Oligopeptide-binding protein from nontypeable Haemophilus influenzae has ligand-specific sites to accommodate peptides and heme in the binding pocket [Membrane Biology]
In nontypeable Haemophilus influenzae (NTHi), the oligopeptide-binding protein (OppA) serves as the substrate-binding protein (SBP) of the oligopeptide transport system responsible for the import of peptides. We solved the crystal structure of nthiOppA in complex with hydrophobic peptides of various sizes. Our novel hexapeptide complex demonstrates the flexibility of the nthiOppA-binding cavity to expand and accommodate the longer peptide while maintaining similar protein–peptide interactions of smaller peptide complexes. In addition to acquiring peptides from the host environment, as a heme auxotroph NTHi utilizes h...
Source: Journal of Biological Chemistry - January 18, 2019 Category: Chemistry Authors: Kari J. Tanaka, Heather W. Pinkett Tags: Molecular Biophysics Source Type: research

Forkhead box protein O1 (FoxO1) regulates hepatic serine protease inhibitor B1 (serpinB1) expression in a non-cell-autonomous fashion [Metabolism]
We reported previously that serpinB1 is a liver-secreted factor (hepatokine) that promotes adaptive β-cell proliferation in response to insulin resistance in the liver-specific insulin receptor knockout (LIRKO) mouse. Here we report that FoxO1 plays a critical role in promoting serpinB1 expression in hepatic insulin resistance in a non-cell-autonomous manner. Mice lacking both the insulin receptor and FoxO1 (LIRFKO) exhibit reduced β-cell mass compared with LIRKO mice because of attenuation of β-cell proliferation. Although hepatic expression of serpinB1 mRNA and protein levels was increased in LIRKO mice, b...
Source: Journal of Biological Chemistry - January 18, 2019 Category: Chemistry Authors: Abdelfattah El Ouaamari, InSug O-Sullivan, Jun Shirakawa, Giorgio Basile, Wenwei Zhang, Sandra Roger, Thomas Thomou, Shanshan Xu, Guifen Qiang, Chong Wee Liew, Rohit N. Kulkarni, Terry G. Unterman Tags: Cell Biology Source Type: research

Parkinson's disease and multiple system atrophy have distinct {alpha}-synuclein seed characteristics [Neurobiology]
Parkinson's disease (PD) and multiple system atrophy (MSA) are distinct clinical syndromes characterized by the pathological accumulation of α-synuclein (α-syn) protein fibrils in neurons and glial cells. These disorders and other neurodegenerative diseases may progress via prion-like mechanisms. The prion model of propagation predicts the existence of “strains” that link pathological aggregate structure and neuropathology. Prion strains are aggregated conformers that stably propagate in vivo and cause disease with defined incubation times and patterns of neuropathology. Indeed, tau prions have been...
Source: Journal of Biological Chemistry - January 18, 2019 Category: Chemistry Authors: Tritia R. Yamasaki, Brandon B. Holmes, Jennifer L. Furman, Dhruva D. Dhavale, Bryant W. Su, Eun-Suk Song, Nigel J. Cairns, Paul T. Kotzbauer, Marc I. Diamond Tags: Molecular Bases of Disease Source Type: research

A cysteine protease-like domain enhances the cytotoxic effects of the Photorhabdus asymbiotica toxin PaTox [Cell Biology]
In this study, we identified a cysteine protease–like domain spanning PaTox residues 1844–2114 (PaToxP), upstream of these two effector domains and characterized by three conserved amino acid residues (Cys-1865, His-1955, and Asp-1975). We determined the crystal structure of the PaToxP C1865A variant by native single-wavelength anomalous diffraction of sulfur atoms (sulfur-SAD). At 2.0 Å resolution, this structure revealed a catalytic site typical for papain-like cysteine proteases, comprising a catalytic triad, oxyanion hole, and typical secondary structural elements. The PaToxP structure had highest sim...
Source: Journal of Biological Chemistry - January 18, 2019 Category: Chemistry Authors: Xenia Bogdanovic, Silvia Schneider, Nadezhda Levanova, Christophe Wirth, Christoph Trillhaase, Marcus Steinemann, Carola Hunte, Klaus Aktories, Thomas Jank Tags: Protein Structure and Folding Source Type: research

Kinetic and catalytic properties of M.HpyAXVII, a phase-variable DNA methyltransferase from Helicobacter pylori [DNA and Chromosomes]
The bacterium Helicobacter pylori is one of the most common infectious agents found in the human stomach. H. pylori has an unusually large number of DNA methyltransferases (MTases), prompting speculation that they may be involved in the cancerization of epithelial cells. The mod-4a/4b locus, consisting of the hp1369 and hp1370 ORFs, encodes for a truncated and inactive MTase in H. pylori strain 26695. However, slipped-strand synthesis within the phase-variable polyguanine tract in hp1369 results in expression of an active HP1369–1370 fusion N6-adenine methyltransferase, designated M.HpyAXVII. Sequence analysis of the...
Source: Journal of Biological Chemistry - January 18, 2019 Category: Chemistry Authors: Yedu Prasad, Ritesh Kumar, Awanish Kumar Chaudhary, Rajkumar Dhanaraju, Soneya Majumdar, Desirazu N. Rao Tags: Enzymology Source Type: research

Elevated histone H3 acetylation and loss of the Sp1-HDAC1 complex de-repress the GM2-synthase gene in renal cell carcinoma [Gene Regulation]
GM2-synthase produces sialic acid–containing glycosphingolipids called gangliosides, and its mRNA overexpression and the gangliosides it generates are linked to tumor progression, migration, and suppression of tumor-specific host immune responses. However, the mechanism underlying GM2-synthase de-repression in renal cell carcinoma (RCC) is poorly understood. Here, we demonstrate that higher GM2-synthase mRNA expression levels in various cancer cells and in human RCC tumors correlate with higher histone acetylation levels (H3K9, H3K14, or both) at region +38/+187 relative to the transcription start site (TSS) of the G...
Source: Journal of Biological Chemistry - January 18, 2019 Category: Chemistry Authors: Avisek Banerjee, Barun Mahata, Arjun Dhir, Tapan Kumar Mandal, Kaushik Biswas Tags: Glycobiology and Extracellular Matrices Source Type: research

Herpes simplex virus 1 ICP6 impedes TNF receptor 1-induced necrosome assembly during compartmentalization to detergent-resistant membrane vesicles [Cell Biology]
Receptor-interacting protein (RIP) kinase 3 (RIPK3)–dependent necroptosis directs inflammation and tissue injury, as well as anti-viral host defense. In human cells, herpes simplex virus 1 (HSV1) UL39-encoded ICP6 blocks RIP homotypic interacting motif (RHIM) signal transduction, preventing this leakage form of cell death and sustaining viral infection. TNF receptor 1 (TNFR1)-induced necroptosis is known to require the formation of a RIPK1–RIPK3–mixed lineage kinase domain–like pseudokinase (MLKL) signaling complex (necrosome) that we find compartmentalizes exclusively to caveolin-1–associated...
Source: Journal of Biological Chemistry - January 18, 2019 Category: Chemistry Authors: Mohammad Ali, Linda Roback, Edward S. Mocarski Tags: Signal Transduction Source Type: research

The bacterial lipid II flippase MurJ functions by an alternating-access mechanism [Microbiology]
The peptidoglycan (PG) cell wall is an essential extracytoplasmic glycopeptide polymer that safeguards bacteria against osmotic lysis and determines cellular morphology. Bacteria use multiprotein machineries for the synthesis of the PG cell wall during cell division and elongation that can be targeted by antibiotics such as the β-lactams. Lipid II, the lipid-linked precursor for PG biogenesis, is synthesized in the inner leaflet of the cytoplasmic membrane and then translocated across the bilayer, where it is ultimately polymerized into PG. In Escherichia coli, MurJ, a member of the MOP exporter superfamily, has been ...
Source: Journal of Biological Chemistry - January 18, 2019 Category: Chemistry Authors: Sujeet Kumar, Frederick A. Rubino, Alicia G. Mendoza, Natividad Ruiz Tags: Membrane Biology Source Type: research

Holliday junction recognition protein interacts with and specifies the centromeric assembly of CENP-T [Cell Biology]
The centromere is an evolutionarily conserved eukaryotic protein machinery essential for precision segregation of the parental genome into two daughter cells during mitosis. Centromere protein A (CENP-A) organizes the functional centromere via a constitutive centromere-associated network composing the CENP-T complex. However, how CENP-T assembles onto the centromere remains elusive. Here we show that CENP-T binds directly to Holliday junction recognition protein (HJURP), an evolutionarily conserved chaperone involved in loading CENP-A. The binding interface of HJURP was mapped to the C terminus of CENP-T. Depletion of HJUR...
Source: Journal of Biological Chemistry - January 18, 2019 Category: Chemistry Authors: Mingrui Ding, Jiying Jiang, Fengrui Yang, Fan Zheng, Jingwen Fang, Qian Wang, Jianyu Wang, William Yao, Xu Liu, Xinjiao Gao, McKay Mullen, Ping He, Cathy Rono, Xia Ding, Jingjun Hong, Chuanhai Fu, Xing Liu, Xuebiao Yao Tags: Cell Biology Source Type: research

Structures of AMP-activated protein kinase bound to novel pharmacological activators in phosphorylated, non-phosphorylated, and nucleotide-free states [Protein Structure and Folding]
AMP-activated protein kinase (AMPK) is an attractive therapeutic target for managing metabolic diseases. A class of pharmacological activators, including Merck 991, binds the AMPK ADaM site, which forms the interaction surface between the kinase domain (KD) of the α-subunit and the carbohydrate-binding module (CBM) of the β-subunit. Here, we report the development of two new 991-derivative compounds, R734 and R739, which potently activate AMPK in a variety of cell types, including β2-specific skeletal muscle cells. Surprisingly, we found that they have only minor effects on direct kinase activity of the rec...
Source: Journal of Biological Chemistry - January 18, 2019 Category: Chemistry Authors: Yan Yan, X. Edward Zhou, Scott J. Novick, Simon J. Shaw, Yingwu Li, Joseph S. Brunzelle, Yasumichi Hitoshi, Patrick R. Griffin, H. Eric Xu, Karsten Melcher Tags: Signal Transduction Source Type: research

Discriminative T-cell receptor recognition of highly homologous HLA-DQ2-bound gluten epitopes [Protein Structure and Folding]
This study underscores the ability of TCRs to recognize subtle differences in the peptide–HLA-II landscape in a human disease setting. (Source: Journal of Biological Chemistry)
Source: Journal of Biological Chemistry - January 18, 2019 Category: Chemistry Authors: Shiva Dahal–Koirala, Laura Ciacchi, Jan Petersen, Louise Fremgaard Risnes, Ralf Stefan Neumann, Asbȷorn Christophersen, Knut E. A. Lundin, Hugh H. Reid, Shuo–Wang Qiao, Jamie Rossȷohn, Ludvig M. Sollid Tags: Immunology Source Type: research

Improved Tol2-mediated enhancer trap identifies weakly expressed genes during liver and {beta} cell development and regeneration in zebrafish [Methods and Resources]
In conclusion, through permanent genetic labeling by Cre/loxP, this improved Tol2-mediated enhancer trap system provides a promising method to identify transiently or weakly expressed, but potentially important, genes during development and regeneration. (Source: Journal of Biological Chemistry)
Source: Journal of Biological Chemistry - January 18, 2019 Category: Chemistry Authors: Yadong Zhong, Wei Huang, Jiang Du, Zekun Wang, Jianbo He, Lingfei Luo Tags: Developmental Biology Source Type: research

Mapping multivalency in the CLIP-170-EB1 microtubule plus-end complex [Cell Biology]
Cytoplasmic linker protein 170 (CLIP-170) is a microtubule plus-end factor that links vesicles to microtubules and recruits the dynein–dynactin complex to microtubule plus ends. CLIP-170 plus-end localization is end binding 1 (EB1)–dependent. CLIP-170 contains two N-terminal cytoskeleton-associated protein glycine-rich (CAP-Gly) domains flanked by serine-rich regions. The CAP-Gly domains are known EB1-binding domains, and the serine-rich regions have also been implicated in CLIP-170's microtubule plus-end localization mechanism. However, the determinants in these serine-rich regions have not been identified. He...
Source: Journal of Biological Chemistry - January 18, 2019 Category: Chemistry Authors: Yaodong Chen, Ping Wang, Kevin C. Slep Tags: Molecular Biophysics Source Type: research

Heat-induced inhibition of phosphorylation of the stress-protective transcription factor DREB2A promotes thermotolerance of Arabidopsis thaliana [Signal Transduction]
Plants have evolved complex systems to rapidly respond to severe stress conditions, such as heat, cold, and dehydration. Dehydration-responsive element-binding protein 2A (DREB2A) is a key transcriptional activator that induces many heat- and drought-responsive genes, increases tolerance to both heat and drought stress, and suppresses plant growth in Arabidopsis thaliana. DREB2A expression is induced by stress, but stabilization of the DREB2A protein in response to stress is essential for activating the expression of downstream stress-inducible genes. Under nonstress growth conditions, an integral negative regulatory domai...
Source: Journal of Biological Chemistry - January 18, 2019 Category: Chemistry Authors: Junya Mizoi, Natsumi Kanazawa, Satoshi Kidokoro, Fuminori Takahashi, Feng Qin, Kyoko Morimoto, Kazuo Shinozaki, Kazuko Yamaguchi-Shinozaki Tags: Plant Biology Source Type: research

Inhibition of ezrin causes PKC{alpha}-mediated internalization of erbb2/HER2 tyrosine kinase in breast cancer cells [Signal Transduction]
Unlike other ErbB family members, HER2 levels are maintained on the cell surface when the receptor is activated, allowing prolonged signaling and contributing to its transforming ability. Interactions between HER2, HSP90, PMCA2, and NHERF1 within specialized plasma membrane domains contribute to the membrane retention of HER2. We hypothesized that the scaffolding protein ezrin, which has been shown to interact with NHERF1, might also help stabilize the HER2–PMCA2–NHERF1 complex at the plasma membrane. Therefore, we examined ezrin expression and its relationship with HER2, NHERF1, and PMCA2 levels in murine and ...
Source: Journal of Biological Chemistry - January 18, 2019 Category: Chemistry Authors: Jaekwang Jeong, Jungmin Choi, Wonnam Kim, Pamela Dann, Farzin Takyar, Julia V. Gefter, Peter A. Friedman, John J. Wysolmerski Tags: Cell Biology Source Type: research

Targeting BCL-xL improves the efficacy of bromodomain and extra-terminal protein inhibitors in triple-negative breast cancer by eliciting the death of senescent cells [Cell Biology]
Inhibitors of bromodomain and extra-terminal proteins (BETi) suppress oncogenic gene expression and have been shown to be efficacious in many in vitro and murine models of cancer, including triple-negative breast cancer (TNBC), a highly aggressive disease. However, in most cancer models, responses to BETi can be highly variable. We previously reported that TNBC cells either undergo senescence or apoptosis in response to BETi, but the specific mechanisms dictating these two cell fates remain unknown. Using six human TNBC cell lines, we show that the terminal response of TNBC cells to BETi is dictated by the intrinsic expres...
Source: Journal of Biological Chemistry - January 18, 2019 Category: Chemistry Authors: Sylvia S. Gayle, Jennifer M. Sahni, Bryan M. Webb, Kristen L. Weber-Bonk, Melyssa S. Shively, Raffaella Spina, Eli E. Bar, Mathew K. Summers, Ruth A. Keri Tags: Cell Biology Source Type: research

Correction: Structure-function analyses reveal the mechanism of the ARH3-dependent hydrolysis of ADP-ribosylation [Additions and Corrections]
VOLUME 293 (2018) PAGES 14470–14480There was an error in the affiliation for Xiaochun Yu. The correct affiliation is only the Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, Duarte, California 91010. (Source: Journal of Biological Chemistry)
Source: Journal of Biological Chemistry - January 18, 2019 Category: Chemistry Authors: Mengxi Wang, Zenglin Yuan, Rong Xie, Yinliang Ma, Xiuhua Liu, Xiaochun Yu Tags: Additions and Corrections Source Type: research

Interactome mapping defines BRG1, a component of the SWI/SNF chromatin remodeling complex, as a new partner of the transcriptional regulator CTCF [DNA and Chromosomes]
The highly conserved zinc finger CCCTC-binding factor (CTCF) regulates genomic imprinting and gene expression by acting as a transcriptional activator or repressor of promoters and insulator of enhancers. The multiple functions of CTCF are accomplished by co-association with other protein partners and are dependent on genomic context and tissue specificity. Despite the critical role of CTCF in the organization of genome structure, to date, only a subset of CTCF interaction partners have been identified. Here we present a large-scale identification of CTCF-binding partners using affinity purification and high-resolution LC-...
Source: Journal of Biological Chemistry - January 18, 2019 Category: Chemistry Authors: Maria Michela Marino, Camilla Rega, Rosita Russo, Mariangela Valletta, Maria Teresa Gentile, Sabrina Esposito, Ilaria Baglivo, Italia De Feis, Claudia Angelini, Tioajiang Xiao, Gary Felsenfeld, Angela Chambery, Paolo Vincenzo Pedone Tags: Genomics and Proteomics Source Type: research

The recombination mediator proteins RecFOR maintain RecA* levels for maximal DNA polymerase V Mut activity [DNA and Chromosomes]
DNA template damage can potentially block DNA replication. Cells have therefore developed different strategies to repair template lesions. Activation of the bacterial lesion bypass DNA polymerase V (Pol V) requires both the cleavage of the UmuD subunit to UmuD′ and the acquisition of a monomer of activated RecA recombinase, forming Pol V Mut. Both of these events are mediated by the generation of RecA* via the formation of a RecA–ssDNA filament during the SOS response. Formation of RecA* is itself modulated by competition with the ssDNA-binding protein (SSB) for binding to ssDNA. Previous observations have demo...
Source: Journal of Biological Chemistry - January 18, 2019 Category: Chemistry Authors: Paromita Raychaudhury, Kenneth J. Marians Tags: DNA and Chromosomes Source Type: research

Tissue-specific kinase expression and activity regulate flux through the pyruvate dehydrogenase complex [Enzymology]
In this study, we analyzed mouse strains carrying targeted mutations of individual isozymes to explore their role in regulating PDC activity. Analysis of protein content of PDK isozymes in major metabolic tissues revealed that PDK1 and PDK2 were ubiquitously expressed, whereas PDK3 and PDK4 displayed a rather limited tissue distribution. Measurement of kinase activity showed that PDK1 is the principal isozyme regulating hepatic PDC. PDK2 was largely responsible for inactivation of PDC in tissues of muscle origin and brown adipose tissue (BAT). PDK3 was the principal kinase regulating pyruvate dehydrogenase activity in kidn...
Source: Journal of Biological Chemistry - January 18, 2019 Category: Chemistry Authors: Alla Klyuyeva, Alina Tuganova, Natalia Kedishvili, Kirill M. Popov Tags: Metabolism Source Type: research

Sirtuin 2-mediated deacetylation of cyclin-dependent kinase 9 promotes STAT1 signaling in type I interferon responses [Signal Transduction]
Type I interferons (IFNs) induce expression of multiple genes that control innate immune responses to invoke both antiviral and antineoplastic activities. Transcription of these interferon-stimulated genes (ISGs) occurs upon activation of the canonical Janus kinase (JAK)–signal transducer and activator of transcription (STAT) signaling pathways. Phosphorylation and acetylation are both events crucial to tightly regulate expression of ISGs. Here, using mouse embryonic fibroblasts and an array of biochemical methods including immunoblotting and kinase assays, we show that sirtuin 2 (SIRT2), a member of the NAD-dependen...
Source: Journal of Biological Chemistry - January 18, 2019 Category: Chemistry Authors: Ewa M. Kosciuczuk, Swarna Mehrotra, Diana Saleiro, Barbara Kroczynska, Beata Majchrzak-Kita, Pawel Lisowski, Caroline Driehaus, Anna Rogalska, Acara Turner, Thomas Lienhoop, David Gius, Eleanor N. Fish, Athanassios Vassilopoulos, Leonidas C. Platanias Tags: Signal Transduction Source Type: research

Sodium channel TRPM4 and sodium/calcium exchangers (NCX) cooperate in the control of Ca2+-induced mucin secretion from goblet cells [Cell Biology]
Regulated mucin secretion is essential for the formation of the mucus layer that protects the underlying epithelial cells from foreign particles. Alterations in the quantity or quality of secreted mucins are therefore detrimental to airway and colon physiology. Based on various biochemical assays in several human cell lines, we report here that Na+/Ca2+ exchanger 2 (NCX2) works in conjunction with transient receptor potential cation channel subfamily M member 4 (TRPM4), and perhaps TRPM5, Na+ channels to control Ca2+-mediated secretion of both mucin 2 (MUC2) and MUC5AC from HT29-18N2 colonic cancer cells. Differentiated no...
Source: Journal of Biological Chemistry - January 18, 2019 Category: Chemistry Authors: Gerard Cantero-Recasens, Cristian M. Butnaru, Nathalie Brouwers, Sandra Mitrovic, Miguel A. Valverde, Vivek Malhotra Tags: Cell Biology Source Type: research

Metabolomics and proteomics identify the toxic form and the associated cellular binding targets of the anti-proliferative drug AICAR [Metabolism]
5-Aminoimidazole-4-carboxamide 1-β-d-ribofuranoside (AICAR, or acadesine) is a precursor of the monophosphate derivative 5-amino-4-imidazole carboxamide ribonucleoside 5′-phosphate (ZMP), an intermediate in de novo purine biosynthesis. AICAR proved to have promising anti-proliferative properties, although the molecular basis of its toxicity is poorly understood. To exert cytotoxicity, AICAR needs to be metabolized, but the AICAR-derived toxic metabolite was not identified. Here, we show that ZMP is the major toxic derivative of AICAR in yeast and establish that its metabolization to succinyl-ZMP, ZDP, or ZTP (di...
Source: Journal of Biological Chemistry - January 18, 2019 Category: Chemistry Authors: Delphine C. Douillet, Benoit Pinson, Johanna Ceschin, Hans C. Hurlimann, Christelle Saint–Marc, Damien Laporte, Stephane Claverol, Manfred Konrad, Marc Bonneu, Bertrand Daignan–Fornier Tags: Metabolism Source Type: research

Non-cryogenic structure of a chloride pump provides crucial clues to temperature-dependent channel transport efficiency [Membrane Biology]
Non-cryogenic protein structures determined at ambient temperature may disclose significant information about protein activity. Chloride-pumping rhodopsin (ClR) exhibits a trend to hyperactivity induced by a change in the photoreaction rate because of a gradual decrease in temperature. Here, to track the structural changes that explain the differences in CIR activity resulting from these temperature changes, we used serial femtosecond crystallography (SFX) with an X-ray free electron laser (XFEL) to determine the non-cryogenic structure of ClR at a resolution of 1.85 Å, and compared this structure with a cryogenic Cl...
Source: Journal of Biological Chemistry - January 18, 2019 Category: Chemistry Authors: Ji-Hye Yun, Xuanxuan Li, Jae-Hyun Park, Yang Wang, Mio Ohki, Zeyu Jin, Wonbin Lee, Sam-Yong Park, Hao Hu, Chufeng Li, Nadia Zatsepin, Mark S. Hunter, Raymond G. Sierra, Jake Koralek, Chun Hong Yoon, Hyun-Soo Cho, Uwe Weierstall, Leihan Tang, Haiguang Liu, Tags: Protein Structure and Folding Source Type: research

The ubiquitin ligase SspH1 from Salmonella uses a modular and dynamic E3 domain to catalyze substrate ubiquitylation [Protein Structure and Folding]
SspH/IpaH bacterial effector E3 ubiquitin (Ub) ligases, unrelated in sequence or structure to eukaryotic E3s, are utilized by a wide variety of Gram-negative bacteria during pathogenesis. These E3s function in a eukaryotic environment, utilize host cell E2 ubiquitin-conjugating enzymes of the Ube2D family, and target host proteins for ubiquitylation. Despite several crystal structures, details of Ube2D∼Ub binding and the mechanism of ubiquitin transfer are poorly understood. Here, we show that the catalytic E3 ligase domain of SspH1 can be divided into two subdomains: an N-terminal subdomain that harbors the active-sit...
Source: Journal of Biological Chemistry - January 18, 2019 Category: Chemistry Authors: Matt Cook, Scott P. Delbecq, Thomas P. Schweppe, Miklos Guttman, Rachel E. Klevit, Peter S. Brzovic Tags: Enzymology Source Type: research

The ER-localized Ca2+-binding protein calreticulin couples ER stress to autophagy by associating with microtubule-associated protein 1A/1B light chain 3 [Signal Transduction]
In this study, in vivo and in vitro approaches were utilized that include gain- and loss-of-function assays and mouse livers and human cell lines with tunicamycin-induced pharmacological ER stress. We report that calreticulin, a quality control chaperone that binds to misfolded glycoproteins for refolding in the ER, is induced under ER stress. Calreticulin overexpression stimulated the formation of autophagosomes and increased autophagic flux. Interestingly, calreticulin was sufficient for attenuating ER stress in tunicamycin- or thapsigargin-treated HeLa cells, whereas lentivirus-mediated shRNA calreticulin knockdown exac...
Source: Journal of Biological Chemistry - January 18, 2019 Category: Chemistry Authors: Yunzhi Yang, Fengguang Ma, Zhengshuai Liu, Qian Su, Yuxiao Liu, Zhixue Liu, Yu Li Tags: Cell Biology Source Type: research

How evolution made the matrix punch at the multicellularity party [Cell Biology]
The basement membrane is a specialized sheet-like form of the extracellular matrix that provides structural support to epithelial cells and tissues, while influencing multiple biological functions, and was essential in the transition to multicellularity. By exploring a variety of genomes, Darris et al. provide evidence that the emergence and divergence of a multifunctional Goodpasture antigen-binding protein (GPBP), a basement membrane constituent, played a role in this transition. These findings help to explain how GPBP contributed to the formation of these extracellular matrices and to more precisely define the transitio...
Source: Journal of Biological Chemistry - January 18, 2019 Category: Chemistry Authors: Fernando Rodriguez–Pascual Tags: Editors ' Picks Highlights Source Type: research

Unicellular ancestry and mechanisms of diversification of Goodpasture antigen-binding protein [Glycobiology and Extracellular Matrices]
The emergence of the basement membrane (BM), a specialized form of extracellular matrix, was essential in the unicellular transition to multicellularity. However, the mechanism is unknown. Goodpasture antigen–binding protein (GPBP), a BM protein, was uniquely poised to play diverse roles in this transition owing to its multiple isoforms (GPBP-1, -2, and -3) with varied intracellular and extracellular functions (ceramide trafficker and protein kinase). We sought to determine the evolutionary origin of GPBP isoforms. Our findings reveal the presence of GPBP in unicellular protists, with GPBP-2 as the most ancient isofo...
Source: Journal of Biological Chemistry - January 18, 2019 Category: Chemistry Authors: Carl Darris, Fernando Revert, Francisco Revert-Ros, Roberto Gozalbo-Rovira, Andrew Feigley, Aaron Fidler, Ernesto Lopez-Pascual, Juan Saus, Billy G. Hudson Tags: Editors ' Picks Source Type: research

Mitochondrial ATP production provides long-range control of endothelial inositol trisphosphate-evoked calcium signaling [Signal Transduction]
In this study, we used high-resolution, wide-field fluorescence imaging to investigate the regulation of Ca2+ signaling by mitochondria in large numbers of endothelial cells (∼50 per field) in intact arteries from rats. We observed that mitochondria were mostly spherical or short-rod structures and were distributed widely throughout the cytoplasm. The density of these organelles did not increase near contact sites with smooth muscle cells. However, local inositol trisphosphate (IP3)-mediated Ca2+ signaling predominated near these contact sites and required polarized mitochondria. Of note, mitochondrial control of Ca2+ ...
Source: Journal of Biological Chemistry - January 18, 2019 Category: Chemistry Authors: Calum Wilson, Matthew D. Lee, Helen R. Heathcote, Xun Zhang, Charlotte Buckley, John M. Girkin, Christopher D. Saunter, John G. McCarron Tags: Signal Transduction Source Type: research

Fatty acid recognition in the Frizzled receptor family [Protein Structure and Folding]
Wnt signaling regulates physiological processes ranging from cell differentiation to bone formation. Dysregulation of Wnt signaling is linked to several human ailments, including colorectal, pancreatic, and breast cancers. As such, modulation of this pathway has been an attractive strategy for therapeutic development of anticancer agents. Since the discovery of Wnt proteins more than 35 years ago, research efforts continue to focus on understanding the biochemistry of their molecular interactions and their biological functions. Wnt is a secreted glycoprotein covalently modified with a cis-unsaturated fatty acyl group at a ...
Source: Journal of Biological Chemistry - January 11, 2019 Category: Chemistry Authors: Aaron H. Nile, Rami N. Hannoush Tags: JBC Reviews Source Type: research

Desensitizing plant EPSP synthase to glyphosate: Optimized global sequence context accommodates a glycine-to-alanine change in the active site [Plant Biology]
5-Enolpyruvylshikimate-3-phosphate synthase (EPSPS) catalyzes the transfer of a carboxyvinyl group from phosphoenolpyruvate (PEP) to shikimate-3-phosphate and in plants is the target of the herbicide glyphosate. EPSPSs with high catalytic efficiency and insensitivity to glyphosate are of microbial origin, including the enzyme from Agrobacterium strain CP4, in which insensitivity is conferred by an active site alanine. In the sequence context of plant EPSPSs, alanine in place of glycine at the equivalent position interferes with the binding of both glyphosate and PEP. We show here that iterative optimization of maize EPSPS ...
Source: Journal of Biological Chemistry - January 11, 2019 Category: Chemistry Authors: Yuxia Dong, Emily Ng, Jian Lu, Tamara Fenwick, Yumin Tao, Sean Bertain, Marian Sandoval, Ericka Bermudez, Zhenglin Hou, Phil Patten, Michael Lassner, Daniel Siehl Tags: Enzymology Source Type: research

Transglutaminase inhibition stimulates hematopoiesis and reduces aggressive behavior of crayfish, Pacifastacus leniusculus [Cell Biology]
In conclusion, we show that cystamine-mediated TGase inhibition directly releases HPT progenitor cells from the HPT into the peripheral circulation in the hemolymph and strongly reduces aggressive behavior in crayfish. (Source: Journal of Biological Chemistry)
Source: Journal of Biological Chemistry - January 11, 2019 Category: Chemistry Authors: Kingkamon Junkunlo, Kenneth Soderhall, Irene Soderhall Tags: Immunology Source Type: research

Deficiency of cathepsin C ameliorates severity of acute pancreatitis by reduction of neutrophil elastase activation and cleavage of E-cadherin [Molecular Bases of Disease]
Acute pancreatitis is characterized by premature intracellular protease activation and infiltration of inflammatory cells, mainly neutrophil granulocytes and macrophages, into the organ. The lysosomal proteases cathepsin B, D, and L have been identified as regulators of early zymogen activation and thus modulators of the severity of pancreatitis. Cathepsin C (CTSC, syn. dipeptidly-peptidase I) is a widely expressed, exo-cystein-protease involved in the proteolytic processing of various other lysosomal enzymes. We have studied its role in pancreatitis. We used CTSC-deleted mice and their WT littermates in two experimental m...
Source: Journal of Biological Chemistry - January 11, 2019 Category: Chemistry Authors: Daniel S. John, Julia Aschenbach, Burkhard Kruger, Matthias Sendler, F. Ulrich Weiss, Julia Mayerle, Markus M. Lerch, Ali A. Aghdassi Tags: Cell Biology Source Type: research

Exploring the quinone/inhibitor-binding pocket in mitochondrial respiratory complex I by chemical biology approaches [Enzymology]
NADH–quinone oxidoreductase (respiratory complex I) couples NADH-to-quinone electron transfer to the translocation of protons across the membrane. Even though the architecture of the quinone-access channel in the enzyme has been modeled by X-ray crystallography and cryo-EM, conflicting findings raise the question whether the models fully reflect physiologically relevant states present throughout the catalytic cycle. To gain further insights into the structural features of the binding pocket for quinone/inhibitor, we performed chemical biology experiments using bovine heart sub-mitochondrial particles. We synthesized ...
Source: Journal of Biological Chemistry - January 11, 2019 Category: Chemistry Authors: Shinpei Uno, Hironori Kimura, Masatoshi Murai, Hideto Miyoshi Tags: Bioenergetics Source Type: research

Neuraminidase 1-mediated desialylation of the mucin 1 ectodomain releases a decoy receptor that protects against Pseudomonas aeruginosa lung infection [Glycobiology and Extracellular Matrices]
Pseudomonas aeruginosa (Pa) expresses an adhesin, flagellin, that engages the mucin 1 (MUC1) ectodomain (ED) expressed on airway epithelia, increasing association of MUC1-ED with neuraminidase 1 (NEU1) and MUC1-ED desialylation. The MUC1-ED desialylation unmasks both cryptic binding sites for Pa and a protease recognition site, permitting its proteolytic release as a hyperadhesive decoy receptor for Pa. We found here that intranasal administration of Pa strain K (PAK) to BALB/c mice increases MUC1-ED shedding into the bronchoalveolar compartment. MUC1-ED levels increased as early as 12 h, peaked at 24–48 h with a 7.8...
Source: Journal of Biological Chemistry - January 11, 2019 Category: Chemistry Authors: Erik P. Lillehoj, Wei Guang, Sang W. Hyun, Anguo Liu, Nicolas Hegerle, Raphael Simon, Alan S. Cross, Hideharu Ishida, Irina G. Luzina, Sergei P. Atamas, Simeon E. Goldblum Tags: Microbiology Source Type: research

Physiological and pathophysiological characteristics of ataxin-3 isoforms [Genomics and Proteomics]
Ataxin-3 is a deubiquitinating enzyme and the affected protein in the neurodegenerative disorder Machado–Joseph disease (MJD). The ATXN3 gene is alternatively spliced, resulting in protein isoforms that differ in the number of ubiquitin-interacting motifs. Additionally, nonsynonymous SNPs in ATXN3 cause amino acid changes in ataxin-3, and one of these polymorphisms introduces a premature stop codon in one isoform. Here, we examined the effects of different ataxin-3 isoforms and of the premature stop codon on ataxin-3's physiological function and on main disease mechanisms. At the physiological level, we show that alt...
Source: Journal of Biological Chemistry - January 11, 2019 Category: Chemistry Authors: Daniel Weishaupl, Juliane Schneider, Barbara Peixoto Pinheiro, Corinna Ruess, Sandra Maria Dold, Felix von Zweydorf, Christian Johannes Gloeckner, Jana Schmidt, Olaf Riess, Thorsten Schmidt Tags: Molecular Bases of Disease Source Type: research

Bombyx mori transcription factors FoxA and SAGE divergently regulate the expression of wing cuticle protein gene 4 during metamorphosis [Signal Transduction]
Stage-specific gene expression governs metamorphosis of the silkworm, Bombyx mori. B. mori wing cuticle protein gene 4 (BmWCP4) is an essential gene for wing disc development expressed specifically during pupation. BmWCP4 transcription is suppressed at the larval stage by unknown mechanisms, which we sought to elucidate here. Bioinformatics analysis predicted seven potential Forkhead box (Fox) cis-regulatory elements (CREs) in the BmWCP4 promoter region, and we found that Fox CRE6 contributes to suppression of BmWCP4 expression. Electrophoretic mobility shift (EMSA) and DNA pull-down assays revealed that BmFoxA suppressed ...
Source: Journal of Biological Chemistry - January 11, 2019 Category: Chemistry Authors: Qihao Hu, Zidan Zhu, Danhui Zhao, Baojuan Zeng, Sichun Zheng, Qisheng Song, Huimin Deng, Qili Feng Tags: Gene Regulation Source Type: research

Formate-nitrite transporters carrying nonprotonatable amide amino acids instead of a central histidine maintain pH-dependent transport [Membrane Biology]
Microbial formate–nitrite transporter-type proteins (FNT) exhibit dual transport functionality. At neutral pH, electrogenic anion currents are detectable, whereas upon acidification transport of the neutral, protonated monoacid predominates. Physiologically, FNT-mediated proton co-transport is vital when monocarboxylic acid products of the energy metabolism, such as l-lactate, are released from the cell. Accordingly, Plasmodium falciparum malaria parasites can be killed by small-molecule inhibitors of PfFNT. Two opposing hypotheses on the site of substrate protonation are plausible. The proton relay mechanism postula...
Source: Journal of Biological Chemistry - January 11, 2019 Category: Chemistry Authors: Folknand Helmstetter, Philipp Arnold, Bastian Hoger, Lea Madlen Petersen, Eric Beitz Tags: Molecular Biophysics Source Type: research

Glucosamine improves survival in a mouse model of sepsis and attenuates sepsis-induced lung injury and inflammation [Glycobiology and Extracellular Matrices]
The aim of the current study was to investigate the effects of glucosamine (GlcN) on septic lethality and sepsis-induced inflammation using animal models of mice and zebrafish. GlcN pretreatment improved survival in the cecal ligation and puncture (CLP)-induced sepsis mouse model and attenuated lipopolysaccharide (LPS)-induced septic lung injury and systemic inflammation. GlcN suppressed LPS-induced M1-specific but not M2-specific gene expression. Furthermore, increased expressions of inflammatory genes in visceral tissue of LPS-injected zebrafish were suppressed by GlcN. GlcN suppressed LPS-induced activation of mitogen-a...
Source: Journal of Biological Chemistry - January 11, 2019 Category: Chemistry Authors: Ji-Sun Hwang, Kyung-Hong Kim, Jiwon Park, Sang-Min Kim, Hyeongjin Cho, Yunkyoung Lee, Inn-Oc Han Tags: Immunology Source Type: research

Membrane-anchored carbonic anhydrase IV interacts with monocarboxylate transporters via their chaperones CD147 and GP70 [Membrane Biology]
Monocarboxylate transporters (MCTs) mediate the proton-coupled exchange of high-energy metabolites, including lactate and pyruvate, between cells and tissues. The transport activity of MCT1, MCT2, and MCT4 can be facilitated by the extracellular carbonic anhydrase IV (CAIV) via a noncatalytic mechanism. Combining physiological measurements in HEK-293 cells and Xenopus oocytes with pulldown experiments, we analyzed the direct interaction between CAIV and the two MCT chaperones basigin (CD147) and embigin (GP70). Our results show that facilitation of MCT transport activity requires direct binding of CAIV to the transporters ...
Source: Journal of Biological Chemistry - January 11, 2019 Category: Chemistry Authors: Linda S. Forero-Quintero, Samantha Ames, Hans-Peter Schneider, Anne Thyssen, Christopher D. Boone, Jacob T. Andring, Robert McKenna, Joseph R. Casey, Joachim W. Deitmer, Holger M. Becker Tags: Cell Biology Source Type: research

Dynamic acetylation of the kinetochore-associated protein HEC1 ensures accurate microtubule-kinetochore attachment [Computational Biology]
Faithful chromosome segregation during mitosis is critical for maintaining genome integrity in cell progeny and relies on accurate and robust kinetochore–microtubule attachments. The NDC80 complex, a tetramer comprising kinetochore protein HEC1 (HEC1), NDC80 kinetochore complex component NUF2 (NUF2), NDC80 kinetochore complex component SPC24 (SPC24), and SPC25, plays a critical role in kinetochore–microtubule attachment. Mounting evidence indicates that phosphorylation of HEC1 is important for regulating the binding of the NDC80 complex to microtubules. However, it remains unclear whether other post-translation...
Source: Journal of Biological Chemistry - January 11, 2019 Category: Chemistry Authors: Gangyin Zhao, Yubao Cheng, Ping Gui, Meiying Cui, Wei Liu, Wenwen Wang, Xueying Wang, Mahboob Ali, Zhen Dou, Liwen Niu, Haiyan Liu, Leonard Anderson, Ke Ruan, Jingjun Hong, Xuebiao Yao Tags: Cell Biology Source Type: research

MAPK- and glycogen synthase kinase 3-mediated phosphorylation regulates the DEAD-box protein modulator Gle1 for control of stress granule dynamics [Gene Regulation]
Rapid expression of critical stress response factors is a key survival strategy for diseased or stressed cells. During cell stress, translation is inhibited, and a pre-existing pool of cytoplasmic mRNA–protein complexes reversibly assembles into cytoplasmic stress granules (SGs). Gle1 is a conserved modulator of RNA-dependent DEAD-box proteins required for mRNA export, translation, and stress responses. Proper Gle1 function is critical as reflected by some human diseases such as developmental and neurodegenerative disorders and some cancers linked to gle1 mutations. However, the mechanism by which Gle1 controls SG fo...
Source: Journal of Biological Chemistry - January 11, 2019 Category: Chemistry Authors: Aditi, Aaron C. Mason, Manisha Sharma, T. Renee Dawson, Susan R. Wente Tags: Cell Biology Source Type: research

Mutation of the gene encoding the circadian clock component PERIOD2 in oncogenic cells confers chemoresistance by up-regulating the Aldh3a1 gene [Gene Regulation]
In this study, we found that oncogene-transformed embryonic fibroblasts prepared from Per2-mutant (Per2m/m) mice, which are susceptible to both spontaneous and radiation-induced tumorigenesis, were resistant against common chemotherapeutic drugs and that this resistance is associated with up-regulation of the aldehyde dehydrogenase 3a1 (Aldh3a1) gene. Co-expression of the oncogenes H-rasV12 and SV40 large T-antigen induced malignant transformation of both WT and Per2m/m cells, but the cytotoxic effects of the chemotherapeutic agents methotrexate, gemcitabine, etoposide, vincristine, and oxaliplatin were significantly allev...
Source: Journal of Biological Chemistry - January 11, 2019 Category: Chemistry Authors: Chiharu Katamune, Satoru Koyanagi, Ken-ichi Hashikawa, Naoki Kusunose, Takahiro Akamine, Naoya Matsunaga, Shigehiro Ohdo Tags: Cell Biology Source Type: research

G{beta}{gamma} signaling to the chemotactic effector P-REX1 and mammalian cell migration is directly regulated by G{alpha}q and G{alpha}13 proteins [Cell Biology]
G protein–coupled receptors stimulate Rho guanine nucleotide exchange factors that promote mammalian cell migration. Rac and Rho GTPases exert opposing effects on cell morphology and are stimulated downstream of Gβγ and Gα12/13 or Gαq, respectively. These Gα subunits might in turn favor Rho pathways by preventing Gβγ signaling to Rac. Here, we investigated whether Gβγ signaling to phosphatidylinositol 3,4,5-trisphosphate–dependent Rac exchange factor 1 (P-REX1), a key Gβγ chemotactic effector, is directly controlled by Rho-activating Gα subunit...
Source: Journal of Biological Chemistry - January 11, 2019 Category: Chemistry Authors: Rodolfo Daniel Cervantes–Villagrana, Sendi Rafael Adame–Garcia, Irving Garcia–Jimenez, Victor Manuel Color–Aparicio, Yarely Mabell Beltran–Navarro, Gabriele M. Konig, Evi Kostenis, Guadalupe Reyes–Cruz, J. Silvio Gutkin Tags: Signal Transduction Source Type: research

Domain analysis of PNKP-XRCC1 interactions: Influence of genetic variants of XRCC1 [DNA and Chromosomes]
Polynucleotide kinase/phosphatase (PNKP) and X-ray repair cross-complementing 1 (XRCC1) are key proteins in the single-strand DNA break repair pathway. Phosphorylated XRCC1 stimulates PNKP by binding to its forkhead-associated (FHA) domain, whereas nonphosphorylated XRCC1 stimulates PNKP by interacting with the PNKP catalytic domain. Here, we have further studied the interactions between these two proteins, including two variants of XRCC1 (R194W and R280H) arising from single-nucleotide polymorphisms (SNPs) that have been associated with elevated cancer risk in some reports. We observed that interaction of the PNKP FHA dom...
Source: Journal of Biological Chemistry - January 11, 2019 Category: Chemistry Authors: Rajam S. Mani, Inbal Mermershtain, Ismail Abdou, Mesfin Fanta, Michael J. Hendzel, J. N. Mark Glover, Michael Weinfeld Tags: Protein Structure and Folding Source Type: research

Receptor-interacting Ser/Thr kinase 1 (RIPK1) and myosin IIA-dependent ceramidosomes form membrane pores that mediate blebbing and necroptosis [Cell Biology]
In conclusion, our findings indicate that the RIPK1–ceramide complex forms large membrane pores we named ceramidosomes. They further suggest that, in addition to their roles in stress-mediated necroptosis, these ceramide-enriched pores also regulate membrane integrity and signaling and might also play a role in D. melanogaster ovary development. (Source: Journal of Biological Chemistry)
Source: Journal of Biological Chemistry - January 11, 2019 Category: Chemistry Authors: Rose Nganga, Natalia Oleinik, Jisun Kim, Shanmugam Panneer Selvam, Ryan De Palma, Kristen A. Johnson, Rasesh Y. Parikh, Vamsi Gangaraju, Yuri Peterson, Mohammed Dany, Robert V. Stahelin, Christina Voelkel-Johnson, Zdzislaw M. Szulc, Erhard Bieberich, Besi Tags: Cell Biology Source Type: research

Dynamic interactions of the homologous pairing 2 (Hop2)-meiotic nuclear divisions 1 (Mnd1) protein complex with meiotic presynaptic filaments in budding yeast [Molecular Biophysics]
Homologous recombination (HR) is a universally conserved DNA repair pathway that can result in the exchange of genetic material. In eukaryotes, HR has evolved into an essential step in meiosis. During meiosis many eukaryotes utilize a two-recombinase pathway. This system consists of Rad51 and the meiosis-specific recombinase Dmc1. Both recombinases have distinct activities during meiotic HR, despite being highly similar in sequence and having closely related biochemical activities, raising the question of how these two proteins can perform separate functions. A likely explanation for their differential regulation involves ...
Source: Journal of Biological Chemistry - January 11, 2019 Category: Chemistry Authors: J. Brooks Crickard, Youngho Kwon, Patrick Sung, Eric C. Greene Tags: DNA and Chromosomes Source Type: research

Proteolysis of methylated SOX2 protein is regulated by L3MBTL3 and CRL4DCAF5 ubiquitin ligase [Protein Synthesis and Degradation]
SOX2 is a dose-dependent master stem cell protein that controls the self-renewal and pluripotency or multipotency of embryonic stem (ES) cells and many adult stem cells. We have previously found that SOX2 protein is monomethylated at lysine residues 42 and 117 by SET7 methyltransferase to promote SOX2 proteolysis, whereas LSD1 and PHF20L1 act on both methylated Lys-42 and Lys-117 to prevent SOX2 proteolysis. However, the mechanism by which the methylated SOX2 protein is degraded remains unclear. Here, we report that L3MBTL3, a protein with the malignant-brain-tumor (MBT) methylation–binding domain, is required for SO...
Source: Journal of Biological Chemistry - January 11, 2019 Category: Chemistry Authors: Chunxiao Zhang, Feng Leng, Lovely Saxena, Nam Hoang, Jiekai Yu, Salvador Alejo, Logan Lee, Dandan Qi, Fei Lu, Hong Sun, Hui Zhang Tags: Cell Biology Source Type: research

Overexpression of the CORVET complex alleviates the fungicidal effects of fludioxonil on the yeast Saccharomyces cerevisiae expressing hybrid histidine kinase 3 [Signal Transduction]
The hybrid histidine kinase 3 (HHK3) is a highly conserved sensor kinase in fungi that regulates the downstream HOG/p38 mitogen-activated protein kinase (MAPK). In addition to its role in osmoadaptation, HHK3 is involved in hyphal morphogenesis, conidiation, virulence, and cellular adaptation to oxidative stress. However, the molecular mechanisms by which it controls these processes remain obscure. Moreover, HHK3 is a molecular target for antifungal agents such as fludioxonil, which thereby interferes with the HOG/p38 pathway, leading to the abnormal accumulation of glycerol and subsequent cell lysis. Here, we used a chemi...
Source: Journal of Biological Chemistry - January 11, 2019 Category: Chemistry Authors: Anmoldeep Randhawa, Debasree Kundu, Anupam Sharma, Rajendra Prasad, Alok K. Mondal Tags: Microbiology Source Type: research

Structure of human cortisol-producing cytochrome P450 11B1 bound to the breast cancer drug fadrozole provides insights for drug design [Molecular Bases of Disease]
Human cytochrome P450 11B1 (CYP11B1) is responsible for the final step generating the steroid hormone cortisol, which controls stress and immune responses and glucose homeostasis. CYP11B1 is a promising drug target to manage Cushing's disease, a disorder arising from excessive cortisol production. However, the design of selective inhibitors has been hampered because structural information for CYP11B1 is unavailable and the enzyme has high amino acid sequence identity (93%) to a closely related enzyme, the aldosterone-producing CYP11B2. Here we report the X-ray crystal structure of human CYP11B1 (at 2.1 Å resolution) ...
Source: Journal of Biological Chemistry - January 11, 2019 Category: Chemistry Authors: Simone Brixius-Anderko, Emily E. Scott Tags: Protein Structure and Folding Source Type: research