Metabolite sensing and signaling in cancer [Metabolism]
Metabolites are not only substrates in metabolic reactions, but also signaling molecules controlling a wide range of cellular processes. Discovery of the oncometabolite 2-hydroxyglutarate provides an important link between metabolic dysfunction and cancer, unveiling the signaling function of metabolites in regulating epigenetic and epitranscriptomic modifications, genome integrity, and signal transduction. It is now known that cancer cells remodel their metabolic network to support biogenesis, caused by or resulting in the dysregulation of various metabolites. Cancer cells can sense alterations in metabolic intermediates t...
Source: Journal of Biological Chemistry - August 14, 2020 Category: Chemistry Authors: Yi-Ping Wang, Jin-Tao Li, Jia Qu, Miao Yin, Qun-Ying Lei Tags: JBC Reviews Source Type: research

Cardiolipin-deficient cells have decreased levels of the iron-sulfur biogenesis protein frataxin [Molecular Bases of Disease]
Cardiolipin (CL) is the signature phospholipid of mitochondrial membranes, where it is synthesized locally and plays an important role in mitochondrial bioenergetics. Previous studies in the yeast model have indicated that CL is required for optimal iron homeostasis, which is disrupted by a mechanism not yet determined in the yeast CL mutant, crd1Δ. This finding has implications for the severe genetic disorder, Barth syndrome (BTHS), in which CL metabolism is perturbed because of mutations in the CL-remodeling enzyme, tafazzin. Here, we investigate the effects of tafazzin deficiency on iron homeostasis in the mouse m...
Source: Journal of Biological Chemistry - August 14, 2020 Category: Chemistry Authors: Yiran Li, Wenȷia Lou, Alexander Grevel, Lena Bottinger, Zhuqing Liang, Jiaȷia Ji, Vinay A. Patil, Jenney Liu, Cunqi Ye, Maik Huttemann, Thomas Becker, Miriam L. Greenberg Tags: Lipids Source Type: research

Disruption of insulin receptor substrate-2 impairs growth but not insulin function in rats [Signal Transduction]
Insulin receptor substrate (IRS)-2, along with IRS-1, is a key signaling molecule that mediates the action of insulin and insulin-like growth factor (IGF)-I. The activated insulin and IGF-I receptors phosphorylate IRSs on tyrosine residues, leading to the activation of downstream signaling pathways and the induction of various physiological functions of insulin and IGF-I. Studies using IRS-2 knockout (KO) mice showed that the deletion of IRS-2 causes type 2 diabetes due to peripheral insulin resistance and impaired β-cell function. However, little is known about the roles of IRS-2 in other animal models. Here, we crea...
Source: Journal of Biological Chemistry - August 14, 2020 Category: Chemistry Authors: Yuka Toyoshima, Katsuyuki Nakamura, Reiko Tokita, Naomi Teramoto, Hidetoshi Sugihara, Hisanori Kato, Keitaro Yamanouchi, Shiro Minami Tags: Metabolism Source Type: research

Axenfeld-Rieger syndrome-associated mutants of the transcription factor FOXC1 abnormally regulate NKX2-5 in model zebrafish embryos [Gene Regulation]
In this study, we demonstrate that FOXC1 does regulate human NKX2-5 expression in a dose-dependent manner via direct binding to its proximal promoter. A comparison of FOXC1 mutant function in the rat cardiac cell line H9c2 and zebrafish embryos suggested that the zebrafish embryos might serve as a more representative model system than the H9c2 cells. Finally, we noted that three of the Axenfeld-Rieger syndrome FOXC1 mutations tested increased, whereas a fourth repressed the expression of NKX2-5. These results imply that mutant FOXC1s might play etiological roles in CHD by abnormally regulating NKX2-5 in the patients. And z...
Source: Journal of Biological Chemistry - August 14, 2020 Category: Chemistry Authors: Qinxin Zhang, Dong Liang, Yunyun Yue, Luqingqing He, Nan Li, Dongya Jiang, Ping Hu, Qingshun Zhao Tags: Molecular Bases of Disease Source Type: research

The maturase HydF enables [FeFe] hydrogenase assembly via transient, cofactor-dependent interactions [Enzymology]
[FeFe] hydrogenases have attracted extensive attention in the field of renewable energy research because of their remarkable efficiency for H2 gas production. H2 formation is catalyzed by a biologically unique hexanuclear iron cofactor denoted the H-cluster. The assembly of this cofactor requires a dedicated maturation machinery including HydF, a multidomain [4Fe4S] cluster protein with GTPase activity. HydF is responsible for harboring and delivering a precatalyst to the apo-hydrogenase, but the details of this process are not well understood. Here, we utilize gas-phase electrophoretic macromolecule analysis to show that ...
Source: Journal of Biological Chemistry - August 14, 2020 Category: Chemistry Authors: Brigitta Nemeth, Henrik Land, Ann Magnuson, Anders Hofer, Gustav Berggren Tags: Molecular Biophysics Source Type: research

The NADPH oxidase NOX4 promotes the directed migration of endothelial cells by stabilizing vascular endothelial growth factor receptor 2 protein [Protein Synthesis and Degradation]
Directed migration of endothelial cells (ECs) is an important process during both physiological and pathological angiogenesis. The binding of vascular endothelial growth factor (VEGF) to VEGF receptor-2 (VEGFR-2) on the EC surface is necessary for directed migration of these cells. Here, we used TAXIScan, an optically accessible real-time horizontal cell dynamics assay approach, and demonstrate that reactive oxygen species (ROS)-producing NADPH oxidase 4 (NOX4), which is abundantly expressed in ECs, mediates VEGF/VEGFR-2-dependent directed migration. We noted that a continuous supply of endoplasmic reticulum (ER)-retained ...
Source: Journal of Biological Chemistry - August 14, 2020 Category: Chemistry Authors: Kei Miyano, Shuichiro Okamoto, Akira Yamauchi, Chikage Kawai, Mizuho Kajikawa, Takuya Kiyohara, Minoru Tamura, Masahiko Taura, Futoshi Kuribayashi Tags: Protein Synthesis and Degradation Source Type: research

Garcinoic acid prevents {beta}-amyloid (A{beta}) deposition in the mouse brain [Lipids]
In conclusion, GA holds potential for preventing Aβ oligomerization and deposition in the brain. The mechanistic aspects of GA's properties appear to be distinct from those of other vitamin E metabolites and of genistein. (Source: Journal of Biological Chemistry)
Source: Journal of Biological Chemistry - August 14, 2020 Category: Chemistry Authors: Rita Marinelli, Pierangelo Torquato, Desiree Bartolini, Cristina Mas–Bargues, Guido Bellezza, Antimo Gioiello, Consuelo Borras, Antonella De Luca, Francesca Fallarino, Bartolomeo Sebastiani, Sridhar Mani, Angelo Sidoni, Jose Vina, Manuela Leri, Moni Tags: Neurobiology Source Type: research

CaMKII enhances voltage-gated sodium channel Nav1.6 activity and neuronal excitability [Neurobiology]
Nav1.6 is the primary voltage-gated sodium channel isoform expressed in mature axon initial segments and nodes, making it critical for initiation and propagation of neuronal impulses. Thus, Nav1.6 modulation and dysfunction may have profound effects on input-output properties of neurons in normal and pathological conditions. Phosphorylation is a powerful and reversible mechanism regulating ion channel function. Because Nav1.6 and the multifunctional Ca2+/CaM-dependent protein kinase II (CaMKII) are independently linked to excitability disorders, we sought to investigate modulation of Nav1.6 function by CaMKII signaling. We...
Source: Journal of Biological Chemistry - August 14, 2020 Category: Chemistry Authors: Agnes S. Zybura, Anthony J. Baucum II, Anthony M. Rush, Theodore R. Cummins, Andy Hudmon Tags: Signal Transduction Source Type: research

Direct evidence for a new mode of plant defense against insects via a novel polygalacturonase-inhibiting protein expression strategy [Glycobiology and Extracellular Matrices]
Plant cell wall–associated polygalacturonase-inhibiting proteins (PGIPs) are widely distributed in the plant kingdom. They play a crucial role in plant defense against phytopathogens by inhibiting microbial polygalacturonases (PGs). PGs hydrolyze the cell wall polysaccharide pectin and are among the first enzymes to be secreted during plant infection. Recent studies demonstrated that herbivorous insects express their own PG multi-gene families, raising the question whether PGIPs also inhibit insect PGs and protect plants from herbivores. Preliminary evidence suggested that PGIPs may negatively influence larval growth...
Source: Journal of Biological Chemistry - August 14, 2020 Category: Chemistry Authors: Wiebke Haeger, Jana Henning, David G. Heckel, Yannick Pauchet, Roy Kirsch Tags: Plant Biology Source Type: research

Methyltransferase-like 21C (METTL21C) methylates alanine tRNA synthetase at Lys-943 in muscle tissue [Enzymology]
Protein-lysine methylation is a common posttranslational modification (PTM) throughout the human proteome that plays important roles in diverse biological processes. In humans, there are>100 known and candidate protein lysine methyltransferases (PKMTs), many of which are linked to human diseases. Methyltransferase-like protein 21C (METTL21C) is a PKMT implicated in muscle biology that has been reported to methylate valosin-containing protein/p97 (VCP) and heat shock 70-kDa protein 8 (HSPA8). However, a clear in vitro methyltransferase activity for METTL21C remains yet to be demonstrated, and whether it is an active enzy...
Source: Journal of Biological Chemistry - August 14, 2020 Category: Chemistry Authors: Muhammad Zoabi, Lichao Zhang, Tie-Mei Li, Josh E. Elias, Scott M. Carlson, Or Gozani Tags: Signal Transduction Source Type: research

Staphylococcus aureus induces cell-surface expression of immune stimulatory NKG2D ligands on human monocytes [Microbiology]
Staphylococcus aureus is among the leading causes of bacterial infections worldwide. The pathogenicity and establishment of S. aureus infections are tightly linked to its ability to modulate host immunity. Persistent infections are often associated with mutant staphylococcal strains that have decreased susceptibility to antibiotics; however, little is known about how these mutations influence bacterial interaction with the host immune system. Here, we discovered that clinical S. aureus isolates activate human monocytes, leading to cell-surface expression of immune stimulatory natural killer group 2D (NKG2D) ligands on the ...
Source: Journal of Biological Chemistry - August 14, 2020 Category: Chemistry Authors: Maiken Mellergaard, Rikke Illum Hogh, Astrid Lund, Blanca Irene Aldana, Romain Guerillot, Sofie Hedlund Moller, Ashleigh S. Hayes, Nafsika Panagiotopoulou, Zofiȷa Frimand, Stine Dam Jepsen, Camilla Hartmann Friis Hansen, Lars Andresen, Anders Rhod Tags: Immunology Source Type: research

Characterization of the nonheme iron center of cysteamine dioxygenase and its interaction with substrates [Enzymology]
Cysteamine dioxygenase (ADO) has been reported to exhibit two distinct biological functions with a nonheme iron center. It catalyzes oxidation of both cysteamine in sulfur metabolism and N-terminal cysteine-containing proteins or peptides, such as regulator of G protein signaling 5 (RGS5). It thereby preserves oxygen homeostasis in a variety of physiological processes. However, little is known about its catalytic center and how it interacts with these two types of primary substrates in addition to O2. Here, using electron paramagnetic resonance (EPR), Mössbauer, and UV-visible spectroscopies, we explored the binding m...
Source: Journal of Biological Chemistry - August 14, 2020 Category: Chemistry Authors: Yifan Wang, Ian Davis, Yan Chan, Sunil G. Naik, Wendell P. Griffith, Aimin Liu Tags: Molecular Biophysics Source Type: research

The WD40-repeat protein WDR-48 promotes the stability of the deubiquitinating enzyme USP-46 by inhibiting its ubiquitination and degradation [Cell Biology]
Ubiquitination is a reversible post-translational modification that has emerged as a critical regulator of synapse development and function. However, the mechanisms that regulate the deubiquitinating enzymes (DUBs) responsible for the removal of ubiquitin from target proteins are poorly understood. We have previously shown that the DUB ubiquitin-specific protease 46 (USP-46) removes ubiquitin from the glutamate receptor GLR-1 and regulates its trafficking and degradation in Caenorhabditis elegans. We found that the WD40-repeat proteins WDR-20 and WDR-48 bind and stimulate the catalytic activity of USP-46. Here, we identifi...
Source: Journal of Biological Chemistry - August 14, 2020 Category: Chemistry Authors: Molly Hodul, Rakesh Ganji, Caroline L. Dahlberg, Malavika Raman, Peter Juo Tags: Protein Synthesis and Degradation Source Type: research

Ubiquitination of interleukin-1{alpha} is associated with increased pro-inflammatory polarization of murine macrophages deficient in the E3 ligase ITCH [Cell Biology]
In conclusion, ubiquitination of IL-1α is associated with increased pro-inflammatory polarization of macrophages deficient in the E3 ligase ITCH. (Source: Journal of Biological Chemistry)
Source: Journal of Biological Chemistry - August 14, 2020 Category: Chemistry Authors: Xi Lin, Hengwei Zhang, Brendan F. Boyce, Lianping Xing Tags: Cell Biology Source Type: research

The deubiquitinase USP7 uses a distinct ubiquitin-like domain to deubiquitinate NF-ĸB subunits [Gene Regulation]
The transcription factor NF-ĸB is a master regulator of the innate immune response and plays a central role in inflammatory diseases by mediating the expression of pro-inflammatory cytokines. Ubiquitination-triggered proteasomal degradation of DNA-bound NF-ĸB strongly limits the expression of its target genes. Conversely, USP7 (deubiquitinase ubiquitin-specific peptidase 7) opposes the activities of E3 ligases, stabilizes DNA-bound NF-ĸB, and thereby promotes NF-ĸB–mediated transcription. Using gene expression and synthetic peptide arrays on membrane support and overlay analyses, we found here that inhibiting USP...
Source: Journal of Biological Chemistry - August 14, 2020 Category: Chemistry Authors: Izaskun Mitxitorena, Domenico Somma, Jennifer P. Mitchell, Matti Lepisto, Christian Tyrchan, Emma L. Smith, Patrick A. Kiely, Helen Walden, Karen Keeshan, Ruaidhri J. Carmody Tags: Protein Synthesis and Degradation Source Type: research

SARS-CoV-2 (COVID-19) structural and evolutionary dynamicome: Insights into functional evolution and human genomics [Computational Biology]
The pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has challenged the speed at which laboratories can discover the viral composition and study health outcomes. The small ∼30-kb ssRNA genome of coronaviruses makes them adept at cross-species spread while enabling a robust understanding of all of the proteins the viral genome encodes. We have employed protein modeling, molecular dynamics simulations, evolutionary mapping, and 3D printing to gain a full proteome- and dynamicome-level understanding of SARS-CoV-2. We established the Viral Integrated Structural Evolution Dynamic Database (VIS...
Source: Journal of Biological Chemistry - August 14, 2020 Category: Chemistry Authors: Ruchir Gupta, Jacob Charron, Cynthia L. Stenger, Jared Painter, Hunter Steward, Taylor W. Cook, William Faber, Austin Frisch, Eric Lind, Jacob Bauss, Xiaopeng Li, Olivia Sirpilla, Xavier Soehnlen, Adam Underwood, David Hinds, Michele Morris, Neil Lamb, Jo Tags: Genomics and Proteomics Source Type: research

In-cell infrared difference spectroscopy of LOV photoreceptors reveals structural responses to light altered in living cells [Methods and Resources]
Proteins are usually studied in well-defined buffer conditions, which differ substantially from those within a host cell. In some cases, the intracellular environment has an impact on the mechanism, which might be missed by in vitro experiments. IR difference spectroscopy previously has been applied to study the light-induced response of photoreceptors and photoenzymes in vitro. Here, we established the in-cell IR difference (ICIRD) spectroscopy in the transmission and attenuated total reflection configuration to investigate the light-induced response of soluble proteins in living bacterial cells. ICIRD spectroscopy on the...
Source: Journal of Biological Chemistry - August 14, 2020 Category: Chemistry Authors: Lukas Goett–Zink, Jessica L. Klocke, Lena A. K. Bogeholz, Tilman Kottke Tags: Molecular Biophysics Source Type: research

Muscarinic-dependent phosphorylation of the cardiac ryanodine receptor by protein kinase G is mediated by PI3K-AKT-nNOS signaling [Cell Biology]
Post-translational modifications of proteins involved in calcium handling in myocytes, such as the cardiac ryanodine receptor (RyR2), critically regulate cardiac contractility. Recent studies have suggested that phosphorylation of RyR2 by protein kinase G (PKG) might contribute to the cardioprotective effects of cholinergic stimulation. However, the specific mechanisms underlying these effects remain unclear. Here, using murine ventricular myocytes, immunoblotting, proximity ligation as-says, and nitric oxide imaging, we report that phosphorylation of Ser-2808 in RyR2 induced by the muscarinic receptor agonist carbachol is...
Source: Journal of Biological Chemistry - August 14, 2020 Category: Chemistry Authors: Stephen Baine, Justin Thomas, Ingrid Bonilla, Marina Ivanova, Andriy Belevych, Jiaoni Li, Rengasayee Veeraraghavan, Przemyslaw B. Radwanski, Cynthia Carnes, Sandor Gyorke Tags: Signal Transduction Source Type: research

The transcriptional repressor BCL11A promotes breast cancer metastasis [RNA]
The phenotypes of each breast cancer subtype are defined by their transcriptomes. However, the transcription factors that regulate differential patterns of gene expression that contribute to specific disease outcomes are not well understood. Here, using gene silencing and overexpression approaches, RNA-Seq, and splicing analysis, we report that the transcription factor B-cell leukemia/lymphoma 11A (BCL11A) is highly expressed in triple-negative breast cancer (TNBC) and drives metastatic disease. Moreover, BCL11A promotes cancer cell invasion by suppressing the expression of muscleblind-like splicing regulator 1 (MBNL1), a ...
Source: Journal of Biological Chemistry - August 14, 2020 Category: Chemistry Authors: Darcie D. Seachrist, Molly M. Hannigan, Natasha N. Ingles, Bryan M. Webb, Kristen L. Weber-Bonk, Peng Yu, Gurkan Bebek, Salendra Singh, Steven T. Sizemore, Vinay Varadan, Donny D. Licatalosi, Ruth A. Keri Tags: Gene Regulation Source Type: research

5'-UTR recruitment of the translation initiation factor eIF4GI or DAP5 drives cap-independent translation of a subset of human mRNAs [Protein Synthesis and Degradation]
During unfavorable conditions (e.g. tumor hypoxia or viral infection), canonical, cap-dependent mRNA translation is suppressed in human cells. Nonetheless, a subset of physiologically important mRNAs (e.g. hypoxia-inducible factor 1α [HIF-1α], fibroblast growth factor 9 [FGF-9], and p53) is still translated by an unknown, cap-independent mechanism. Additionally, expression levels of eukaryotic translation initiation factor 4GI (eIF4GI) and of its homolog, death-associated protein 5 (DAP5), are elevated. By examining the 5′ UTRs of HIF-1α, FGF-9, and p53 mRNAs and using fluorescence anisotropy bindin...
Source: Journal of Biological Chemistry - August 14, 2020 Category: Chemistry Authors: Solomon A. Haizel, Usha Bhardwaj, Ruben L. Gonzalez Jr., Somdeb Mitra, Dixie J. Goss Tags: Gene Regulation Source Type: research

PRL3 pseudophosphatase activity is necessary and sufficient to promote metastatic growth [Protein Structure and Folding]
Phosphatases of regenerating liver (PRLs) are markers of cancer and promote tumor growth. They have been implicated in a variety of biochemical pathways but the physiologically relevant target of phosphatase activity has eluded 20 years of investigation. Here, we show that PRL3 catalytic activity is not required in a mouse model of metastasis. PRL3 binds and inhibits CNNM4, a membrane protein associated with magnesium transport. Analysis of PRL3 mutants specifically defective in either CNNM-binding or phosphatase activity demonstrate that CNNM binding is necessary and sufficient to promote tumor metastasis. As PRLs do have...
Source: Journal of Biological Chemistry - August 14, 2020 Category: Chemistry Authors: Guennadi Kozlov, Yosuke Funato, Yu Seby Chen, Zhidian Zhang, Katalin Illes, Hiroaki Miki, Kalle Gehring Tags: Signal Transduction Source Type: research

Runt-related transcription factor 1 is required for murine osteoblast differentiation and bone formation [Gene Regulation]
In conclusion, RUNX1 up-regulates the expression of Runx2 and multiple bone-specific genes, and plays an indispensable role in bone formation and homeostasis in both trabecular and cortical bone. We propose that stimulating Runx1 activity may be useful in therapeutic approaches for managing some bone diseases such as osteoporosis. (Source: Journal of Biological Chemistry)
Source: Journal of Biological Chemistry - August 14, 2020 Category: Chemistry Authors: Jun Tang, Jing Xie, Wei Chen, Chenyi Tang, Jinjin Wu, Yiping Wang, Xue-Dong Zhou, Hou-De Zhou, Yi-Ping Li Tags: Cell Biology Source Type: research

Crystal structures of human PAICS reveal substrate and product binding of an emerging cancer target [Enzymology]
The bifunctional human enzyme phosphoribosylaminoimidazole carboxylase and phosphoribosylaminoimidazolesuccinocarboxamide synthetase (PAICS) catalyzes two essential steps in the de novo purine biosynthesis pathway. PAICS is overexpressed in many cancers and could be a promising target for the development of cancer therapeutics. Here, using gene knockdowns and clonogenic survival and cell viability assays, we demonstrate that PAICS is required for growth and survival of prostate cancer cells. PAICS catalyzes the carboxylation of aminoimidazole ribonucleotide (AIR) and the subsequent conversion of carboxyaminoimidazole ribon...
Source: Journal of Biological Chemistry - August 14, 2020 Category: Chemistry Authors: Jana Škerlova, Judith Unterlass, Mona Gottmann, Petra Marttila, Evert Homan, Thomas Helleday, Ann–Sofie Jemth, Pal Stenmark Tags: Enzymology Source Type: research

A Lynch syndrome-associated mutation at a Bergerat ATP-binding fold destabilizes the structure of the DNA mismatch repair endonuclease MutL [DNA and Chromosomes]
In humans, mutations in genes encoding homologs of the DNA mismatch repair endonuclease MutL cause a hereditary cancer that is known as Lynch syndrome. Here, we determined the crystal structures of the N-terminal domain (NTD) of MutL from the thermophilic eubacterium Aquifex aeolicus (aqMutL) complexed with ATP analogs at 1.69–1.73 Å. The structures revealed significant structural similarities to those of a human MutL homolog, postmeiotic segregation increased 2 (PMS2). We introduced five Lynch syndrome-associated mutations clinically found in human PMS2 into the aqMutL NTD and investigated the protein stabilit...
Source: Journal of Biological Chemistry - August 14, 2020 Category: Chemistry Authors: Keisuke Izuhara, Kenji Fukui, Takeshi Murakawa, Seiki Baba, Takashi Kumasaka, Kazuhisa Uchiyama, Takato Yano Tags: Molecular Bases of Disease Source Type: research

Structural insights into emergent signaling modes of G protein-coupled receptors [Protein Structure and Folding]
G protein–coupled receptors (GPCRs) represent the largest family of cell membrane proteins, with>800 GPCRs in humans alone, and recognize highly diverse ligands, ranging from photons to large protein molecules. Very important to human medicine, GPCRs are targeted by about 35% of prescription drugs. GPCRs are characterized by a seven-transmembrane α-helical structure, transmitting extracellular signals into cells to regulate major physiological processes via heterotrimeric G proteins and β-arrestins. Initially viewed as receptors whose signaling via G proteins is delimited to the plasma membrane, it is n...
Source: Journal of Biological Chemistry - August 14, 2020 Category: Chemistry Authors: Ieva Sutkeviciute, Jean-Pierre Vilardaga Tags: JBC Reviews Source Type: research

The RNA-binding protein PTBP1 promotes ATPase-dependent dissociation of the RNA helicase UPF1 to protect transcripts from nonsense-mediated mRNA decay [RNA]
The sequence-specific RNA-binding proteins PTBP1 (polypyrimidine tract–binding protein 1) and HNRNP L (heterogeneous nuclear ribonucleoprotein L) protect mRNAs from nonsense-mediated decay (NMD) by preventing the UPF1 RNA helicase from associating with potential decay targets. Here, by analyzing in vitro helicase activity, dissociation of UPF1 from purified mRNPs, and transcriptome-wide UPF1 RNA binding, we present the mechanistic basis for inhibition of NMD by PTBP1. Unlike mechanisms of RNA stabilization that depend on direct competition for binding sites among protective RNA-binding proteins and decay factors, PTB...
Source: Journal of Biological Chemistry - August 14, 2020 Category: Chemistry Authors: Sarah E. Fritz, Soumya Ranganathan, Clara D. Wang, J. Robert Hogg Tags: Gene Regulation Source Type: research

Unique features of the ketosynthase domain in a nonribosomal peptide synthetase-polyketide synthase hybrid enzyme, tenuazonic acid synthetase 1 [Protein Structure and Folding]
Many microbial secondary metabolites are produced by multienzyme complexes comprising nonribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs). The ketosynthase (KS) domains of polyketide synthase normally catalyze the decarboxylative Claisen condensation of acyl and malonyl blocks to extend the polyketide chain. However, the terminal KS domain in tenuazonic acid synthetase 1 (TAS1) from the fungus Pyricularia oryzae conducts substrate cyclization. Here, we report on the unique features of the KS domain in TAS1. We observed that this domain is monomeric, not dimeric as is typical for KSs. Analysis of a 1.68...
Source: Journal of Biological Chemistry - August 14, 2020 Category: Chemistry Authors: Choong-Soo Yun, Kazuki Nishimoto, Takayuki Motoyama, Takeshi Shimizu, Tomoya Hino, Naoshi Dohmae, Shingo Nagano, Hiroyuki Osada Tags: Enzymology Source Type: research

Pterocarpan synthase (PTS) structures suggest a common quinone methide-stabilizing function in dirigent proteins and proteins with dirigent-like domains [Plant Biology]
The biochemical activities of dirigent proteins (DPs) give rise to distinct complex classes of plant phenolics. DPs apparently began to emerge during the aquatic-to-land transition, with phylogenetic analyses revealing the presence of numerous DP subfamilies in the plant kingdom. The vast majority (>95%) of DPs in these large multigene families still await discovery of their biochemical functions. Here, we elucidated the 3D structures of two pterocarpan-forming proteins with dirigent-like domains. Both proteins stereospecifically convert distinct diastereomeric chiral isoflavonoid precursors to the chiral pterocarpans, ...
Source: Journal of Biological Chemistry - August 14, 2020 Category: Chemistry Authors: Qingyan Meng, Syed G. A. Moinuddin, Sung-Jin Kim, Diana L. Bedgar, Michael A. Costa, Dennis G. Thomas, Robert P. Young, Clyde A. Smith, John R. Cort, Laurence B. Davin, Norman G. Lewis Tags: Protein Structure and Folding Source Type: research

An astrocyte cell line that differentially propagates murine prions [Microbiology]
Prion diseases are fatal infectious neurodegenerative disorders in human and animals caused by misfolding of the cellular prion protein (PrPC) into the pathological isoform PrPSc. Elucidating the molecular and cellular mechanisms underlying prion propagation may help to develop disease interventions. Cell culture systems for prion propagation have greatly advanced molecular insights into prion biology, but translation of in vitro to in vivo findings is often disappointing. A wider range of cell culture systems might help overcome these shortcomings. Here, we describe an immortalized mouse neuronal astrocyte cell line (C8D1...
Source: Journal of Biological Chemistry - August 14, 2020 Category: Chemistry Authors: Waqas Tahir, Basant Abdulrahman, Dalia H. Abdelaziz, Simrika Thapa, Rupali Walia, Hermann M. Schatzl Tags: Molecular Bases of Disease Source Type: research

The guanine nucleotide exchange factor VAV3 participates in ERBB4-mediated cancer cell migration [Cell Biology]
ERBB4 is a member of the epidermal growth factor receptor (EGFR)/ERBB subfamily of receptor tyrosine kinases that regulates cellular processes including proliferation, migration, and survival. ERBB4 signaling is involved in embryogenesis and homeostasis of healthy adult tissues, but also in human pathologies such as cancer, neurological disorders, and cardiovascular diseases. Here, an MS-based analysis revealed the Vav guanine nucleotide exchange factor 3 (VAV3), an activator of Rho family GTPases, as a critical ERBB4-interacting protein in breast cancer cells. We confirmed the ERBB4–VAV3 interaction by targeted MS a...
Source: Journal of Biological Chemistry - August 14, 2020 Category: Chemistry Authors: Veera K. Oȷala, Anna M. Knittle, Peppi Kirȷalainen, Johannes A. M. Merilahti, Maarit Kortesoȷa, Denis Tvorogov, Katri Vaparanta, Shuȷun Lin, Jurgen Kast, Arto T. Pulliainen, Kari J. Kurppa, Klaus Elenius Tags: Signal Transduction Source Type: research

The polycomb proteins EZH1 and EZH2 co-regulate chromatin accessibility and nephron progenitor cell lifespan in mice [Developmental Biology]
SIX2 (SIX homeobox 2)–positive nephron progenitor cells (NPCs) give rise to all epithelial cell types of the nephron, the filtering unit of the kidney. NPCs have a limited lifespan and are depleted near the time of birth. Epigenetic factors are implicated in the maintenance of organ-restricted progenitors such as NPCs, but the chromatin-based mechanisms are incompletely understood. Here, using a combination of gene targeting, chromatin profiling, and single-cell RNA analysis, we examined the role of the murine histone 3 Lys-27 (H3K27) methyltransferases EZH1 (enhancer of zeste 1) and EZH2 in NPC maintenance. We found...
Source: Journal of Biological Chemistry - August 14, 2020 Category: Chemistry Authors: Hongbing Liu, Sylvia Hilliard, Elizabeth Kelly, Chao-Hui Chen, Zubaida Saifudeen, Samir S. El-Dahr Tags: Developmental Biology Source Type: research

Discordance between GLP-1R gene and protein expression in mouse pancreatic islet cells [Molecular Bases of Disease]
The insulinotropic actions of glucagon-like peptide 1 receptor (GLP-1R) in β-cells have made it a useful target to manage type 2 diabetes. Metabolic stress reduces β-cell sensitivity to GLP-1, yet the underlying mechanisms are unknown. We hypothesized that Glp1r expression is heterogeneous among β-cells and that metabolic stress decreases the number of GLP-1R–positive β-cells. Here, analyses of publicly available single-cell RNA-Seq sequencing (scRNASeq) data from mouse and human β-cells indicated that significant populations of β-cells do not express the Glp1r gene, supporting heterogen...
Source: Journal of Biological Chemistry - August 14, 2020 Category: Chemistry Authors: Sarah M. Gray, Yurong Xin, Elizabeth C. Ross, Bryanna M. Chazotte, Megan E. Capozzi, Kimberley El, Berit Svendsen, Peter Ravn, Kyle W. Sloop, Jenny Tong, Jesper Gromada, Jonathan E. Campbell, David A. D'Alessio Tags: Metabolism Source Type: research

Viperin: An ancient radical SAM enzyme finds its place in modern cellular metabolism and innate immunity [Immunology]
Viperin plays an important and multifaceted role in the innate immune response to viral infection. Viperin is also notable as one of very few radical SAM–dependent enzymes present in higher animals; however, the enzyme appears broadly conserved across all kingdoms of life, which suggests that it represents an ancient defense mechanism against viral infections. Although viperin was discovered some 20 years ago, only recently was the enzyme's structure determined and its catalytic activity elucidated. The enzyme converts CTP to 3′-deoxy-3′,4′-didehydro-CTP, which functions as novel chain-terminating a...
Source: Journal of Biological Chemistry - August 14, 2020 Category: Chemistry Authors: Soumi Ghosh, E. Neil G. Marsh Tags: JBC Reviews Source Type: research

Photoaffinity labeling identifies an intersubunit steroid-binding site in heteromeric GABA type A (GABAA) receptors [Neurobiology]
Allopregnanolone (3α5α-P), pregnanolone, and their synthetic derivatives are potent positive allosteric modulators (PAMs) of GABAA receptors (GABAARs) with in vivo anesthetic, anxiolytic, and anti-convulsant effects. Mutational analysis, photoaffinity labeling, and structural studies have provided evidence for intersubunit and intrasubunit steroid-binding sites in the GABAAR transmembrane domain, but revealed only little definition of their binding properties. Here, we identified steroid-binding sites in purified human α1β3 and α1β3γ2 GABAARs by photoaffinity labeling with [3H]21-[4-...
Source: Journal of Biological Chemistry - August 14, 2020 Category: Chemistry Authors: Selwyn S. Jayakar, David C. Chiara, Xiaojuan Zhou, Bo Wu, Karol S. Bruzik, Keith W. Miller, Jonathan B. Cohen Tags: Protein Structure and Folding Source Type: research

T cell receptor interactions with human leukocyte antigen govern indirect peptide selectivity for the cancer testis antigen MAGE-A4 [Molecular Biophysics]
T cell-mediated immunity is governed primarily by T cell receptor (TCR) recognition of peptide-human leukocyte antigen (pHLA) complexes and is essential for immunosurveillance and disease control. This interaction is generally stabilized by interactions between the HLA surface and TCR germline-encoded complementarity-determining region (CDR) loops 1 and 2, whereas peptide selectivity is guided by direct interactions with the TCR CDR3 loops. Here, we solved the structure of a newly identified TCR in complex with a clinically relevant peptide derived from the cancer testis antigen melanoma antigen-A4 (MAGE-A4). The TCR bound...
Source: Journal of Biological Chemistry - August 14, 2020 Category: Chemistry Authors: Charlotte H. Coles, Catriona McMurran, Angharad Lloyd, Miriam Hock, Linda Hibbert, Marine C. C. Raman, Conor Hayes, Patrick Lupardus, David K. Cole, Stephen Harper Tags: Immunology Source Type: research

The Spo7 sequence LLI is required for Nem1-Spo7/Pah1 phosphatase cascade function in yeast lipid metabolism [Signal Transduction]
The Nem1-Spo7 complex in the yeast Saccharomyces cerevisiae is a protein phosphatase that catalyzes the dephosphory-lation of Pah1 phosphatidate phosphatase, required for its translocation to the nuclear/endoplasmic reticulum membrane. The Nem1–Spo7/Pah1 phosphatase cascade plays a major role in triacylglycerol synthesis and in the regulation of phospholipid synthesis. In this work, we examined Spo7, a regulatory subunit required for Nem1 catalytic function, to identify residues that govern formation of the Nem1-Spo7 complex. By deletion analysis of Spo7, we identified a hydrophobic Leu-Leu-Ile (LLI) sequence compris...
Source: Journal of Biological Chemistry - August 14, 2020 Category: Chemistry Authors: Mona Mirheydari, Prabuddha Dey, Geordan J. Stukey, Yeonhee Park, Gil-Soo Han, George M. Carman Tags: Lipids Source Type: research

Loss of the RNA-binding protein Rbm15 disrupts liver maturation in zebrafish [Developmental Biology]
Liver organogenesis begins with hepatic precursors in the foregut endoderm, followed by hepatoblast specification, differentiation, outgrowth, and maturation for the formation of functional hepatocytes. Although several signaling pathways and critical factors that regulate liver specification, differentiation, and proliferation have been identified, little is known about how liver maturation is regulated. Here, we used a screen for mutations affecting liver development in zebrafish and identified a cq96 mutant that exhibits a specific defect in liver maturation. Results from positional cloning revealed that cq96 encodes an...
Source: Journal of Biological Chemistry - August 14, 2020 Category: Chemistry Authors: Liang Hu, Hongyan Li, Zhiping Chi, Jianbo He Tags: Developmental Biology Source Type: research

Cytochrome c nitrite reductase from the bacterium Geobacter lovleyi represents a new NrfA subclass [Protein Structure and Folding]
Cytochrome c nitrite reductase (NrfA) catalyzes the reduction of nitrite to ammonium in the dissimilatory nitrate reduction to ammonium (DNRA) pathway, a process that competes with denitrification, conserves nitrogen, and minimizes nutrient loss in soils. The environmental bacterium Geobacter lovleyi has recently been recognized as a key driver of DNRA in nature, but its enzymatic pathway is still uncharacterized. To address this limitation, here we overexpressed, purified, and characterized G. lovleyi NrfA. We observed that the enzyme crystallizes as a dimer but remains monomeric in solution. Importantly, its crystal stru...
Source: Journal of Biological Chemistry - August 14, 2020 Category: Chemistry Authors: Julius Campecino, Satyanarayana Lagishetty, Zdzislaw Wawrzak, Victor Sosa Alfaro, Nicolai Lehnert, Gemma Reguera, Jian Hu, Eric L. Hegg Tags: Enzymology Source Type: research

The yeast exoribonuclease Xrn1 and associated factors modulate RNA polymerase II processivity in 5' and 3' gene regions [Cell Biology]
mRNA levels are determined by the balance between mRNA synthesis and decay. Protein factors that mediate both processes, including the 5'-3' exonuclease Xrn1, are responsible for a cross-talk between the two processes that buffers steady-state mRNA levels. However, the roles of these proteins in transcription remain elusive and controversial. Applying native elongating transcript sequencing (NET-seq) to yeast cells, we show that Xrn1 functions mainly as a transcriptional activator and that its disruption manifests as a reduction of RNA polymerase II (Pol II) occupancy downstream of transcription start sites. By combining o...
Source: Journal of Biological Chemistry - August 14, 2020 Category: Chemistry Authors: Jonathan Fischer, Yun S. Song, Nir Yosef, Julia di Iulio, L. Stirling Churchman, Mordechai Choder Tags: Gene Regulation Source Type: research

Phase-separated condensate-aided enrichment of biomolecular interactions for high-throughput drug screening in test tubes [Molecular Biophysics]
Modification-dependent and -independent biomolecular interactions, including protein–protein, protein–DNA/RNA, protein–sugar, and protein–lipid interactions, play crucial roles in all cellular processes. Dysregulation of these biomolecular interactions or malfunction of the associated enzymes results in various diseases; therefore, these interactions and enzymes are attractive targets for therapies. High-throughput screening can greatly facilitate the discovery of drugs for these targets. Here, we describe a biomolecular interaction detection method, called phase-separated condensate-aided enrichmen...
Source: Journal of Biological Chemistry - August 14, 2020 Category: Chemistry Authors: Min Zhou, Weiping Li, Jian Li, Leiming Xie, Rongbo Wu, Liang Wang, Shuai Fu, Wei Su, Jianyang Hu, Jing Wang, Pilong Li Tags: Methods and Resources Source Type: research

A protein folding intermediate pulls its weight [Molecular Biophysics]
Proteins must acquire and maintain a specific fold to execute their biochemical function(s). In solution, unfolded proteins typically find this native structure through a biased sampling of preferred intermediate conformations. However, the initial search for these structures begins during protein synthesis, and it is unclear how much interactions between the ribosome and nascent polypeptide skew folding pathways. In this issue, Jensen and colleagues use a ribosomal force–profiling assay to show that RNase H forms a similar folding intermediate on and off the ribosome. In conjunction with measurements of the rate of ...
Source: Journal of Biological Chemistry - August 14, 2020 Category: Chemistry Authors: Jonathan P. Schlebach Tags: Editors ' Picks Highlights Source Type: research

The folding and unfolding behavior of ribonuclease H on the ribosome [Protein Synthesis and Degradation]
The health of a cell depends on accurate translation and proper protein folding, whereas misfolding can lead to aggregation and disease. The first opportunity for a protein to fold occurs during translation, when the ribosome and surrounding environment can affect the nascent chain energy landscape. However, quantifying these environmental effects is challenging because ribosomal proteins and rRNA preclude most spectroscopic measurements of protein energetics. Here, we have applied two gel-based approaches, pulse proteolysis and force-profile analysis, to probe the folding and unfolding pathways of RNase H (RNH) nascent ch...
Source: Journal of Biological Chemistry - August 14, 2020 Category: Chemistry Authors: Madeleine K. Jensen, Avi J. Samelson, Annette Steward, Jane Clarke, Susan Marqusee Tags: Editors ' Picks Source Type: research

Finding proteases that make cells go viral [Molecular Bases of Disease]
The activation of influenza virus hemagglutinin (HA) glycoprotein via cleavage by host cell proteases is essential for viral infectivity, and understanding the mechanisms for HA protein cleavage and how they may differ depending on the biological context is important for the development of flu treatments. However, the HA proteases involved in the activation of many viral strains remain unidentified. In this issue, Harbig et al. identify a repertoire of proteases that cleave HA and determine the proteases' functionality against specific HA glycoproteins. (Source: Journal of Biological Chemistry)
Source: Journal of Biological Chemistry - August 14, 2020 Category: Chemistry Authors: Hector C. Aguilar, David W. Buchholz Tags: Editors ' Picks Highlights Source Type: research

Transcriptome profiling and protease inhibition experiments identify proteases that activate H3N2 influenza A and influenza B viruses in murine airways [Microbiology]
Cleavage of influenza virus hemagglutinin (HA) by host proteases is essential for virus infectivity. HA of most influenza A and B (IAV/IBV) viruses is cleaved at a monobasic motif by trypsin-like proteases. Previous studies have reported that transmembrane serine protease 2 (TMPRSS2) is essential for activation of H7N9 and H1N1pdm IAV in mice but that H3N2 IAV and IBV activation is independent of TMPRSS2 and carried out by as-yet-undetermined protease(s). Here, to identify additional H3 IAV- and IBV-activating proteases, we used RNA-Seq to investigate the protease repertoire of murine lower airway tissues, primary type II ...
Source: Journal of Biological Chemistry - August 14, 2020 Category: Chemistry Authors: Anne Harbig, Marco Mernberger, Linda Bittel, Stephan Pleschka, Klaus Schughart, Torsten Steinmetzer, Thorsten Stiewe, Andrea Nist, Eva Bottcher–Friebertshauser Tags: Editors ' Picks Source Type: research

Comparative study of the stabilities of synthetic in vitro and natural ex vivo transthyretin amyloid fibrils [Molecular Bases of Disease]
Systemic amyloidosis caused by extracellular deposition of insoluble fibrils derived from the pathological aggregation of circulating proteins, such as transthyretin, is a severe and usually fatal condition. Elucidation of the molecular pathogenic mechanism of the disease and discovery of effective therapies still represents a challenging medical issue. The in vitro preparation of amyloid fibrils that exhibit structural and biochemical properties closely similar to those of natural fibrils is central to improving our understanding of the biophysical basis of amyloid formation in vivo and may offer an important tool for dru...
Source: Journal of Biological Chemistry - August 14, 2020 Category: Chemistry Authors: Sara Raimondi, P. Patrizia Mangione, Guglielmo Verona, Diana Canetti, Paola Nocerino, Loredana Marchese, Rebecca Piccarducci, Valentina Mondani, Giulia Faravelli, Graham W. Taylor, Julian D. Gillmore, Alessandra Corazza, Mark B. Pepys, Sofia Giorgetti, Vi Tags: Editors ' Picks Source Type: research

Correction: The E3 ubiquitin ligase STUB1 attenuates cell senescence by promoting the ubiquitination and degradation of the core circadian regulator BMAL1 [Additions and Corrections]
VOLUME 295 (2020) PAGES 4696–4708There was an error in one of the grant numbers. The correct grant number for the National Key R&D Program of China Grant is 2019YFA0802400. (Source: Journal of Biological Chemistry)
Source: Journal of Biological Chemistry - August 7, 2020 Category: Chemistry Authors: Kifayat Ullah, Suping Chen, Jiaqi Lu, Xiaohui Wang, Qing Liu, Yang Zhang, Yaqiu Long, Zhanhong Hu, Guoqiang Xu Tags: Additions and Corrections Source Type: research

Correction: Binding studies of TNF receptor superfamily (TNFRSF) receptors on intact cells. [Additions and Corrections]
VOLUME 291 (2015) PAGES 5022–5037During preparation of Fig. 3, the p100/p52 immunoblot of Flag-TNC-CD27L–treated cells was inadvertently used in the Flag-TNC-CD40L immunoblot panel. This error has now been corrected and does not affect the results or conclusions of this work. The authors apologize for the error.jbc;295/32/11377/F3F1F3Figure 3. (Source: Journal of Biological Chemistry)
Source: Journal of Biological Chemistry - August 7, 2020 Category: Chemistry Authors: Isabell Lang, Simone Fullsack, Agnes Wyzgol, Andrea Fick, Johannes Trebing, Jose Antonio Carmona Arana, Viktoria Schafer, Daniela Weisenberger, Harald Waȷant Tags: Additions and Corrections Source Type: research

The bacterial copper resistance protein CopG contains a cysteine-bridged tetranuclear copper cluster [Protein Structure and Folding]
CopG is an uncharacterized protein ubiquitous in Gram-negative bacteria whose gene frequently occurs in clusters of copper resistance genes and can be recognized by the presence of a conserved CxCC motif. To investigate its contribution to copper resistance, here we undertook a structural and biochemical characterization of the CopG protein from Pseudomonas aeruginosa. Results from biochemical analyses of CopG purified under aerobic conditions indicate that it is a green copper-binding protein that displays absorbance maxima near 411, 581, and 721 nm and is monomeric in solution. Determination of the three-dimensional stru...
Source: Journal of Biological Chemistry - August 7, 2020 Category: Chemistry Authors: Andrew C. Hausrath, Nicholas A. Ramirez, Alan T. Ly, Megan M. McEvoy Tags: Microbiology Source Type: research

New analysis pipeline for high-throughput domain-peptide affinity experiments improves SH2 interaction data [Computational Biology]
We present revised SH2–pTyr affinity results and propose a new analysis pipeline for future HTP measurements of domain–peptide interactions. (Source: Journal of Biological Chemistry)
Source: Journal of Biological Chemistry - August 7, 2020 Category: Chemistry Authors: Tom Ronan, Roman Garnett, Kristen M. Naegle Tags: Methods and Resources Source Type: research

A conserved evolutionary mechanism permits {Delta}9 desaturation of very-long-chain fatty acyl lipids [Lipids]
Δ9 fatty acyl desaturases introduce a cis–double bond between C9 and C10 of saturated fatty acyl chains. From the crystal structure of the mouse stearoyl-CoA desaturase (mSCD1) it was proposed that Tyr-104, a surface residue located at the distal end of the fatty acyl binding pocket plays a key role in specifying 18C selectivity. We created mSCD1-Y104G to test the hypothesis that eliminating this bulky side chain would create an opening and permit the substrate's methyl end to protrude through the enzyme into the lipid bilayer, facilitating the desaturation of very-long-chain (VLC) substrates. Consistent with t...
Source: Journal of Biological Chemistry - August 7, 2020 Category: Chemistry Authors: Yuanheng Cai, Xiao-Hong Yu, Jin Chai, Chang-Jun Liu, John Shanklin Tags: Lipids Source Type: research