Generated by SRI International Pathway Tools Version 25.0, Authors S

Total Page:16

File Type:pdf, Size:1020Kb

Generated by SRI International Pathway Tools Version 25.0, Authors S Authors: Pallavi Subhraveti Ron Caspi Quang Ong Peter D Karp An online version of this diagram is available at BioCyc.org. Biosynthetic pathways are positioned in the left of the cytoplasm, degradative pathways on the right, and reactions not assigned to any pathway are in the far right of the cytoplasm. Transporters and membrane proteins are shown on the membrane. Ingrid Keseler Periplasmic (where appropriate) and extracellular reactions and proteins may also be shown. Pathways are colored according to their cellular function. Gcf_001570945Cyc: Janibacter anophelis NBRC 107843 Cellular Overview Connections between pathways are omitted for legibility.
Recommended publications
  • METACYC ID Description A0AR23 GO:0004842 (Ubiquitin-Protein Ligase
    Electronic Supplementary Material (ESI) for Integrative Biology This journal is © The Royal Society of Chemistry 2012 Heat Stress Responsive Zostera marina Genes, Southern Population (α=0.
    [Show full text]
  • Gene Symbol Gene Description ACVR1B Activin a Receptor, Type IB
    Table S1. Kinase clones included in human kinase cDNA library for yeast two-hybrid screening Gene Symbol Gene Description ACVR1B activin A receptor, type IB ADCK2 aarF domain containing kinase 2 ADCK4 aarF domain containing kinase 4 AGK multiple substrate lipid kinase;MULK AK1 adenylate kinase 1 AK3 adenylate kinase 3 like 1 AK3L1 adenylate kinase 3 ALDH18A1 aldehyde dehydrogenase 18 family, member A1;ALDH18A1 ALK anaplastic lymphoma kinase (Ki-1) ALPK1 alpha-kinase 1 ALPK2 alpha-kinase 2 AMHR2 anti-Mullerian hormone receptor, type II ARAF v-raf murine sarcoma 3611 viral oncogene homolog 1 ARSG arylsulfatase G;ARSG AURKB aurora kinase B AURKC aurora kinase C BCKDK branched chain alpha-ketoacid dehydrogenase kinase BMPR1A bone morphogenetic protein receptor, type IA BMPR2 bone morphogenetic protein receptor, type II (serine/threonine kinase) BRAF v-raf murine sarcoma viral oncogene homolog B1 BRD3 bromodomain containing 3 BRD4 bromodomain containing 4 BTK Bruton agammaglobulinemia tyrosine kinase BUB1 BUB1 budding uninhibited by benzimidazoles 1 homolog (yeast) BUB1B BUB1 budding uninhibited by benzimidazoles 1 homolog beta (yeast) C9orf98 chromosome 9 open reading frame 98;C9orf98 CABC1 chaperone, ABC1 activity of bc1 complex like (S. pombe) CALM1 calmodulin 1 (phosphorylase kinase, delta) CALM2 calmodulin 2 (phosphorylase kinase, delta) CALM3 calmodulin 3 (phosphorylase kinase, delta) CAMK1 calcium/calmodulin-dependent protein kinase I CAMK2A calcium/calmodulin-dependent protein kinase (CaM kinase) II alpha CAMK2B calcium/calmodulin-dependent
    [Show full text]
  • A Putative Cystathionine Beta-Synthase Homolog of Mycolicibacterium Smegmatis Is Involved in De Novo Cysteine Biosynthesis
    University of Arkansas, Fayetteville ScholarWorks@UARK Theses and Dissertations 5-2020 A Putative Cystathionine Beta-Synthase Homolog of Mycolicibacterium smegmatis is Involved in de novo Cysteine Biosynthesis Saroj Kumar Mahato University of Arkansas, Fayetteville Follow this and additional works at: https://scholarworks.uark.edu/etd Part of the Cell Biology Commons, Molecular Biology Commons, and the Pathogenic Microbiology Commons Citation Mahato, S. K. (2020). A Putative Cystathionine Beta-Synthase Homolog of Mycolicibacterium smegmatis is Involved in de novo Cysteine Biosynthesis. Theses and Dissertations Retrieved from https://scholarworks.uark.edu/etd/3639 This Thesis is brought to you for free and open access by ScholarWorks@UARK. It has been accepted for inclusion in Theses and Dissertations by an authorized administrator of ScholarWorks@UARK. For more information, please contact [email protected]. A Putative Cystathionine Beta-Synthase Homolog of Mycolicibacterium smegmatis is Involved in de novo Cysteine Biosynthesis A thesis submitted in partial fulfillment of the requirement for the degree of Master of Science in Cell and Molecular Biology by Saroj Kumar Mahato Purbanchal University Bachelor of Science in Biotechnology, 2016 May 2020 University of Arkansas This thesis is approved for recommendation to the Graduate Council. ___________________________________ Young Min Kwon, Ph.D. Thesis Director ___________________________________ ___________________________________ Suresh Thallapuranam, Ph.D. Inés Pinto, Ph.D. Committee Member Committee Member ABSTRACT Mycobacteria include serious pathogens of humans and animals. Mycolicibacterium smegmatis is a non-pathogenic model that is widely used to study core mycobacterial metabolism. This thesis explores mycobacterial pathways of cysteine biosynthesis by generating and study of genetic mutants of M. smegmatis. Published in vitro biochemical studies had revealed three independent routes to cysteine synthesis in mycobacteria involving separate homologs of cysteine synthase, namely CysK1, CysK2, and CysM.
    [Show full text]
  • Comparative Analysis of Mutants in the Mycothiol Biosynthesis Pathway in Mycobacterium Smegmatis
    Biochemical and Biophysical Research Communications 363 (2007) 71–76 www.elsevier.com/locate/ybbrc Comparative analysis of mutants in the mycothiol biosynthesis pathway in Mycobacterium smegmatis Mamta Rawat a, Chantale Johnson a, Vanessa Cadiz a, Yossef Av-Gay b,* a Department of Biology, California State University-Fresno, Fresno, CA 937401, USA b Department of Medicine, Division of Infectious Diseases, University of British Columbia, Vancouver, BC, Canada V5Z 3J5 Received 17 August 2007 Available online 31 August 2007 Abstract The role of mycothiol in mycobacteria was examined by comparative analysis of mutants disrupted in the four known genes encoding the protein machinery needed for mycothiol biosynthesis. These mutants were sensitive to acid stress, antibiotic stress, alkylating stress, and oxidative stress indicating that mycothiol and mycothiol-dependent enzymes protect the mycobacterial cell against attack from various different types of stresses and toxic agents. Ó 2007 Elsevier Inc. All rights reserved. Keywords: Mycothiol; Mycothiol deacetylase; Mycothiol ligase; Mycothiol synthase; Oxidative stress; Toxins; Xenobiotics Mycobacteria, like most other Gram-positive bacteria do We have previously reported that Mycobacterium not make glutathione but produce another low molecular smegmatis mutants disrupted in the four known genes weight thiol, mycothiol (MSH) (Fig. 1), 1-D-myoinosityl- [3,9–11] involved in mycothiol biosynthesis are resistant to 2-(n-acetyl-L-cysteinyl)-amido-2-deoxy-a-D-glucopyranoside. isoniazid, a front-line drug used in the treatment of tubercu- Since MSH is unique to actinomycetales [1], enzymes losis. We have also reported that M. smegmatis mutants involved in MSH biosynthesis and metabolism are poten- lacking mycothiol ligase activity and thus mycothiol are tial targets for drugs directed against pathogenic mycobac- sensitive to a wide range of antibiotics, alkylating agents, teria like Mycobacterium tuberculosis.
    [Show full text]
  • Supplementary Materials
    1 Supplementary Materials: Supplemental Figure 1. Gene expression profiles of kidneys in the Fcgr2b-/- and Fcgr2b-/-. Stinggt/gt mice. (A) A heat map of microarray data show the genes that significantly changed up to 2 fold compared between Fcgr2b-/- and Fcgr2b-/-. Stinggt/gt mice (N=4 mice per group; p<0.05). Data show in log2 (sample/wild-type). 2 Supplemental Figure 2. Sting signaling is essential for immuno-phenotypes of the Fcgr2b-/-lupus mice. (A-C) Flow cytometry analysis of splenocytes isolated from wild-type, Fcgr2b-/- and Fcgr2b-/-. Stinggt/gt mice at the age of 6-7 months (N= 13-14 per group). Data shown in the percentage of (A) CD4+ ICOS+ cells, (B) B220+ I-Ab+ cells and (C) CD138+ cells. Data show as mean ± SEM (*p < 0.05, **p<0.01 and ***p<0.001). 3 Supplemental Figure 3. Phenotypes of Sting activated dendritic cells. (A) Representative of western blot analysis from immunoprecipitation with Sting of Fcgr2b-/- mice (N= 4). The band was shown in STING protein of activated BMDC with DMXAA at 0, 3 and 6 hr. and phosphorylation of STING at Ser357. (B) Mass spectra of phosphorylation of STING at Ser357 of activated BMDC from Fcgr2b-/- mice after stimulated with DMXAA for 3 hour and followed by immunoprecipitation with STING. (C) Sting-activated BMDC were co-cultured with LYN inhibitor PP2 and analyzed by flow cytometry, which showed the mean fluorescence intensity (MFI) of IAb expressing DC (N = 3 mice per group). 4 Supplemental Table 1. Lists of up and down of regulated proteins Accession No.
    [Show full text]
  • Activation of Sphingosine Kinase 1 by ERK1/2Mediated Phosphorylation
    The EMBO Journal Vol. 22 No. 20 pp. 5491±5500, 2003 Activation of sphingosine kinase 1 by ERK1/2-mediated phosphorylation Stuart M.Pitson1,2, Paul A.B.Moretti1, second messenger and a ligand for cell-surface receptors Julia R.Zebol1, Helen E.Lynn1, Pu Xia1,3, (Hla et al., 2001; Spiegel and Milstien, 2002). MathewA.Vadas 1,3 and The cellular levels of S1P are controlled by its Binks W.Wattenberg1,4 formation from sphingosine through the activity of sphingosine kinase, and by its degradation by S1P lyase 1Hanson Institute, Division of Human Immunology, Institute of (Van Veldhoven et al., 2000) and S1P phosphatases Medical and Veterinary Science, Frome Road, Adelaide, SA 5000 and (Mandala, 2001). In the basal state, this balance between 3Department of Medicine, Adelaide University, Frome Road, Adelaide, Australia S1P generation and degradation results in low cellular levels of S1P (Pyne and Pyne, 2000). However, when cells 4Present address: James Graham Brown Cancer Center, Dehlia Baxter Research Building, 580 S. Preston Avenue, Louisville, KY 40202, are exposed to speci®c growth factors and other agonists USA like tumour necrosis factor-a (TNFa) or phorbol esters the cellular levels of S1P can increase rapidly and transiently 2Corresponding author e-mail: [email protected] (Pitson et al., 2000b). This results in the triggering of various signalling pathways through as yet unidenti®ed Sphingosine kinase 1 is an agonist-activated signalling intracellular S1P targets, as well as through the engage- enzyme that catalyses the formation of sphingosine ment of cell surface S1P receptors following its release 1-phosphate, a lipid second messenger that has been from cells (Hobson et al., 2001).
    [Show full text]
  • Lipid Metabolic Reprogramming: Role in Melanoma Progression and Therapeutic Perspectives
    cancers Review Lipid metabolic Reprogramming: Role in Melanoma Progression and Therapeutic Perspectives 1, 1, 1 2 1 Laurence Pellerin y, Lorry Carrié y , Carine Dufau , Laurence Nieto , Bruno Ségui , 1,3 1, , 1, , Thierry Levade , Joëlle Riond * z and Nathalie Andrieu-Abadie * z 1 Centre de Recherches en Cancérologie de Toulouse, Equipe Labellisée Fondation ARC, Université Fédérale de Toulouse Midi-Pyrénées, Université Toulouse III Paul-Sabatier, Inserm 1037, 2 avenue Hubert Curien, tgrCS 53717, 31037 Toulouse CEDEX 1, France; [email protected] (L.P.); [email protected] (L.C.); [email protected] (C.D.); [email protected] (B.S.); [email protected] (T.L.) 2 Institut de Pharmacologie et de Biologie Structurale, CNRS, Université Toulouse III Paul-Sabatier, UMR 5089, 205 Route de Narbonne, 31400 Toulouse, France; [email protected] 3 Laboratoire de Biochimie Métabolique, CHU Toulouse, 31059 Toulouse, France * Correspondence: [email protected] (J.R.); [email protected] (N.A.-A.); Tel.: +33-582-7416-20 (J.R.) These authors contributed equally to this work. y These authors jointly supervised this work. z Received: 15 September 2020; Accepted: 23 October 2020; Published: 27 October 2020 Simple Summary: Melanoma is a devastating skin cancer characterized by an impressive metabolic plasticity. Melanoma cells are able to adapt to the tumor microenvironment by using a variety of fuels that contribute to tumor growth and progression. In this review, the authors summarize the contribution of the lipid metabolic network in melanoma plasticity and aggressiveness, with a particular attention to specific lipid classes such as glycerophospholipids, sphingolipids, sterols and eicosanoids.
    [Show full text]
  • Investigations Into Intracellular Thiols of Biological Importance
    Investigations into Intracellular Thiols of Biological Importance by Christine Elizabeth Hand A thesis presented to the University of Waterloo in fulfillment of the thesis requirement for the degree of Doctor of Philosophy in Chemistry Waterloo, Ontario, Canada, 2007 © Christine Elizabeth Hand 2007 AUTHOR'S DECLARATION I hereby declare that I am the sole author of this thesis. This is a true copy of the thesis, including any required final revisions, as accepted by my examiners. I understand that my thesis may be made electronically available to the public. ii Abstract The presence of thiols in living systems is critical for the maintenance of cellular redox homeostasis, the maintenance of protein thiol-disulfide ratios and the protection of cells from reactive oxygen species. In addition to the well studied tripeptide glutathione (γ-Glu-Cys-Gly), a number of compounds have been identified that contribute to these essential cellular roles. Many of these molecules are of great clinical interest due to their essential role in the biochemistry of a number of deadly pathogens, as well as their possible role as therapeutic agents in the treatment of a number of diseases. A series of studies were undertaken using theoretical, chemical and biochemical approaches on a selection of thiols, ergothioneine, the ovothiols and mycothiol, to further our understanding of these necessary biological components. Ergothioneine is present at significant physiological levels in humans and other mammals; however, a definitive role for this thiol has yet to be determined. It has been implicated in radical scavenging in vivo and shows promise as a therapeutic agent against disease states caused by oxidative damage.
    [Show full text]
  • 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
    [Show full text]
  • Building a Metabolic Bridge Between Glycolysis and Sphingolipid Biosynthesis : Implications in Cancer
    University of Louisville ThinkIR: The University of Louisville's Institutional Repository Electronic Theses and Dissertations 8-2014 Building a metabolic bridge between glycolysis and sphingolipid biosynthesis : implications in cancer. Morgan L. Stathem University of Louisville Follow this and additional works at: https://ir.library.louisville.edu/etd Part of the Pharmacy and Pharmaceutical Sciences Commons Recommended Citation Stathem, Morgan L., "Building a metabolic bridge between glycolysis and sphingolipid biosynthesis : implications in cancer." (2014). Electronic Theses and Dissertations. Paper 1374. https://doi.org/10.18297/etd/1374 This Master's Thesis is brought to you for free and open access by ThinkIR: The nivU ersity of Louisville's Institutional Repository. It has been accepted for inclusion in Electronic Theses and Dissertations by an authorized administrator of ThinkIR: The nivU ersity of Louisville's Institutional Repository. This title appears here courtesy of the author, who has retained all other copyrights. For more information, please contact [email protected]. BUILDING A METABOLIC BRIDGE BETWEEN GLYCOLYSIS AND SPHINGOLIPID BIOSYNTHESIS: IMPLICATIONS IN CANCER By Morgan L. Stathem B.S., University of Georgia, 2010 A Thesis Submitted to the Faculty of the School of Medicine of the University of Louisville In Partial Fulfillment of the Requirements for the Degree of Master of Science Department of Pharmacology and Toxicology University of Louisville Louisville, KY August 2014 BUILDING A METABOLIC BRIDGE BETWEEN GLYCOLYSIS AND SPHINGOLIPID BIOSYNTHESIS: IMPLICATIONS IN CANCER By Morgan L. Stathem B.S., University of Georgia, 2010 Thesis Approved on 08/07/2014 by the following Thesis Committee: __________________________________ Leah Siskind, Ph.D. __________________________________ Levi Beverly, Ph.D.
    [Show full text]
  • Structure and Functional Diversity of GCN5-Related N-Acetyltransferases (GNAT)
    International Journal of Molecular Sciences Review Structure and Functional Diversity of GCN5-Related N-Acetyltransferases (GNAT) Abu Iftiaf Md Salah Ud-Din 1, Alexandra Tikhomirova 1 and Anna Roujeinikova 1,2,* 1 Infection and Immunity Program, Monash Biomedicine Discovery Institute; Department of Microbiology, Monash University, Clayton, Victoria 3800, Australia; [email protected] (A.I.M.S.U.-D.); [email protected] (A.T.) 2 Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia * Correspondence: [email protected]; Tel.: +61-3-9902-9194; Fax: +61-3-9902-9222 Academic Editor: Claudiu T. Supuran Received: 30 May 2016; Accepted: 20 June 2016; Published: 28 June 2016 Abstract: General control non-repressible 5 (GCN5)-related N-acetyltransferases (GNAT) catalyze the transfer of an acyl moiety from acyl coenzyme A (acyl-CoA) to a diverse group of substrates and are widely distributed in all domains of life. This review of the currently available data acquired on GNAT enzymes by a combination of structural, mutagenesis and kinetic methods summarizes the key similarities and differences between several distinctly different families within the GNAT superfamily, with an emphasis on the mechanistic insights obtained from the analysis of the complexes with substrates or inhibitors. It discusses the structural basis for the common acetyltransferase mechanism, outlines the factors important for the substrate recognition, and describes the mechanism of action of inhibitors of these enzymes. It is anticipated that understanding of the structural basis behind the reaction and substrate specificity of the enzymes from this superfamily can be exploited in the development of novel therapeutics to treat human diseases and combat emerging multidrug-resistant microbial infections.
    [Show full text]
  • Targeting the Sphingosine Kinase/Sphingosine-1-Phosphate Signaling Axis in Drug Discovery for Cancer Therapy
    cancers Review Targeting the Sphingosine Kinase/Sphingosine-1-Phosphate Signaling Axis in Drug Discovery for Cancer Therapy Preeti Gupta 1, Aaliya Taiyab 1 , Afzal Hussain 2, Mohamed F. Alajmi 2, Asimul Islam 1 and Md. Imtaiyaz Hassan 1,* 1 Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India; [email protected] (P.G.); [email protected] (A.T.); [email protected] (A.I.) 2 Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia; afi[email protected] (A.H.); [email protected] (M.F.A.) * Correspondence: [email protected] Simple Summary: Cancer is the prime cause of death globally. The altered stimulation of signaling pathways controlled by human kinases has often been observed in various human malignancies. The over-expression of SphK1 (a lipid kinase) and its metabolite S1P have been observed in various types of cancer and metabolic disorders, making it a potential therapeutic target. Here, we discuss the sphingolipid metabolism along with the critical enzymes involved in the pathway. The review provides comprehensive details of SphK isoforms, including their functional role, activation, and involvement in various human malignancies. An overview of different SphK inhibitors at different phases of clinical trials and can potentially be utilized as cancer therapeutics has also been reviewed. Citation: Gupta, P.; Taiyab, A.; Hussain, A.; Alajmi, M.F.; Islam, A.; Abstract: Sphingolipid metabolites have emerged as critical players in the regulation of various Hassan, M..I. Targeting the Sphingosine Kinase/Sphingosine- physiological processes. Ceramide and sphingosine induce cell growth arrest and apoptosis, whereas 1-Phosphate Signaling Axis in Drug sphingosine-1-phosphate (S1P) promotes cell proliferation and survival.
    [Show full text]