asp t 36), one of the dominant IgE (IgE)-reactive proteins. The gene was cloned and expressed in Escherichia coli. Phylogenetic analysis showed Asp t 36 to be highly conserved with close...
Source: Journal of Biological Chemistry - December 18, 2020 Category: Chemistry Authors: Bijoya Karmakar, Bodhisattwa Saha, Kuladip Jana, Swati Gupta Bhattacharya Tags: Immunology Source Type: research

Biochemical transformation of bacterial lipopolysaccharides by acyloxyacyl hydrolase reduces host injury and promotes recovery [Enzymology]
Animals can sense the presence of microbes in their tissues and mobilize their own defenses by recognizing and responding to conserved microbial structures (often called microbe-associated molecular patterns (MAMPs)). Successful host defenses may kill the invaders, yet the host animal may fail to restore homeostasis if the stimulatory microbial structures are not silenced. Although mice have many mechanisms for limiting their responses to lipopolysaccharide (LPS), a major Gram-negative bacterial MAMP, a highly conserved host lipase is required to extinguish LPS sensing in tissues and restore homeostasis. We review recent p...
Source: Journal of Biological Chemistry - December 18, 2020 Category: Chemistry Authors: Robert S. Munford, Jerrold P. Weiss, Mingfang Lu Tags: JBC Reviews Source Type: research

Clearance of intracellular tau protein from neuronal cells via VAMP8-induced secretion [Cell Biology]
In Alzheimer's disease (AD), tau, a microtubule-associated protein (MAP), becomes hyperphosphorylated, aggregates, and accumulates in the somato-dendritic compartment of neurons. In parallel to its intracellular accumulation in AD, tau is also released in the extracellular space, as revealed by its increased presence in cerebrospinal fluid (CSF). Consistent with this, recent studies, including ours, have reported that neurons secrete tau, and several therapeutic strategies aim to prevent the intracellular tau accumulation. Previously, we reported that late endosomes were implicated in tau secretion. Here, we explore the po...
Source: Journal of Biological Chemistry - December 18, 2020 Category: Chemistry Authors: Julie Pilliod, Alexandre Desȷardins, Camille Pernegre, Helene Jamann, Catherine Larochelle, Edward A. Fon, Nicole Leclerc Tags: Molecular Bases of Disease Source Type: research

A novel method produces native light-harvesting complex II aggregates from the photosynthetic membrane revealing their role in nonphotochemical quenching [Bioenergetics]
Nonphotochemical quenching (NPQ) is a mechanism of regulating light harvesting that protects the photosynthetic apparatus from photodamage by dissipating excess absorbed excitation energy as heat. In higher plants, the major light-harvesting antenna complex (LHCII) of photosystem (PS) II is directly involved in NPQ. The aggregation of LHCII is proposed to be involved in quenching. However, the lack of success in isolating native LHCII aggregates has limited the direct interrogation of this process. The isolation of LHCII in its native state from thylakoid membranes has been problematic because of the use of detergent, whic...
Source: Journal of Biological Chemistry - December 18, 2020 Category: Chemistry Authors: Mahendra K. Shukla, Akimasa Watanabe, Sam Wilson, Vasco Giovagnetti, Ece Imam Moustafa, Jun Minagawa, Alexander V. Ruban Tags: Bioenergetics Source Type: research

Polymerase {gamma} efficiently replicates through many natural template barriers but stalls at the HSP1 quadruplex [Enzymology]
Faithful replication of the mitochondrial genome is carried out by a set of key nuclear-encoded proteins. DNA polymerase γ is a core component of the mtDNA replisome and the only replicative DNA polymerase localized to mitochondria. The asynchronous mechanism of mtDNA replication predicts that the replication machinery encounters dsDNA and unique physical barriers such as structured genes, G-quadruplexes, and other obstacles. In vitro experiments here provide evidence that the polymerase γ heterotrimer is well-adapted to efficiently synthesize DNA, despite the presence of many naturally occurring roadblocks. Ho...
Source: Journal of Biological Chemistry - December 18, 2020 Category: Chemistry Authors: Eric D. Sullivan, Matthew J. Longley, William C. Copeland Tags: DNA and Chromosomes Source Type: research

Mouse Ifit1b is a cap1-RNA-binding protein that inhibits mouse coronavirus translation and is regulated by complexing with Ifit1c [RNA]
Knockout mouse models have been extensively used to study the antiviral activity of IFIT (interferon-induced protein with tetratricopeptide repeats). Human IFIT1 binds to cap0 (m7GpppN) RNA, which lacks methylation on the first and second cap-proximal nucleotides (cap1, m7GpppNm, and cap2, m7GpppNmNm, respectively). These modifications are signatures of “self” in higher eukaryotes, whereas unmodified cap0-RNA is recognized as foreign and, therefore, potentially harmful to the host cell. IFIT1 inhibits translation at the initiation stage by competing with the cap-binding initiation factor complex, eIF4F, restric...
Source: Journal of Biological Chemistry - December 18, 2020 Category: Chemistry Authors: Harriet V. Mears, Trevor R. Sweeney Tags: Immunology Source Type: research

The C-terminal region of the plasmid partitioning protein TubY is a tetramer that can bind membranes and DNA [Protein Structure and Folding]
This study determined the crystal structure of the C-terminal domain of TubY from the Bacillus cereus pXO1-like plasmid and showed that it forms a tetrameric parallel four-helix bundle that differs from the typical MerR family proteins with a dimeric anti-parallel coiled-coil. Biochemical analyses revealed that the C-terminal tail with the conserved lysine cluster helps TubY to stably associate with the TubR-centromere complex as well as to nonspecifically bind DNA. Furthermore, this C-terminal tail forms an amphipathic helix in the presence of lipids but must oligomerize to localize the protein to the membrane in vivo. Ta...
Source: Journal of Biological Chemistry - December 18, 2020 Category: Chemistry Authors: Ikuko Hayashi Tags: Protein Structure and Folding Source Type: research

A structural and kinetic survey of GH5_4 endoglucanases reveals determinants of broad substrate specificity and opportunities for biomass hydrolysis [Protein Structure and Folding]
Broad-specificity glycoside hydrolases (GHs) contribute to plant biomass hydrolysis by degrading a diverse range of polysaccharides, making them useful catalysts for renewable energy and biocommodity production. Discovery of new GHs with improved kinetic parameters or more tolerant substrate-binding sites could increase the efficiency of renewable bioenergy production even further. GH5 has over 50 subfamilies exhibiting selectivities for reaction with β-(1,4)–linked oligo- and polysaccharides. Among these, subfamily 4 (GH5_4) contains numerous broad-selectivity endoglucanases that hydrolyze cellulose, xyloglucan...
Source: Journal of Biological Chemistry - December 18, 2020 Category: Chemistry Authors: Evan M. Glasgow, Elias I. Kemna, Craig A. Bingman, Nicole Ing, Kai Deng, Christopher M. Bianchetti, Taichi E. Takasuka, Trent R. Northen, Brian G. Fox Tags: Enzymology Source Type: research

ARID4B is critical for mouse embryonic stem cell differentiation towards mesoderm and endoderm, linking epigenetics to pluripotency exit [Developmental Biology]
Distinct cell types emerge from embryonic stem cells through a precise and coordinated execution of gene expression programs during lineage commitment. This is established by the action of lineage specific transcription factors along with chromatin complexes. Numerous studies have focused on epigenetic factors that affect embryonic stem cells (ESC) self-renewal and pluripotency. However, the contribution of chromatin to lineage decisions at the exit from pluripotency has not been as extensively studied. Using a pooled epigenetic shRNA screen strategy, we identified chromatin-related factors critical for differentiation tow...
Source: Journal of Biological Chemistry - December 18, 2020 Category: Chemistry Authors: Nihal Terzi Cizmecioglu, Jialiang Huang, Ezgi G. Keskin, Xiaofeng Wang, Idil Esen, Fei Chen, Stuart H. Orkin Tags: Gene Regulation Source Type: research

Snapshots during the catalytic cycle of a histidine acid phytase reveal an induced-fit structural mechanism [Protein Structure and Folding]
Highly engineered phytases, which sequentially hydrolyze the hexakisphosphate ester of inositol known as phytic acid, are routinely added to the feeds of monogastric animals to improve phosphate bioavailability. New phytases are sought as starting points to further optimize the rate and extent of dephosphorylation of phytate in the animal digestive tract. Multiple inositol polyphosphate phosphatases (MINPPs) are clade 2 histidine phosphatases (HP2P) able to carry out the stepwise hydrolysis of phytate. MINPPs are not restricted by a strong positional specificity making them attractive targets for development as feed enzyme...
Source: Journal of Biological Chemistry - December 18, 2020 Category: Chemistry Authors: Isabella M. Acquistapace, Monika A. Zi{cedilla}etek, Arthur W. H. Li, Melissa Salmon, Imke Kuhn, Mike R. Bedford, Charles A. Brearley, Andrew M. Hemmings Tags: Enzymology Source Type: research

Hdac3 regulates bone modeling by suppressing osteoclast responsiveness to RANKL [Signal Transduction]
In this study we conditionally deleted Hdac3 within Ctsk-expressing cells and examined the effects on bone modeling and osteoclast differentiation in mice. Hdac3 deficiency reduced femur and tibia periosteal circumference and increased cortical periosteal osteoclast number. Trabecular bone was likewise reduced and was accompanied by increased osteoclast number per trabecular bone surface. We previously showed that Hdac3 deacetylates the p65 subunit of the NF-κB transcriptional complex to decrease DNA-binding and transcriptional activity. Hdac3-deficient osteoclasts demonstrate increased K310 NF-κB acetylation a...
Source: Journal of Biological Chemistry - December 18, 2020 Category: Chemistry Authors: David H. H. Molstad, Anna M. Mattson, Dana L. Begun, Jennifer J. Westendorf, Elizabeth W. Bradley Tags: Molecular Bases of Disease Source Type: research

Mapping the transition state for a binding reaction between ancient intrinsically disordered proteins [Molecular Biophysics]
Intrinsically disordered protein domains often have multiple binding partners. It is plausible that the strength of pairing with specific partners evolves from an initial low affinity to a higher affinity. However, little is known about the molecular changes in the binding mechanism that would facilitate such a transition. We previously showed that the interaction between two intrinsically disordered domains, NCBD and CID, likely emerged in an ancestral deuterostome organism as a low-affinity interaction that subsequently evolved into a higher-affinity interaction before the radiation of modern vertebrate groups. Here we m...
Source: Journal of Biological Chemistry - December 18, 2020 Category: Chemistry Authors: Elin Karlsson, Cristina Paissoni, Amanda M. Erkelens, Zeinab A. Tehranizadeh, Frieda A. Sorgenfrei, Eva Andersson, Weihua Ye, Carlo Camilloni, Per Jemth Tags: Protein Structure and Folding Source Type: research

Mycobacterium tuberculosis infection up-regulates MFN2 expression to promote NLRP3 inflammasome formation [Cell Biology]
Tuberculosis (TB), caused by the infection of Mycobacterium tuberculosis (MTB), is one of the leading causes of death worldwide, especially in children. However, the mechanisms by which MTB infects its cellular host, activates an immune response, and triggers inflammation remain unknown. Mitochondria play important roles in the initiation and activation of the nucleotide-binding oligomerization domain-like receptor with a pyrin domain 3 (NLRP3) inflammasome, where mitochondria-associated endoplasmic reticulum membranes (MAMs) may serve as the platform for inflammasome assembly and activation. Additionally, mitofusin 2 (MFN...
Source: Journal of Biological Chemistry - December 18, 2020 Category: Chemistry Authors: Fang Xu, Hui Qi, Jieqiong Li, Lin Sun, Juanjuan Gong, Yuanying Chen, Adong Shen, Wei Li Tags: Microbiology Source Type: research

AggreCount: an unbiased image analysis tool for identifying and quantifying cellular aggregates in a spatially defined manner [Methods and Resources]
Protein quality control is maintained by a number of integrated cellular pathways that monitor the folding and functionality of the cellular proteome. Defects in these pathways lead to the accumulation of misfolded or faulty proteins that may become insoluble and aggregate over time. Protein aggregates significantly contribute to the development of a number of human diseases such as amyotrophic lateral sclerosis, Huntington's disease, and Alzheimer's disease. In vitro, imaging-based, cellular studies have defined key biomolecular components that recognize and clear aggregates; however, no unifying method is available to qu...
Source: Journal of Biological Chemistry - December 18, 2020 Category: Chemistry Authors: Jacob Aaron Klickstein, Sirisha Mukkavalli, Malavika Raman Tags: Cell Biology Source Type: research

AMPK{beta}1 and AMPK{beta}2 define an isoform-specific gene signature in human pluripotent stem cells, differentially mediating cardiac lineage specification [Cell Biology]
AMP-activated protein kinase (AMPK) is a key regulator of energy metabolism that phosphorylates a wide range of proteins to maintain cellular homeostasis. AMPK consists of three subunits: α, β, and γ. AMPKα and β are encoded by two genes, the γ subunit by three genes, all of which are expressed in a tissue-specific manner. It is not fully understood, whether individual isoforms have different functions. Using RNA-Seq technology, we provide evidence that the loss of AMPKβ1 and AMPKβ2 lead to different gene expression profiles in human induced pluripotent stem cells (hiPSCs), indic...
Source: Journal of Biological Chemistry - December 18, 2020 Category: Chemistry Authors: Nicole Ziegler, Erik Bader, Alexey Epanchintsev, Daniel Margerie, Aimo Kannt, Dieter Schmoll Tags: Metabolism Source Type: research

The HRDC domain oppositely modulates the unwinding activity of E. coli RecQ helicase on duplex DNA and G-quadruplex [Enzymology]
In this study, we systematically characterized the roles of the HRDC domain in E. coli RecQ in various DNA transactions by single-molecule FRET. We found that RecQ repetitively unwinds the 3′-partial duplex and fork DNA with a moderate processivity and periodically patrols on the ssDNA in the 5′-partial duplex by translocation. The HRDC domain significantly suppresses RecQ activities in the above transactions. In sharp contrast, the HRDC domain is essential for the deep and long-time unfolding of the G4 DNA structure by RecQ. Based on the observations that the HRDC domain dynamically switches between RecA core-...
Source: Journal of Biological Chemistry - December 18, 2020 Category: Chemistry Authors: Fang-Yuan Teng, Ting-Ting Wang, Hai-Lei Guo, Ben-Ge Xin, Bo Sun, Shuo-Xing Dou, Xu-Guang Xi, Xi-Miao Hou Tags: Molecular Biophysics Source Type: research

Importance of endothelial Hey1 expression for thoracic great vessel development and its distal enhancer for Notch-dependent endothelial transcription [Gene Regulation]
In this study, we revealed that Hey1 in vascular endothelial cells, but not in smooth muscle cells, played essential roles for PAA development and great vessel morphogenesis in mouse embryos. Tek-Cre–mediated Hey1 deletion in endothelial cells affected endothelial tube formation and smooth muscle differentiation in embryonic fourth PAAs and resulted in interruption of the aortic arch and other great vessel malformations. Cell specificity and signal responsiveness of Hey1 expression were controlled through multiple cis-regulatory regions. We found two distal genomic regions that had enhancer activity in endothelial ce...
Source: Journal of Biological Chemistry - December 18, 2020 Category: Chemistry Authors: Yusuke Watanabe, Daiki Seya, Dai Ihara, Shuhei Ishii, Taiki Uemoto, Atsushi Kubo, Yuji Arai, Yoshie Isomoto, Atsushi Nakano, Takaya Abe, Mayo Shigeta, Teruhisa Kawamura, Yoshihiko Saito, Toshihiko Ogura, Osamu Nakagawa Tags: Developmental Biology Source Type: research

NETosis occurs independently of neutrophil serine proteases [Enzymology]
Neutrophils are primary host innate immune cells defending against pathogens. One proposed mechanism by which neutrophils prevent the spread of pathogens is NETosis, the extrusion of cellular DNA resulting in neutrophil extracellular traps (NETs). The protease neutrophil elastase (NE) has been implicated in the formation of NETs through proteolysis of nuclear proteins leading to chromatin decondensation. In addition to NE, neutrophils contain three other serine proteases that could compensate if the activity of NE was neutralized. However, whether they do play such a role is unknown. Thus, we deployed recently described sp...
Source: Journal of Biological Chemistry - December 18, 2020 Category: Chemistry Authors: Paulina Kasperkiewicz, Anne Hempel, Tomasz Janiszewski, Sonia Kołt, Scott J. Snipas, Marcin Drag, Guy S. Salvesen Tags: Cell Biology Source Type: research

Bacterial iron detoxification at the molecular level [Protein Structure and Folding]
Iron is an essential micronutrient, and, in the case of bacteria, its availability is commonly a growth-limiting factor. However, correct functioning of cells requires that the labile pool of chelatable “free” iron be tightly regulated. Correct metalation of proteins requiring iron as a cofactor demands that such a readily accessible source of iron exist, but overaccumulation results in an oxidative burden that, if unchecked, would lead to cell death. The toxicity of iron stems from its potential to catalyze formation of reactive oxygen species that, in addition to causing damage to biological molecules, can al...
Source: Journal of Biological Chemistry - December 18, 2020 Category: Chemistry Authors: Justin M. Bradley, Dimitry A. Svistunenko, Michael T. Wilson, Andrew M. Hemmings, Geoffrey R. Moore, Nick E. Le Brun Tags: JBC Reviews Source Type: research

Visualizing, quantifying, and manipulating mitochondrial DNA in vivo [Methods and Resources]
Mitochondrial DNA (mtDNA) encodes proteins and RNAs that support the functions of mitochondria and thereby numerous physiological processes. Mutations of mtDNA can cause mitochondrial diseases and are implicated in aging. The mtDNA within cells is organized into nucleoids within the mitochondrial matrix, but how mtDNA nucleoids are formed and regulated within cells remains incompletely resolved. Visualization of mtDNA within cells is a powerful means by which mechanistic insight can be gained. Manipulation of the amount and sequence of mtDNA within cells is important experimentally and for developing therapeutic interventi...
Source: Journal of Biological Chemistry - December 18, 2020 Category: Chemistry Authors: David L. Prole, Patrick F. Chinnery, Nick S. Jones Tags: JBC Reviews Source Type: research

Wildtype {sigma}1 receptor and the receptor agonist improve ALS-associated mutation-induced insolubility and toxicity [Neurobiology]
Genetic mutations related to ALS, a progressive neurological disease, have been discovered in the gene encoding σ-1 receptor (σ1R). We previously reported that σ1RE102Q elicits toxicity in cells. The σ1R forms oligomeric states that are regulated by ligands. Nevertheless, little is known about the effect of ALS-related mutations on oligomer formation. Here, we transfected NSC-34 cells, a motor neuronal cell line, and HEK293T cells with σ1R-mCherry (mCh), σ1RE102Q-mCh, or nontagged forms to investigate detergent solubility and subcellular distribution using immunocytochemistry and fluores...
Source: Journal of Biological Chemistry - December 18, 2020 Category: Chemistry Authors: Yasuharu Shinoda, Yudai Haga, Koichiro Akagawa, Kohji Fukunaga Tags: Cell Biology Source Type: research

Hepatocyte nuclear factor 1{beta} suppresses canonical Wnt signaling through transcriptional repression of lymphoid enhancer-binding factor 1 [Molecular Bases of Disease]
Hepatocyte nuclear factor-1β (HNF-1β) is a tissue-specific transcription factor that is required for normal kidney development and renal epithelial differentiation. Mutations of HNF-1β produce congenital kidney abnormalities and inherited renal tubulopathies. Here, we show that ablation of HNF-1β in mIMCD3 renal epithelial cells results in activation of β-catenin and increased expression of lymphoid enhancer–binding factor 1 (LEF1), a downstream effector in the canonical Wnt signaling pathway. Increased expression and nuclear localization of LEF1 are also observed in cystic kidneys from Hnf1b...
Source: Journal of Biological Chemistry - December 18, 2020 Category: Chemistry Authors: Siu Chiu Chan, Sachin S. Hajarnis, Sophia M. Vrba, Vishal Patel, Peter Igarashi Tags: Gene Regulation Source Type: research

Post-translational control of the long and winding road to cholesterol [Lipids]
The synthesis of cholesterol requires more than 20 enzymes, many of which are intricately regulated. Post-translational control of these enzymes provides a rapid means for modifying flux through the pathway. So far, several enzymes have been shown to be rapidly degraded through the ubiquitin–proteasome pathway in response to cholesterol and other sterol intermediates. Additionally, several enzymes have their activity altered through phosphorylation mechanisms. Most work has focused on the two rate-limiting enzymes: 3-hydroxy-3-methylglutaryl CoA reductase and squalene monooxygenase. Here, we review current literature...
Source: Journal of Biological Chemistry - December 18, 2020 Category: Chemistry Authors: Laura J. Sharpe, Hudson W. Coates, Andrew J. Brown Tags: JBC Reviews Source Type: research

The role of uncoupling protein 2 in macrophages and its impact on obesity-induced adipose tissue inflammation and insulin resistance [Immunology]
The development of a chronic, low-grade inflammation originating from adipose tissue in obese subjects is widely recognized to induce insulin resistance, leading to the development of type 2 diabetes. The adipose tissue microenvironment drives specific metabolic reprogramming of adipose tissue macrophages, contributing to the induction of tissue inflammation. Uncoupling protein 2 (UCP2), a mitochondrial anion carrier, is thought to separately modulate inflammatory and metabolic processes in macrophages and is up-regulated in macrophages in the context of obesity and diabetes. Here, we investigate the role of UCP2 in macrop...
Source: Journal of Biological Chemistry - December 18, 2020 Category: Chemistry Authors: Xanthe A. M. H. van Dierendonck, Tiphaine Sancerni, Marie-Clotilde Alves-Guerra, Rinke Stienstra Tags: Metabolism Source Type: research

Evolving the naturally compromised chorismate mutase from Mycobacterium tuberculosis to top performance [Protein Structure and Folding]
Chorismate mutase (CM), an essential enzyme at the branch-point of the shikimate pathway, is required for the biosynthesis of phenylalanine and tyrosine in bacteria, archaea, plants, and fungi. MtCM, the CM from Mycobacterium tuberculosis, has less than 1% of the catalytic efficiency of a typical natural CM and requires complex formation with 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase for high activity. To explore the full potential of MtCM for catalyzing its native reaction, we applied diverse iterative cycles of mutagenesis and selection, thereby raising kcat/Km 270-fold to 5 × 105 m−1s−1, whi...
Source: Journal of Biological Chemistry - December 18, 2020 Category: Chemistry Authors: Jūrate˙ Fahrig–Kamarauskait≑, Kathrin Wurth–Roderer, Helen V. Thorbȷornsrud, Susanne Mailand, Ute Krengel, Peter Kast Tags: Enzymology Source Type: research

Fibrillar {alpha}-synuclein toxicity depends on functional lysosomes [Cell Biology]
Neurodegeneration in Parkinson's disease (PD) can be recapitulated in animals by administration of α-synuclein preformed fibrils (PFFs) into the brain. However, the mechanism by which these PFFs induce toxicity is unknown. Iron is implicated in PD pathophysiology, so we investigated whether α-synuclein PFFs induce ferroptosis, an iron-dependent cell death pathway. A range of ferroptosis inhibitors were added to a striatal neuron-derived cell line (STHdhQ7/7 cells), a dopaminergic neuron–derived cell line (SN4741 cells), and WT primary cortical neurons, all of which had been intoxicated with α-synucl...
Source: Journal of Biological Chemistry - December 18, 2020 Category: Chemistry Authors: Stephanie J. Guiney, Paul A. Adlard, Peng Lei, Celeste H. Mawal, Ashley I. Bush, David I. Finkelstein, Scott Ayton Tags: Neurobiology Source Type: research

Novel fluorescent GPCR biosensor detects retinal equilibrium binding to opsin and active G protein and arrestin signaling conformations [Molecular Biophysics]
Rhodopsin is a canonical class A photosensitive G protein–coupled receptor (GPCR), yet relatively few pharmaceutical agents targeting this visual receptor have been identified, in part due to the unique characteristics of its light-sensitive, covalently bound retinal ligands. Rhodopsin becomes activated when light isomerizes 11-cis-retinal into an agonist, all-trans-retinal (ATR), which enables the receptor to activate its G protein. We have previously demonstrated that, despite being covalently bound, ATR can display properties of equilibrium binding, yet how this is accomplished is unknown. Here, we describe a new ...
Source: Journal of Biological Chemistry - December 18, 2020 Category: Chemistry Authors: Christopher T. Schafer, Anthony Shumate, David L. Farrens Tags: Signal Transduction Source Type: research

Shared requirements for key residues in the antibiotic resistance enzymes ErmC and ErmE suggest a common mode of RNA recognition [Enzymology]
Erythromycin-resistance methyltransferases are SAM dependent Rossmann fold methyltransferases that convert A2058 of 23S rRNA to m6 2A2058. This modification sterically blocks binding of several classes of antibiotics to 23S rRNA, resulting in a multidrug-resistant phenotype in bacteria expressing the enzyme. ErmC is an erythromycin resistance methyltransferase found in many Gram-positive pathogens, whereas ErmE is found in the soil bacterium that biosynthesizes erythromycin. Whether ErmC and ErmE, which possess only 24% sequence identity, use similar structural elements for rRNA substrate recognition and positioning is not...
Source: Journal of Biological Chemistry - December 18, 2020 Category: Chemistry Authors: Sebastian J. Rowe, Ryan J. Mecaskey, Mohamed Nasef, Rachel C. Talton, Rory E. Sharkey, Joshua C. Halliday, Jack A. Dunkle Tags: RNA Source Type: research

Genetic evidence for the involvement of mismatch repair proteins, PMS2 and MLH3, in a late step of homologous recombination [Cell Biology]
Homologous recombination (HR) repairs DNA double-strand breaks using intact homologous sequences as template DNA. Broken DNA and intact homologous sequences form joint molecules (JMs), including Holliday junctions (HJs), as HR intermediates. HJs are resolved to form crossover and noncrossover products. A mismatch repair factor, MLH3 endonuclease, produces the majority of crossovers during meiotic HR, but it remains elusive whether mismatch repair factors promote HR in nonmeiotic cells. We disrupted genes encoding the MLH3 and PMS2 endonucleases in the human B cell line, TK6, generating null MLH3−/− and PMS2&min...
Source: Journal of Biological Chemistry - December 18, 2020 Category: Chemistry Authors: Md Maminur Rahman, Mohiuddin Mohiuddin, Islam Shamima Keka, Kousei Yamada, Masataka Tsuda, Hiroyuki Sasanuma, Jessica Andreani, Raphael Guerois, Valerie Borde, Jean-Baptiste Charbonnier, Shunichi Takeda Tags: DNA and Chromosomes Source Type: research

Methylarginine metabolites are associated with attenuated muscle protein synthesis in cancer-associated muscle wasting [Protein Synthesis and Degradation]
Cancer cachexia is characterized by reductions in peripheral lean muscle mass. Prior studies have primarily focused on increased protein breakdown as the driver of cancer-associated muscle wasting. Therapeutic interventions targeting catabolic pathways have, however, largely failed to preserve muscle mass in cachexia, suggesting that other mechanisms might be involved. In pursuit of novel pathways, we used untargeted metabolomics to search for metabolite signatures that may be linked with muscle atrophy. We injected 7-week–old C57/BL6 mice with LLC1 tumor cells or vehicle. After 21 days, tumor-bearing mice exhibited ...
Source: Journal of Biological Chemistry - December 18, 2020 Category: Chemistry Authors: Hawley E. Kunz, Jessica M. Dorschner, Taylor E. Berent, Thomas Meyer, Xuewei Wang, Aminah Jatoi, Rajiv Kumar, Ian R. Lanza Tags: Metabolism Source Type: research

Structural basis for allosteric regulation of pyruvate kinase M2 by phosphorylation and acetylation [Molecular Biophysics]
Pyruvate kinase muscle isoform 2 (PKM2) is a key glycolytic enzyme and transcriptional coactivator and is critical for tumor metabolism. In cancer cells, native tetrameric PKM2 is phosphorylated or acetylated, which initiates a switch to a dimeric/monomeric form that translocates into the nucleus, causing oncogene transcription. However, it is not known how these post-translational modifications (PTMs) disrupt the oligomeric state of PKM2. We explored this question via crystallographic and biophysical analyses of PKM2 mutants containing residues that mimic phosphorylation and acetylation. We find that the PTMs elicit major...
Source: Journal of Biological Chemistry - December 18, 2020 Category: Chemistry Authors: Suparno Nandi, Mortezaali Razzaghi, Dhiraj Srivastava, Mishtu Dey Tags: Enzymology Source Type: research

N-acetylglucosamine drives myelination by triggering oligodendrocyte precursor cell differentiation [Molecular Bases of Disease]
Myelination plays an important role in cognitive development and in demyelinating diseases like multiple sclerosis (MS), where failure of remyelination promotes permanent neuro-axonal damage. Modification of cell surface receptors with branched N-glycans coordinates cell growth and differentiation by controlling glycoprotein clustering, signaling, and endocytosis. GlcNAc is a rate-limiting metabolite for N-glycan branching. Here we report that GlcNAc and N-glycan branching trigger oligodendrogenesis from precursor cells by inhibiting platelet-derived growth factor receptor-α cell endocytosis. Supplying oral GlcNAc to...
Source: Journal of Biological Chemistry - December 18, 2020 Category: Chemistry Authors: Michael Sy, Alexander U. Brandt, Sung-Uk Lee, Barbara L. Newton, Judy Pawling, Autreen Golzar, Anas M. A. Rahman, Zhaoxia Yu, Graham Cooper, Michael Scheel, Friedemann Paul, James W. Dennis, Michael Demetriou Tags: Glycobiology and Extracellular Matrices Source Type: research

Mapping invisible epitopes by NMR spectroscopy [Molecular Biophysics]
Defining discontinuous antigenic epitopes remains a substantial challenge, as exemplified by the case of lipid transfer polyproteins, which are common pollen allergens. Hydrogen/deuterium exchange monitored by NMR can be used to map epitopes onto folded protein surfaces, but only if the complex rapidly dissociates. Modifying the standard NMR-exchange measurement to detect substoichiometric complexes overcomes this time scale limitation and provides new insights into recognition of lipid transfer polyprotein by antibodies. In the future, this new and exciting development should see broad application to a range of tight macr...
Source: Journal of Biological Chemistry - December 18, 2020 Category: Chemistry Authors: Emery T. Usher, Scott A. Showalter Tags: Editors ' Picks Highlights Source Type: research

Hydrogen/deuterium exchange memory NMR reveals structural epitopes involved in IgE cross-reactivity of allergenic lipid transfer proteins [Protein Structure and Folding]
Identification of antibody-binding epitopes is crucial to understand immunological mechanisms. It is of particular interest for allergenic proteins with high cross-reactivity as observed in the lipid transfer protein (LTP) syndrome, which is characterized by severe allergic reactions. Art v 3, a pollen LTP from mugwort, is frequently involved in this cross-reactivity, but no antibody-binding epitopes have been determined so far. To reveal human IgE-binding regions of Art v 3, we produced three murine high-affinity mAbs, which showed 70–90% coverage of the allergenic epitopes from mugwort pollen–allergic patient...
Source: Journal of Biological Chemistry - December 18, 2020 Category: Chemistry Authors: Martina Di Muzio, Sabrina Wildner, Sara Huber, Michael Hauser, Eva Vejvar, Werner Auzinger, Christof Regl, Josef Laimer, Danila Zennaro, Nicole Wopfer, Christian G. Huber, Ronald van Ree, Adriano Mari, Peter Lackner, Fatima Ferreira, Mario Schubert, Gabri Tags: Editors ' Picks Source Type: research

FRET and optical trapping reveal mechanisms of actin activation of the power stroke and phosphate release in myosin V [Enzymology]
Myosins generate force and motion by precisely coordinating their mechanical and chemical cycles, but the nature and timing of this coordination remains controversial. We utilized a FRET approach to examine the kinetics of structural changes in the force-generating lever arm in myosin V. We directly compared the FRET results with single-molecule mechanical events examined by optical trapping. We introduced a mutation (S217A) in the conserved switch I region of the active site to examine how myosin couples structural changes in the actin- and nucleotide-binding regions with force generation. Specifically, S217A enhanced the...
Source: Journal of Biological Chemistry - December 18, 2020 Category: Chemistry Authors: Laura K. Gunther, John A. Rohde, Wanjian Tang, Joseph A. Cirilo Jr., Christopher P. Marang, Brent D. Scott, David D. Thomas, Edward P. Debold, Christopher M. Yengo Tags: Editors ' Picks Source Type: research

Correction: Functional domain and motif analyses of androgen receptor coregulator ARA70 and its differential expression in prostate cancer. [Additions and Corrections]
VOLUME 279 (2004) PAGES 33438–33446For Fig. 1B, the second, third, and fifth panels were mistakenly duplicated during article preparation as no yeast colonies were observed in these conditions. The corrected images are presented in the revised Fig. 1B. This correction does not affect the results or conclusions of the work. The authors apologize for the error.jbc;295/50/17382/F1F1F1Figure 1B. (Source: Journal of Biological Chemistry)
Source: Journal of Biological Chemistry - December 11, 2020 Category: Chemistry Authors: Yueh-Chiang Hu, Shuyuan Yeh, Shauh-Der Yeh, Erik R. Sampson, Jiaoti Huang, Peng Li, Cheng-Lung Hsu, Huei-Ju Ting, Hui-Kuan Lin, Liang Wang, Eungseok Kim, Jing Ni, Chawnshang Chang Tags: Additions and Corrections Source Type: research

Withdrawal: FGF16 promotes invasive behavior of SKOV-3 ovarian cancer cells through activation of mitogen-activated protein kinase (MAPK) signaling pathway. [Withdrawals/Retractions]
This article has been withdrawn by the authors. There were undeclared splices in Fig. 2 (d and e). In addition, the bands in Fig. 2e are shown as migrating at the same molecular weight; however, upon analysis of the original data, they were migrating at different molecular weights. The immunoblots of Fig. 4b active β-catenin and Fig. 8B CaMKII of Basu and Roy (2013) J. Biol. Chem. 288, 4355–4367 have been reused as Fig. 5g, corresponding to FGF16, and as Fig. 6a, corresponding to tubulin, respectively. Panels A and D from Fig. 6e presented the same data with different brightness. The authors affirm that the expe...
Source: Journal of Biological Chemistry - December 11, 2020 Category: Chemistry Authors: Moitri Basu, Satinath Mukhopadhyay, Uttara Chatterjee, Sib Sankar Roy Tags: Withdrawals/Retractions Source Type: research

Mycobacteria excise DNA damage in 12- or 13-nucleotide-long oligomers by prokaryotic-type dual incisions and performs transcription-coupled repair [Genomics and Proteomics]
In nucleotide excision repair, bulky DNA lesions such as UV-induced cyclobutane pyrimidine dimers are removed from the genome by concerted dual incisions bracketing the lesion, followed by gap filling and ligation. So far, two dual-incision patterns have been discovered: the prokaryotic type, which removes the damage in 11–13-nucleotide-long oligomers, and the eukaryotic type, which removes the damage in 24–32-nucleotide-long oligomers. However, a recent study reported that the UvrC protein of Mycobacterium tuberculosis removes damage in a manner analogous to yeast and humans in a 25-mer oligonucleotide arising...
Source: Journal of Biological Chemistry - December 11, 2020 Category: Chemistry Authors: Christopher P. Selby, Laura A. Lindsey-Boltz, Yanyan Yang, Aziz Sancar Tags: Accelerated Communications Source Type: research

Unusual zwitterionic catalytic site of SARS-CoV-2 main protease revealed by neutron crystallography [Enzymology]
The main protease (3CL Mpro) from SARS–CoV-2, the etiological agent of COVID-19, is an essential enzyme for viral replication. 3CL Mpro possesses an unusual catalytic dyad composed of Cys145 and His41 residues. A critical question in the field has been what the protonation states of the ionizable residues in the substrate-binding active-site cavity are; resolving this point would help understand the catalytic details of the enzyme and inform rational drug development against this pernicious virus. Here, we present the room-temperature neutron structure of 3CL Mpro, which allowed direct determination of hydrogen atom ...
Source: Journal of Biological Chemistry - December 11, 2020 Category: Chemistry Authors: Daniel W. Kneller, Gwyndalyn Phillips, Kevin L. Weiss, Swati Pant, Qiu Zhang, Hugh M. O'Neill, Leighton Coates, Andrey Kovalevsky Tags: Molecular Bases of Disease Source Type: research

Post-translational regulation of the maȷor drug transporters in the families of organic anion transporters and organic anion-transporting polypeptides [Protein Structure and Folding]
The organic anion transporters (OATs) and organic anion–transporting polypeptides (OATPs) belong to the solute carrier (SLC) transporter superfamily and play important roles in handling various endogenous and exogenous compounds of anionic charge. The OATs and OATPs are often implicated in drug therapy by impacting the pharmacokinetics of clinically important drugs and, thereby, drug exposure in the target organs or cells. Various mechanisms (e.g. genetic, environmental, and disease-related factors, drug-drug interactions, and food-drug interactions) can lead to variations in the expression and activity of the anion ...
Source: Journal of Biological Chemistry - December 11, 2020 Category: Chemistry Authors: Wooin Lee, Jeong-min Ha, Yuichi Sugiyama Tags: JBC Reviews Source Type: research

Site-specific contacts enable distinct modes of TRPV1 regulation by the potassium channel Kv{beta}1 subunit [Molecular Biophysics]
Transient receptor potential vanilloid 1 (TRPV1) channel is a multimodal receptor that is responsible for nociceptive, thermal, and mechanical sensations. However, which biomolecular partners specifically interact with TRPV1 remains to be elucidated. Here, we used cDNA library screening of genes from mouse dorsal root ganglia combined with patch-clamp electrophysiology to identify the voltage-gated potassium channel auxiliary subunit Kvβ1 physically interacting with TRPV1 channel and regulating its function. The interaction was validated in situ using endogenous dorsal root ganglia neurons, as well as a recombinant ex...
Source: Journal of Biological Chemistry - December 11, 2020 Category: Chemistry Authors: Yuanyuan Wang, Xiaoyi Mo, Conghui Ping, Qian Huang, Hao Zhang, Chang Xie, Bo Zhong, Dongdong Li, Jing Yao Tags: Cell Biology Source Type: research

A trade-off switch of two immunological memories in Caenorhabditis elegans reinfected by bacterial pathogens [Microbiology]
Recent studies have suggested that innate immune responses exhibit characteristics associated with memory linked to modulations in both vertebrates and invertebrates. However, the diverse evolutionary paths taken, particularly within the invertebrate taxa, should lead to similarly diverse innate immunity memory processes. Our understanding of innate immune memory in invertebrates primarily comes from studies of the fruit fly Drosophila melanogaster, the generality of which is unclear. Caenorhabditis elegans typically inhabits soil harboring a variety of fatal microbial pathogens; for this invertebrate, the innate immune sy...
Source: Journal of Biological Chemistry - December 11, 2020 Category: Chemistry Authors: Jinyuan Yan, Ninghui Zhao, Zhongshan Yang, Yuhong Li, Hua Bai, Wei Zou, Keqin Zhang, Xiaowei Huang Tags: Immunology Source Type: research

CDKN2A/p16INK4a suppresses hepatic fatty acid oxidation through the AMPK{alpha}2-SIRT1-PPAR{alpha} signaling pathway [Metabolism]
In addition to their well-known role in the control of cellular proliferation and cancer, cell cycle regulators are increasingly identified as important metabolic modulators. Several GWAS have identified SNPs near CDKN2A, the locus encoding for p16INK4a (p16), associated with elevated risk for cardiovascular diseases and type-2 diabetes development, two pathologies associated with impaired hepatic lipid metabolism. Although p16 was recently shown to control hepatic glucose homeostasis, it is unknown whether p16 also controls hepatic lipid metabolism. Using a combination of in vivo and in vitro approaches, we found that p16...
Source: Journal of Biological Chemistry - December 11, 2020 Category: Chemistry Authors: Yann Deleye, Alexia Karen Cotte, Sarah Anissa Hannou, Nathalie Hennuyer, Lucie Bernard, Bruno Derudas, Sandrine Caron, Vanessa Legry, Emmanuelle Vallez, Emilie Dorchies, Nathalie Martin, Steve Lancel, Jean Sebastien Annicotte, Kadiombo Bantubungi, Albin P Tags: Metabolism Source Type: research

Nonspecific DNA binding by P1 ParA determines the distribution of plasmid partition and repressor activities [Microbiology]
The faithful segregation, or “partition,” of many low-copy number bacterial plasmids is driven by plasmid-encoded ATPases that are represented by the P1 plasmid ParA protein. ParA binds to the bacterial nucleoid via an ATP-dependent nonspecific DNA (nsDNA)-binding activity, which is essential for partition. ParA also has a site-specific DNA-binding activity to the par operator (parOP), which requires either ATP or ADP, and which is essential for it to act as a transcriptional repressor but is dispensable for partition. Here we examine how DNA binding by ParA contributes to the relative distribution of its plasm...
Source: Journal of Biological Chemistry - December 11, 2020 Category: Chemistry Authors: Jamie C. Baxter, William G. Waples, Barbara E. Funnell Tags: DNA and Chromosomes Source Type: research

Leptin modulates pancreatic {beta}-cell membrane potential through Src kinase-mediated phosphorylation of NMDA receptors [Membrane Biology]
The adipocyte-derived hormone leptin increases trafficking of KATP and Kv2.1 channels to the pancreatic β-cell surface, resulting in membrane hyperpolarization and suppression of insulin secretion. We have previously shown that this effect of leptin is mediated by the NMDA subtype of glutamate receptors (NMDARs). It does so by potentiating NMDAR activity, thus enhancing Ca2+ influx and the ensuing downstream signaling events that drive channel trafficking to the cell surface. However, the molecular mechanism by which leptin potentiates NMDARs in β-cells remains unknown. Here, we report that leptin augments NMDAR ...
Source: Journal of Biological Chemistry - December 11, 2020 Category: Chemistry Authors: Veronica A. Cochrane, Yi Wu, Zhongying Yang, Assmaa ElSheikh, Jeremy Dunford, Paul Kievit, Dale A. Fortin, Show-Ling Shyng Tags: Signal Transduction Source Type: research

Optimized incorporation of an unnatural fluorescent amino acid affords measurement of conformational dynamics governing high-fidelity DNA replication [DNA and Chromosomes]
DNA polymerase from bacteriophage T7 undergoes large, substrate-induced conformational changes that are thought to account for high replication fidelity, but prior studies were adversely affected by mutations required to construct a Cys-lite variant needed for site-specific fluorescence labeling. Here we have optimized the direct incorporation of a fluorescent un-natural amino acid, (7-hydroxy-4-coumarin-yl)-ethylglycine, using orthogonal amber suppression machinery in Escherichia coli. MS methods verify that the unnatural amino acid is only incorporated at one position with minimal background. We show that the single fluo...
Source: Journal of Biological Chemistry - December 11, 2020 Category: Chemistry Authors: Tyler L. Dangerfield, Kenneth A. Johnson Tags: Enzymology Source Type: research