Pdf 2019; 572: 402-6
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
Structure of the Human Frataxin-Bound Iron-Sulfur Cluster Assembly Complex Provides Insight Into Its Activation Mechanism
bioRxiv preprint doi: https://doi.org/10.1101/561795; this version posted February 28, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. Structure of the human frataxin-bound iron-sulfur cluster assembly complex provides insight into its activation mechanism Nicholas G. Fox1,4, Xiaodi Yu2,4, Xidong Feng2, Henry J. Bailey1, Alain Martelli3, Joseph F. Nabhan3, Claire Strain-Damerell1, Christine Bulawa3, Wyatt W. Yue1,*, Seungil Han2,* 1Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, UK OX3 7DQ 2Discovery Sciences, Worldwide Research and Development, Pfizer Inc., Eastern Point Road, Groton, CT, 06340, United States 3Rare Disease Research Unit, Worldwide Research and Development, Pfizer Inc., 610 Main Street, Cambridge, MA, 02139, United States 4These authors contributed equally. *Correspondence should be addressed to Wyatt W. Yue, [email protected] Seungil Han, [email protected] 1 bioRxiv preprint doi: https://doi.org/10.1101/561795; this version posted February 28, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. Abstract Iron-sulfur clusters (ISC) are essential in all life forms and carry out many crucial cellular functions. The core machinery for de novo ISC biosynthesis, located in the mitochondria matrix, is a five- protein complex containing the cysteine desulfurase NFS1 that is activated by frataxin (FXN), scaffold protein ISCU, accessory protein ISD11, and acyl-carrier protein ACP. -
High-Throughput Discovery of Novel Developmental Phenotypes
High-throughput discovery of novel developmental phenotypes The Harvard community has made this article openly available. Please share how this access benefits you. Your story matters Citation Dickinson, M. E., A. M. Flenniken, X. Ji, L. Teboul, M. D. Wong, J. K. White, T. F. Meehan, et al. 2016. “High-throughput discovery of novel developmental phenotypes.” Nature 537 (7621): 508-514. doi:10.1038/nature19356. http://dx.doi.org/10.1038/nature19356. Published Version doi:10.1038/nature19356 Citable link http://nrs.harvard.edu/urn-3:HUL.InstRepos:32071918 Terms of Use This article was downloaded from Harvard University’s DASH repository, and is made available under the terms and conditions applicable to Other Posted Material, as set forth at http:// nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of- use#LAA HHS Public Access Author manuscript Author ManuscriptAuthor Manuscript Author Nature. Manuscript Author Author manuscript; Manuscript Author available in PMC 2017 March 14. Published in final edited form as: Nature. 2016 September 22; 537(7621): 508–514. doi:10.1038/nature19356. High-throughput discovery of novel developmental phenotypes A full list of authors and affiliations appears at the end of the article. Abstract Approximately one third of all mammalian genes are essential for life. Phenotypes resulting from mouse knockouts of these genes have provided tremendous insight into gene function and congenital disorders. As part of the International Mouse Phenotyping Consortium effort to generate and phenotypically characterize 5000 knockout mouse lines, we have identified 410 Users may view, print, copy, and download text and data-mine the content in such documents, for the purposes of academic research, subject always to the full Conditions of use:http://www.nature.com/authors/editorial_policies/license.html#terms #Corresponding author: [email protected]. -
Anti-NFS1 Antibody (ARG56331)
Product datasheet [email protected] ARG56331 Package: 100 μl anti-NFS1 antibody Store at: -20°C Summary Product Description Rabbit Polyclonal antibody recognizes NFS1 Tested Reactivity Hu, Ms, Rat Tested Application ICC/IF, IHC-P, WB Host Rabbit Clonality Polyclonal Isotype IgG Target Name NFS1 Antigen Species Human Immunogen Recombinant protein of Human NFS1 Conjugation Un-conjugated Alternate Names HUSSY-08; NIFS; EC 2.8.1.7; IscS; Cysteine desulfurase, mitochondrial Application Instructions Application table Application Dilution ICC/IF 1:50 - 1:200 IHC-P 1:50 - 1:200 WB 1:500 - 1:2000 Application Note * The dilutions indicate recommended starting dilutions and the optimal dilutions or concentrations should be determined by the scientist. Positive Control Rat liver Calculated Mw 50 kDa Properties Form Liquid Purification Affinity purification with immunogen. Buffer PBS (pH 7.3), 0.02% Sodium azide and 50% Glycerol. Preservative 0.02% Sodium azide Stabilizer 50% Glycerol Storage instruction For continuous use, store undiluted antibody at 2-8°C for up to a week. For long-term storage, aliquot and store at -20°C. Storage in frost free freezers is not recommended. Avoid repeated freeze/thaw cycles. Suggest spin the vial prior to opening. The antibody solution should be gently mixed before use. www.arigobio.com 1/3 Note For laboratory research only, not for drug, diagnostic or other use. Bioinformation Database links GeneID: 18041 Mouse GeneID: 9054 Human Swiss-port # Q9Y697 Human Swiss-port # Q9Z1J3 Mouse Gene Symbol NFS1 Gene Full Name NFS1 cysteine desulfurase Background Iron-sulfur clusters are required for the function of many cellular enzymes. -
NFS1 Mouse Monoclonal Antibody [Clone ID: OTI5D1] Product Data
OriGene Technologies, Inc. 9620 Medical Center Drive, Ste 200 Rockville, MD 20850, US Phone: +1-888-267-4436 [email protected] EU: [email protected] CN: [email protected] Product datasheet for TA805820 NFS1 Mouse Monoclonal Antibody [Clone ID: OTI5D1] Product data: Product Type: Primary Antibodies Clone Name: OTI5D1 Applications: IHC, WB Recommended Dilution: WB 1:500, IHC 1:150 Reactivity: Human, Mouse, Rat Host: Mouse Isotype: IgG2a Clonality: Monoclonal Immunogen: Human recombinant protein fragment corresponding to amino acids 1-299 of human NFS1(NP_066923) produced in E.coli. Formulation: PBS (PH 7.3) containing 1% BSA, 50% glycerol and 0.02% sodium azide. Concentration: 1 mg/ml Purification: Purified from mouse ascites fluids or tissue culture supernatant by affinity chromatography (protein A/G) Conjugation: Unconjugated Storage: Store at -20°C as received. Stability: Stable for 12 months from date of receipt. Predicted Protein Size: 50 kDa Gene Name: NFS1 cysteine desulfurase Database Link: NP_066923 Entrez Gene 18041 MouseEntrez Gene 84594 RatEntrez Gene 9054 Human Q9Y697 This product is to be used for laboratory only. Not for diagnostic or therapeutic use. View online » ©2021 OriGene Technologies, Inc., 9620 Medical Center Drive, Ste 200, Rockville, MD 20850, US 1 / 3 NFS1 Mouse Monoclonal Antibody [Clone ID: OTI5D1] – TA805820 Background: Iron-sulfur clusters are required for the function of many cellular enzymes. The proteins encoded by this gene supply inorganic sulfur to these clusters by removing the sulfur from cysteine, creating alanine in the process. This gene uses alternate in-frame translation initiation sites to generate mitochondrial forms and cytoplasmic/nuclear forms. -
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 -
Fe-S Protein Synthesis in Green Algae Mitochondria
plants Review Fe-S Protein Synthesis in Green Algae Mitochondria Diego F. Gomez-Casati * , Maria V. Busi *, Julieta Barchiesi, Maria A. Pagani , Noelia S. Marchetti-Acosta and Agustina Terenzi Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Universidad Nacional de Rosario, 2000 Rosario, Argentina; [email protected] (J.B.); [email protected] (M.A.P.); [email protected] (N.S.M.-A.); [email protected] (A.T.) * Correspondence: [email protected] (D.F.G.-C.); [email protected] (M.V.B.); Tel.: +54-341-4391955 (ext. 113) (D.F.G.-C. & M.V.B.) Abstract: Iron and sulfur are two essential elements for all organisms. These elements form the Fe-S clusters that are present as cofactors in numerous proteins and protein complexes related to key processes in cells, such as respiration and photosynthesis, and participate in numerous enzymatic reactions. In photosynthetic organisms, the ISC and SUF Fe-S cluster synthesis pathways are located in organelles, mitochondria, and chloroplasts, respectively. There is also a third biosynthetic machinery in the cytosol (CIA) that is dependent on the mitochondria for its function. The genes and proteins that participate in these assembly pathways have been described mainly in bacteria, yeasts, humans, and recently in higher plants. However, little is known about the proteins that participate in these processes in algae. This review work is mainly focused on releasing the information on the existence of genes and proteins of green algae (chlorophytes) that could participate in the assembly process of Fe-S groups, especially in the mitochondrial ISC and CIA pathways. -
Nanopore Sequencing Enables Near-Complete De Novo Assembly of 2 Saccharomyces Cerevisiae Reference Strain CEN.PK113-7D
bioRxiv preprint doi: https://doi.org/10.1101/175984; this version posted August 14, 2017. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 Nanopore sequencing enables near-complete de novo assembly of 2 Saccharomyces cerevisiae reference strain CEN.PK113-7D 3 #,1,3 #,2 2 4 Alex N. Salazar , Arthur R. Gorter de Vries , Marcel van den Broek , Melanie 2 2 2 2 5 Wijsman , Pilar de la Torre Cortés , Anja Brickwedde , Nick Brouwers , Jean-Marc 2 ,1,3 6 G. Daran and Thomas Abeel* # 7 These authors contributed equally to this publication and should be 8 considered co-first authors. 9 * Corresponding author 10 1. Delft Bioinformatics Lab, Delft University of Technology, Delft, The 11 Netherlands 12 2. Department of Biotechnology, Delft University of Technology, Delft, The 13 Netherlands 14 3. Broad Institute of MIT and Harvard, Boston, Massachusetts, USA 15 16 Alex N. Salazar [email protected] 17 Arthur R. Gorter de Vries [email protected] 18 Marcel van den Broek [email protected] 19 Melanie Wijsman [email protected] 20 Pilar de la Torre Cortés [email protected] 21 Anja Brickwedde [email protected] 22 Nick Brouwers [email protected] 23 Jean-Marc G. Daran [email protected] 24 Thomas Abeel [email protected] 25 Manuscript for publication in FEMS Yeast Research 1 bioRxiv preprint doi: https://doi.org/10.1101/175984; this version posted August 14, 2017. -
Structure and Functional Dynamics of the Mitochondrial Fe/S Cluster Synthesis Complex
ARTICLE DOI: 10.1038/s41467-017-01497-1 OPEN Structure and functional dynamics of the mitochondrial Fe/S cluster synthesis complex Michal T. Boniecki1, Sven A. Freibert 2, Ulrich Mühlenhoff2, Roland Lill 2,3 & Miroslaw Cygler 1,4 Iron–sulfur (Fe/S) clusters are essential protein cofactors crucial for many cellular functions including DNA maintenance, protein translation, and energy conversion. De novo Fe/S cluster synthesis occurs on the mitochondrial scaffold protein ISCU and requires cysteine 1234567890 desulfurase NFS1, ferredoxin, frataxin, and the small factors ISD11 and ACP (acyl carrier protein). Both the mechanism of Fe/S cluster synthesis and function of ISD11-ACP are poorly understood. Here, we present crystal structures of three different NFS1-ISD11-ACP complexes with and without ISCU, and we use SAXS analyses to define the 3D architecture of the complete mitochondrial Fe/S cluster biosynthetic complex. Our structural and biochemical studies provide mechanistic insights into Fe/S cluster synthesis at the catalytic center defined by the active-site Cys of NFS1 and conserved Cys, Asp, and His residues of ISCU. We assign specific regulatory rather than catalytic roles to ISD11-ACP that link Fe/S cluster synthesis with mitochondrial lipid synthesis and cellular energy status. 1 Department of Biochemistry, University of Saskatchewan, 107 Wiggins Road, Saskatoon, SK, Canada S7N 5E5. 2 Institut für Zytobiologie und Zytopathologie, Philipps-Universität, Robert-Koch-Strasse 6, 35032 Marburg, Germany. 3 LOEWE Zentrum für Synthetische Mikrobiologie SynMikro, Hans- Meerwein-Strasse, 35043 Marburg, Germany. 4 Department of Biochemistry, McGill University, 3649 Promenade Sir William Osler, Montreal, QC, Canada H3G 0B1. -
Glutamine Deprivation Triggers NAGK-Dependent Hexosamine Salvage
bioRxiv preprint doi: https://doi.org/10.1101/2020.09.13.294116; this version posted September 13, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Glutamine deprivation triggers NAGK-dependent hexosamine salvage Campbell, S.L.1,2, Mesaros, C.3, Affronti, H.1,2, Tsang, T.1,2, Noji, M.1,2, Sun, K.4, Izzo, L.1,2, Trefely, S.1,2,5, Kruijning, S.1,2, Blair, I.A.3, Wellen, K.E.1,2,6 1Department of Cancer Biology, 2Abramson Family Cancer Research Institute, 3Department of Systems Pharmacology and Translational Therapeutics, 4Pancreatic Cancer Research Center, Perelman School of Medicine, University of Pennsylvania; 5Center for Metabolic Disease Research, Department of Microbiology and Immunology, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140. 6Corresponding author. Abstract Tumors of many types exhibit aberrant glycosylation, which can impact cancer progression and therapeutic responses. The hexosamine biosynthesis pathway (HBP) branches from glycolysis at fructose-6-phosphate to synthesize uridine diphosphate N-acetylglucosamine (UDP-GlcNAc), a major substrate for glycosylation in the cell. HBP enzyme gene expression is elevated in pancreatic ductal adenocarcinoma (PDA), and studies have pointed to the potential significance of the HBP as a therapeutic target. Yet, the PDA tumor microenvironment is nutrient poor, and adaptive nutrient acquisition strategies support tumorigenesis. Here, we identify that pancreatic cancer cells salvage GlcNAc via N-acetylglucosamine kinase (NAGK), particularly under glutamine limitation. Glutamine deprivation suppresses de novo HBP flux and triggers upregulation of NAGK. -
The DNA Sequence and Comparative Analysis of Human Chromosome 20
articles The DNA sequence and comparative analysis of human chromosome 20 P. Deloukas, L. H. Matthews, J. Ashurst, J. Burton, J. G. R. Gilbert, M. Jones, G. Stavrides, J. P. Almeida, A. K. Babbage, C. L. Bagguley, J. Bailey, K. F. Barlow, K. N. Bates, L. M. Beard, D. M. Beare, O. P. Beasley, C. P. Bird, S. E. Blakey, A. M. Bridgeman, A. J. Brown, D. Buck, W. Burrill, A. P. Butler, C. Carder, N. P. Carter, J. C. Chapman, M. Clamp, G. Clark, L. N. Clark, S. Y. Clark, C. M. Clee, S. Clegg, V. E. Cobley, R. E. Collier, R. Connor, N. R. Corby, A. Coulson, G. J. Coville, R. Deadman, P. Dhami, M. Dunn, A. G. Ellington, J. A. Frankland, A. Fraser, L. French, P. Garner, D. V. Grafham, C. Grif®ths, M. N. D. Grif®ths, R. Gwilliam, R. E. Hall, S. Hammond, J. L. Harley, P. D. Heath, S. Ho, J. L. Holden, P. J. Howden, E. Huckle, A. R. Hunt, S. E. Hunt, K. Jekosch, C. M. Johnson, D. Johnson, M. P. Kay, A. M. Kimberley, A. King, A. Knights, G. K. Laird, S. Lawlor, M. H. Lehvaslaiho, M. Leversha, C. Lloyd, D. M. Lloyd, J. D. Lovell, V. L. Marsh, S. L. Martin, L. J. McConnachie, K. McLay, A. A. McMurray, S. Milne, D. Mistry, M. J. F. Moore, J. C. Mullikin, T. Nickerson, K. Oliver, A. Parker, R. Patel, T. A. V. Pearce, A. I. Peck, B. J. C. T. Phillimore, S. R. Prathalingam, R. W. Plumb, H. Ramsay, C. M. -
Cdna Cloning and Characterization of Mouse Nifs-Like Protein, M-Nfs1: Mitochondrial Localization of Eukaryotic Nifs-Like Proteins
View metadata,FEBS 20659 citation and similar papers at core.ac.uk FEBS Letters 433 (1998)brought to143^148 you by CORE provided by Elsevier - Publisher Connector cDNA cloning and characterization of mouse nifS-like protein, m-Nfs1: mitochondrial localization of eukaryotic NifS-like proteins Yumi Nakai, Yoshihiro Yoshihara, Hideyuki Hayashi, Hiroyuki Kagamiyama* Department of Biochemistry, Osaka Medical College, 2-7 Daigaku-machi, Takatsuki, Osaka 569-8686, Japan Received 15 June 1998; revised version received 17 July 1998 In the present study, we have cloned the mouse nifS-like Abstract We have isolated a mouse cDNA which shows significant sequence similarity to the yeast nifS-like gene (y- cDNA (named m-Nfs1) and identi¢ed its product, the m-Nfs1 NFS1), and termed it m-Nfs1. The deduced protein sequence protein, in various tissues. Mitochondrial localization of both (459 amino acids long) has several characteristic features the m-Nfs1 protein and its yeast counterpart has also been common to those of bacterial NifS proteins, but distinct from demonstrated. This is the ¢rst report of the identi¢cation and them by its amino-terminal extension which contains a typical characterization of eukaryotic NifS-like proteins. mitochondrial targeting presequence. m-Nfs1 was found to be a soluble 47-kDa protein in the matrix fraction of mouse liver 2. Materials and methods mitochondria. The m-Nfs1 gene was ubiquitously expressed in most tissues, suggesting its housekeeping function in vivo. We 2.1. Isolation of the mouse NifS-like gene from cDNA library also found that the y-NFS1 protein was localized in the Two degenerate oligonucleotide primers which correspond to the mitochondrial matrix in yeast cells. -
Functional Dependency Analysis Identifies Potential Druggable
cancers Article Functional Dependency Analysis Identifies Potential Druggable Targets in Acute Myeloid Leukemia 1, 1, 2 3 Yujia Zhou y , Gregory P. Takacs y , Jatinder K. Lamba , Christopher Vulpe and Christopher R. Cogle 1,* 1 Division of Hematology and Oncology, Department of Medicine, College of Medicine, University of Florida, Gainesville, FL 32610-0278, USA; yzhou1996@ufl.edu (Y.Z.); gtakacs@ufl.edu (G.P.T.) 2 Department of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Gainesville, FL 32610-0278, USA; [email protected]fl.edu 3 Department of Physiological Sciences, College of Veterinary Medicine, University of Florida, Gainesville, FL 32610-0278, USA; cvulpe@ufl.edu * Correspondence: [email protected]fl.edu; Tel.: +1-(352)-273-7493; Fax: +1-(352)-273-5006 Authors contributed equally. y Received: 3 November 2020; Accepted: 7 December 2020; Published: 10 December 2020 Simple Summary: New drugs are needed for treating acute myeloid leukemia (AML). We analyzed data from genome-edited leukemia cells to identify druggable targets. These targets were necessary for AML cell survival and had favorable binding sites for drug development. Two lists of genes are provided for target validation, drug discovery, and drug development. The deKO list contains gene-targets with existing compounds in development. The disKO list contains gene-targets without existing compounds yet and represent novel targets for drug discovery. Abstract: Refractory disease is a major challenge in treating patients with acute myeloid leukemia (AML). Whereas the armamentarium has expanded in the past few years for treating AML, long-term survival outcomes have yet to be proven. To further expand the arsenal for treating AML, we searched for druggable gene targets in AML by analyzing screening data from a lentiviral-based genome-wide pooled CRISPR-Cas9 library and gene knockout (KO) dependency scores in 15 AML cell lines (HEL, MV411, OCIAML2, THP1, NOMO1, EOL1, KASUMI1, NB4, OCIAML3, MOLM13, TF1, U937, F36P, AML193, P31FUJ).