Bid, One of the First Family Members Described with a BH3 Domain Only, Is a Cytosolic Protein and Lacks a Membrane Targeting Sequence
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Supplementary Materials: Evaluation of Cytotoxicity and Α-Glucosidase Inhibitory Activity of Amide and Polyamino-Derivatives of Lupane Triterpenoids
Supplementary Materials: Evaluation of cytotoxicity and α-glucosidase inhibitory activity of amide and polyamino-derivatives of lupane triterpenoids Oxana B. Kazakova1*, Gul'nara V. Giniyatullina1, Akhat G. Mustafin1, Denis A. Babkov2, Elena V. Sokolova2, Alexander A. Spasov2* 1Ufa Institute of Chemistry of the Ufa Federal Research Centre of the Russian Academy of Sciences, 71, pr. Oktyabrya, 450054 Ufa, Russian Federation 2Scientific Center for Innovative Drugs, Volgograd State Medical University, Novorossiyskaya st. 39, Volgograd 400087, Russian Federation Correspondence Prof. Dr. Oxana B. Kazakova Ufa Institute of Chemistry of the Ufa Federal Research Centre of the Russian Academy of Sciences 71 Prospeсt Oktyabrya Ufa, 450054 Russian Federation E-mail: [email protected] Prof. Dr. Alexander A. Spasov Scientific Center for Innovative Drugs of the Volgograd State Medical University 39 Novorossiyskaya st. Volgograd, 400087 Russian Federation E-mail: [email protected] Figure S1. 1H and 13C of compound 2. H NH N H O H O H 2 2 Figure S2. 1H and 13C of compound 4. NH2 O H O H CH3 O O H H3C O H 4 3 Figure S3. Anticancer screening data of compound 2 at single dose assay 4 Figure S4. Anticancer screening data of compound 7 at single dose assay 5 Figure S5. Anticancer screening data of compound 8 at single dose assay 6 Figure S6. Anticancer screening data of compound 9 at single dose assay 7 Figure S7. Anticancer screening data of compound 12 at single dose assay 8 Figure S8. Anticancer screening data of compound 13 at single dose assay 9 Figure S9. Anticancer screening data of compound 14 at single dose assay 10 Figure S10. -
Role of CCCH-Type Zinc Finger Proteins in Human Adenovirus Infections
viruses Review Role of CCCH-Type Zinc Finger Proteins in Human Adenovirus Infections Zamaneh Hajikhezri 1, Mahmoud Darweesh 1,2, Göran Akusjärvi 1 and Tanel Punga 1,* 1 Department of Medical Biochemistry and Microbiology, Uppsala University, 75123 Uppsala, Sweden; [email protected] (Z.H.); [email protected] (M.D.); [email protected] (G.A.) 2 Department of Microbiology and Immunology, Al-Azhr University, Assiut 11651, Egypt * Correspondence: [email protected]; Tel.: +46-733-203-095 Received: 28 October 2020; Accepted: 16 November 2020; Published: 18 November 2020 Abstract: The zinc finger proteins make up a significant part of the proteome and perform a huge variety of functions in the cell. The CCCH-type zinc finger proteins have gained attention due to their unusual ability to interact with RNA and thereby control different steps of RNA metabolism. Since virus infections interfere with RNA metabolism, dynamic changes in the CCCH-type zinc finger proteins and virus replication are expected to happen. In the present review, we will discuss how three CCCH-type zinc finger proteins, ZC3H11A, MKRN1, and U2AF1, interfere with human adenovirus replication. We will summarize the functions of these three cellular proteins and focus on their potential pro- or anti-viral activities during a lytic human adenovirus infection. Keywords: human adenovirus; zinc finger protein; CCCH-type; ZC3H11A; MKRN1; U2AF1 1. Zinc Finger Proteins Zinc finger proteins are a big family of proteins with characteristic zinc finger (ZnF) domains present in the protein sequence. The ZnF domains consists of various ZnF motifs, which are short 30–100 amino acid sequences, coordinating zinc ions (Zn2+). -
A Computational Approach for Defining a Signature of Β-Cell Golgi Stress in Diabetes Mellitus
Page 1 of 781 Diabetes A Computational Approach for Defining a Signature of β-Cell Golgi Stress in Diabetes Mellitus Robert N. Bone1,6,7, Olufunmilola Oyebamiji2, Sayali Talware2, Sharmila Selvaraj2, Preethi Krishnan3,6, Farooq Syed1,6,7, Huanmei Wu2, Carmella Evans-Molina 1,3,4,5,6,7,8* Departments of 1Pediatrics, 3Medicine, 4Anatomy, Cell Biology & Physiology, 5Biochemistry & Molecular Biology, the 6Center for Diabetes & Metabolic Diseases, and the 7Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202; 2Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202; 8Roudebush VA Medical Center, Indianapolis, IN 46202. *Corresponding Author(s): Carmella Evans-Molina, MD, PhD ([email protected]) Indiana University School of Medicine, 635 Barnhill Drive, MS 2031A, Indianapolis, IN 46202, Telephone: (317) 274-4145, Fax (317) 274-4107 Running Title: Golgi Stress Response in Diabetes Word Count: 4358 Number of Figures: 6 Keywords: Golgi apparatus stress, Islets, β cell, Type 1 diabetes, Type 2 diabetes 1 Diabetes Publish Ahead of Print, published online August 20, 2020 Diabetes Page 2 of 781 ABSTRACT The Golgi apparatus (GA) is an important site of insulin processing and granule maturation, but whether GA organelle dysfunction and GA stress are present in the diabetic β-cell has not been tested. We utilized an informatics-based approach to develop a transcriptional signature of β-cell GA stress using existing RNA sequencing and microarray datasets generated using human islets from donors with diabetes and islets where type 1(T1D) and type 2 diabetes (T2D) had been modeled ex vivo. To narrow our results to GA-specific genes, we applied a filter set of 1,030 genes accepted as GA associated. -
Structural and Functional Diversity of Caspase Homologues in Non-Metazoan Organisms
Protoplasma DOI 10.1007/s00709-017-1145-5 REVIEW ARTICLE Structural and functional diversity of caspase homologues in non-metazoan organisms Marina Klemenčič1,2 & Christiane Funk1 Received: 1 June 2017 /Accepted: 5 July 2017 # The Author(s) 2017. This article is an open access publication Abstract Caspases, the proteases involved in initiation and supports the role of metacaspases and orthocaspases as im- execution of metazoan programmed cell death, are only pres- portant contributors to cell homeostasis during normal physi- ent in animals, while their structural homologues can be ological conditions or cell differentiation and ageing. found in all domains of life, spanning from simple prokary- otes (orthocaspases) to yeast and plants (metacaspases). All members of this wide protease family contain the p20 do- Keywords Algae . Cyanobacteria . Cell death . Cysteine main, which harbours the catalytic dyad formed by the two protease . Metacaspase . Orthocaspase amino acid residues, histidine and cysteine. Despite the high structural similarity of the p20 domain, metacaspases and orthocaspases were found to exhibit different substrate speci- ficities than caspases. While the former cleave their substrates Introduction after basic amino acid residues, the latter accommodate sub- strates with negative charge. This observation is crucial for BOut of life’s school of war: What does not destroy me, the re-evaluation of non-metazoan caspase homologues being makes me stronger.^ wrote the German philosopher involved in processes of programmed cell death. In this re- Friedrich Nietzsche in his book Twilight of the Idols or view, we analyse the structural diversity of enzymes contain- how to philosophize with a hammer. Even though ing the p20 domain, with focus on the orthocaspases, and reformatted to more common use, this phrase has been summarise recent advances in research of orthocaspases and used to describe the dual nature of caspase homologues metacaspases of cyanobacteria, algae and higher plants. -
Yeast Genome Gazetteer P35-65
gazetteer Metabolism 35 tRNA modification mitochondrial transport amino-acid metabolism other tRNA-transcription activities vesicular transport (Golgi network, etc.) nitrogen and sulphur metabolism mRNA synthesis peroxisomal transport nucleotide metabolism mRNA processing (splicing) vacuolar transport phosphate metabolism mRNA processing (5’-end, 3’-end processing extracellular transport carbohydrate metabolism and mRNA degradation) cellular import lipid, fatty-acid and sterol metabolism other mRNA-transcription activities other intracellular-transport activities biosynthesis of vitamins, cofactors and RNA transport prosthetic groups other transcription activities Cellular organization and biogenesis 54 ionic homeostasis organization and biogenesis of cell wall and Protein synthesis 48 plasma membrane Energy 40 ribosomal proteins organization and biogenesis of glycolysis translation (initiation,elongation and cytoskeleton gluconeogenesis termination) organization and biogenesis of endoplasmic pentose-phosphate pathway translational control reticulum and Golgi tricarboxylic-acid pathway tRNA synthetases organization and biogenesis of chromosome respiration other protein-synthesis activities structure fermentation mitochondrial organization and biogenesis metabolism of energy reserves (glycogen Protein destination 49 peroxisomal organization and biogenesis and trehalose) protein folding and stabilization endosomal organization and biogenesis other energy-generation activities protein targeting, sorting and translocation vacuolar and lysosomal -
TRAF5, a Novel Tumor Necrosis Factor Receptor-Associated Factor Family
Proc. Natl. Acad. Sci. USA Vol. 93, pp. 9437-9442, September 1996 Biochemistry TRAF5, a novel tumor necrosis factor receptor-associated factor family protein, mediates CD40 signaling (signal transduction/protein-protein interaction/yeast two-hybrid system) TAKAoMI ISHIDA*, TADASHI ToJo*, TSUTOMU AOKI*, NORIHIKO KOBAYASHI*, TSUKASA OHISHI*, TOSHIKI WATANABEt, TADASHI YAMAMOTO*, AND JUN-ICHIRO INOUE*t Departments of *Oncology and tPathology, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108, Japan Communicated by David Baltimore, Massachusetts Institute of Technology, Cambridge, MA, May 22, 1996 (received for review March 8, 1996) ABSTRACT Signals emanating from CD40 play crucial called a death domain, suggesting that these receptors could roles in B-cell function. To identify molecules that transduce have either common or similar signaling mechanisms (13). CD40 signalings, we have used the yeast two-hybrid system to Biochemical purification of receptor-associated proteins or the clone cDNAs encoding proteins that bind the cytoplasmic tail recently developed cDNA cloning system that uses yeast of CD40. A cDNA encoding a putative signal transducer genetic selection led to the discovery of two groups of signal protein, designated TRAF5, has been molecularly cloned. transducer molecules. Members of the first group are proteins TRAF5 has a tumor necrosis factor receptor-associated factor with a TRAF domain for TNFR2 and CD40 such as TRAF1, (TRAF) domain in its carboxyl terminus and is most homol- TRAF2 (17), and TRAF3, also known as CD40bp, LAP-1, or ogous to TRAF3, also known as CRAF1, CD40bp, or LAP-1, CRAF1 or CD40 receptor-associated factor (18-20). -
Comparative Study of Apoptosis-Related Gene Loci in Human, Mouse and Rat Genomes
ISSN 1672-9145 Acta Biochimica et Biophysica Sinica 2005, 37(5): 341–348 CN 31-1940/Q Comparative Study of Apoptosis-related Gene Loci in Human, Mouse and Rat Genomes Yan-Bin YIN, Yong ZHANG, Peng YU, Jing-Chu LUO, Ying JIANG*, and Song-Gang LI* Center of Bioinformatics, National Laboratory of Genetic Engineering and Protein Engineering, College of Life Sciences, Peking University, Beijing 100871, China Downloaded from Abstract Many genes are involved in mammalian cell apoptosis pathway. These apoptosis genes often contain characteristic functional domains, and can be classified into at least 15 functional groups, according to previous reports. Using an integrated bioinformatics platform for motif or domain search from three public mammalian proteomes (International Protein Index database for human, mouse, and rat), we system- atically cataloged all of the proteins involved in mammalian apoptosis pathway. By localizing those proteins http://abbs.oxfordjournals.org/ onto the genomes, we obtained a gene locus centric apoptosis gene catalog for human, mouse and rat. Further phylogenetic analysis showed that most of the apoptosis related gene loci are conserved among these three mammals. Interestingly, about one-third of apoptosis gene loci form gene clusters on mammal chromosomes, and exist in the three species, which indicated that mammalian apoptosis gene orders are also conserved. In addition, some tandem duplicated gene loci were revealed by comparing gene loci clusters in the three species. All data produced in this work were stored in a relational database and may be viewed at http://pcas.cbi.pku.edu.cn/database/apd.php. at Institute of Zoology, CAS on November 2, 2011 Key words apoptosis; gene cluster; comparative genomics; bioinformatics Apoptosis is a regulated program by which cells destroy between mouse and human, they revealed that most themselves [1]. -
FLIP and the Death Effector Domain Family
Oncogene (2008) 27, 6216–6227 & 2008 Macmillan Publishers Limited All rights reserved 0950-9232/08 $32.00 www.nature.com/onc REVIEW FLIP and the death effector domain family JW Yu and Y Shi Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, Princeton, NJ, USA Death effector domains (DEDs) are protein interaction and stress that impinge on the mitochondria or modules found in a number of proteins known to regulate ‘extrinsically’ from extracellular ligands that activate apoptosis from death receptors. The core DED family death receptors at the cell surface. In either scenario, members that orchestrate programmed cell death from each pathway critically relies on the action of a family of death receptors include the adaptor protein FADD, the cysteine proteases known as caspases to initiate and initiator caspases procaspases-8 and -10 and the regulatory execute the cell death process through a two-step protein c-FLIP. Through homotypic DED interactions, cascade (Riedl and Shi, 2004). In the apoptotic these proteins assemble into the death-inducingsignaling proteolytic cascade, the initiator caspases (caspases-2, complex (DISC) to regulate initiator caspase activation -8, -9 and -10) cleave and consequently activate the and launch the apoptotic proteolytic cascade. A consider- effector caspases (caspases-3, -6 and -7), and the effector able body of evidence, however, is revealingthat the same caspases in turn cleave a large array of substrates to core group of DED-containing proteins also paradoxically dismantle and package the cell into apoptotic bodies. promotes survival and proliferation in lymphocytes and Activation of initiator caspases for both the intrinsic possibly other cell types. -
Supplementary Table S4. FGA Co-Expressed Gene List in LUAD
Supplementary Table S4. FGA co-expressed gene list in LUAD tumors Symbol R Locus Description FGG 0.919 4q28 fibrinogen gamma chain FGL1 0.635 8p22 fibrinogen-like 1 SLC7A2 0.536 8p22 solute carrier family 7 (cationic amino acid transporter, y+ system), member 2 DUSP4 0.521 8p12-p11 dual specificity phosphatase 4 HAL 0.51 12q22-q24.1histidine ammonia-lyase PDE4D 0.499 5q12 phosphodiesterase 4D, cAMP-specific FURIN 0.497 15q26.1 furin (paired basic amino acid cleaving enzyme) CPS1 0.49 2q35 carbamoyl-phosphate synthase 1, mitochondrial TESC 0.478 12q24.22 tescalcin INHA 0.465 2q35 inhibin, alpha S100P 0.461 4p16 S100 calcium binding protein P VPS37A 0.447 8p22 vacuolar protein sorting 37 homolog A (S. cerevisiae) SLC16A14 0.447 2q36.3 solute carrier family 16, member 14 PPARGC1A 0.443 4p15.1 peroxisome proliferator-activated receptor gamma, coactivator 1 alpha SIK1 0.435 21q22.3 salt-inducible kinase 1 IRS2 0.434 13q34 insulin receptor substrate 2 RND1 0.433 12q12 Rho family GTPase 1 HGD 0.433 3q13.33 homogentisate 1,2-dioxygenase PTP4A1 0.432 6q12 protein tyrosine phosphatase type IVA, member 1 C8orf4 0.428 8p11.2 chromosome 8 open reading frame 4 DDC 0.427 7p12.2 dopa decarboxylase (aromatic L-amino acid decarboxylase) TACC2 0.427 10q26 transforming, acidic coiled-coil containing protein 2 MUC13 0.422 3q21.2 mucin 13, cell surface associated C5 0.412 9q33-q34 complement component 5 NR4A2 0.412 2q22-q23 nuclear receptor subfamily 4, group A, member 2 EYS 0.411 6q12 eyes shut homolog (Drosophila) GPX2 0.406 14q24.1 glutathione peroxidase -
Nutrient Limitation Inactivates Mrc1-To-Cds1 Checkpoint Signalling in Schizosaccharomyces Pombe
cells Article Nutrient Limitation Inactivates Mrc1-to-Cds1 Checkpoint Signalling in Schizosaccharomyces pombe Jessica Fletcher 1,2 ID , Liam Griffiths 1 and Thomas Caspari 1,3,* ID 1 School of Medical Sciences, Bangor University, Bangor LL57 2UW, UK; j.f.fl[email protected] (J.F.); lbgriffi[email protected] (L.G.) 2 Medical School, Swansea University, Swansea SA2 8PP, UK 3 Postgraduate Doctoral Studies, Paracelsus Medical University, 5020 Salzburg, Austria * Correspondence: [email protected]; Tel.: +43-662-2420-80245 Received: 11 February 2018; Accepted: 21 February 2018; Published: 23 February 2018 Abstract: The S. pombe checkpoint kinase, Cds1, protects the integrity of stalled DNA replication forks after its phosphorylation at threonine-11 by Rad3 (ATR). Modified Cds1 associates through its N-terminal forkhead-associated domain (FHA)-domain with Mrc1 (Claspin) at stalled forks. We report here that nutrient starvation results in post-translational changes to Cds1 and the loss of Mrc1. A drop in glucose after a down-shift from 3% to 0.1–0.3%, or when cells enter the stationary phase, triggers a sharp decline in Mrc1 and the accumulation of insoluble Cds1. Before this transition, Cds1 is transiently activated and phosphorylated by Rad3 when glucose levels fall. Because this coincides with the phosphorylation of histone 2AX at S129 by Rad3, an event that occurs towards the end of every unperturbed S phase, we suggest that a glucose limitation promotes the exit from the S phase. Since nitrogen starvation also depletes Mrc1 while Cds1 is post-translationally modified, we suggest that nutrient limitation is the general signal that promotes exit from S phase before it inactivates the Mrc1–Cds1 signalling component. -
The Microbiota-Produced N-Formyl Peptide Fmlf Promotes Obesity-Induced Glucose
Page 1 of 230 Diabetes Title: The microbiota-produced N-formyl peptide fMLF promotes obesity-induced glucose intolerance Joshua Wollam1, Matthew Riopel1, Yong-Jiang Xu1,2, Andrew M. F. Johnson1, Jachelle M. Ofrecio1, Wei Ying1, Dalila El Ouarrat1, Luisa S. Chan3, Andrew W. Han3, Nadir A. Mahmood3, Caitlin N. Ryan3, Yun Sok Lee1, Jeramie D. Watrous1,2, Mahendra D. Chordia4, Dongfeng Pan4, Mohit Jain1,2, Jerrold M. Olefsky1 * Affiliations: 1 Division of Endocrinology & Metabolism, Department of Medicine, University of California, San Diego, La Jolla, California, USA. 2 Department of Pharmacology, University of California, San Diego, La Jolla, California, USA. 3 Second Genome, Inc., South San Francisco, California, USA. 4 Department of Radiology and Medical Imaging, University of Virginia, Charlottesville, VA, USA. * Correspondence to: 858-534-2230, [email protected] Word Count: 4749 Figures: 6 Supplemental Figures: 11 Supplemental Tables: 5 1 Diabetes Publish Ahead of Print, published online April 22, 2019 Diabetes Page 2 of 230 ABSTRACT The composition of the gastrointestinal (GI) microbiota and associated metabolites changes dramatically with diet and the development of obesity. Although many correlations have been described, specific mechanistic links between these changes and glucose homeostasis remain to be defined. Here we show that blood and intestinal levels of the microbiota-produced N-formyl peptide, formyl-methionyl-leucyl-phenylalanine (fMLF), are elevated in high fat diet (HFD)- induced obese mice. Genetic or pharmacological inhibition of the N-formyl peptide receptor Fpr1 leads to increased insulin levels and improved glucose tolerance, dependent upon glucagon- like peptide-1 (GLP-1). Obese Fpr1-knockout (Fpr1-KO) mice also display an altered microbiome, exemplifying the dynamic relationship between host metabolism and microbiota. -
Two-Stage Mechanism for Activation of the DNA Replication Checkpoint Kinase Cds1 in Fission Yeast
Downloaded from genesdev.cshlp.org on September 27, 2021 - Published by Cold Spring Harbor Laboratory Press Two-stage mechanism for activation of the DNA replication checkpoint kinase Cds1 in fission yeast Yong-jie Xu,1,2 Matthew Davenport,1 and Thomas J. Kelly1,3 1Program in Molecular Biology, Sloan-Kettering Institute, New York, New York 10021, USA; 2Biochemistry, Cellular and Molecular Biology Program, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA The DNA replication checkpoint is a complex signal transduction pathway, present in all eukaryotic cells, that functions to maintain genomic integrity and cell viability when DNA replication is perturbed. In Schizosaccharomyces pombe the major effector of the replication checkpoint is the protein kinase Cds1. Activation of Cds1 is known to require the upstream kinase Rad3 and the mediator Mrc1, but the biochemical mechanism of activation is not well understood. We report that the replication checkpoint is activated in two stages. In the first stage, Mrc1 recruits Cds1 to stalled replication forks by interactions between the FHA domain of Cds1 and specific phosphorylated Rad3 consensus sites in Mrc1. Cds1 is then primed for activation by Rad3-dependent phosphorylation. In the second stage, primed Cds1 molecules dimerize via phospho-specific interactions mediated by the FHA domains and are activated by autophosphorylation. This two-stage activation mechanism for the replication checkpoint allows for rapid activation with a high signal-to-noise ratio. [Keywords: Cds1 autoactivation; Cds1 autophosphorylation; Cds1 dimerization; Mrc1 SQ cluster; Mrc1 TQ repeats; replication checkpoint] Supplemental material is available at http://www.genesdev.org. Received December 30, 2005; revised version accepted February 9, 2006.