DOCSLIB.ORG

Rice Metabolic Map Based on Proteomics Results

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Rice Metabolic Map Based on Proteomics Results RICE METABOLIC MAP BASED ON PROTEOMICS RESULTS Leuco- pelargonidin Pelargonidin Anthocyanidin (Flavan- Anthocyanidin (Anthocyanidin) Anthocyanidin 3-O-glucoside 3,4-diol) synthase 3-glucosyl- IAA (1.13.11.-) transferase Anthocyanidin glucoside (n.a.) Dihydroflav onol 3-glucoside 4-reductase rhamnosyl- (1.1.1.219) transferase IAA (n.a.) 3-β-glucosyl- Respiratory chain transferase TOCOPHEROLS (localization: inner mitochondrial membrane) (n.a.) (plastidial antioxidant) Chalcone Naringenin Dihydroflavonol Anthocyanidin Chalcone (Flavanone) Flav anone 3-O-rhamno- Flav onol isomerase 3-β-hydroxylase Flav onol glucoside (5.5.1.6) (1.14.11.9) synthase Chalcone (1.13.11.-) 3-glucosyl- Indole 3-acetic ðà ðà synthase NADH O2 H2O ADP ATP transferase acid (IAA) NADH-CoQ QH -cytochrome c Cytochrome c Caffeoyl-CoA (2.3.1.74) (2.4.1.91) 2 O-methyltransferase 4-Coumaroyl-CoA (plant hormone) reductase reductase oxidase O-methyl- ATP synthase complex (2.1.1.104) 3-hydroxylase Kaempferol BRASSINOSTEROIDS (????) (1.10.2.2) (1.9.3.1) transferase ? (n.a.) Kaempferol (plant hormones) (3.6.3.14) (n.a.) 4-Coumaroyl- 3-O-glucoside FMN Cyt. b Cyt. a subunits: F0 4-Coumaryl- Sinapoyl- 5-Hydroxy- Feruloyl-CoA Caffeoyl-CoA 4-Coumarate Cinnamate 4-Coumar- CoA F1 alcohol CoA feruloyl-CoA 4-Coumarate: Cinnamate 2-Methyl- FeS Cluster Cyt. a3 4-Coumarate: 4-Coumarate: aldehyde 4-Coumarate: CoA-ligase 4-hydroxylase FeS Cluster CoA-ligase CoA-ligase 6-phytyl- CoA-ligase (6.2.1.12) (1.14.13.11) Cyt. c1 Cu α , (2.6.1.12) (6.2.1.12) Phenylalanine Phenylalanyl Conifer- (6.2.1.12) 4-Coumarate quinol Coniferyl ? ammonia lyase tRNA β 3-hydroxylase Cyt. c Peroxidases alcohol aldehyde (4.3.1.5) synthetase (n.a.) (6.1.1.20) PROTEIN L-Trypto- 5-Hydroxy- Ferulate Caffeate L-Phenyl- γ Sinapyl Sinap- Sinapate phanyl O-methyl- ferulate Ferulate Caffeate O-methyl- alanyl- alcohol aldehyde important: this enzyme may not exist ! tRNA ∆ transferase 5-hydroxylase transferase There is eviden ce th at 3-h ydro xylation h appen s on tRNA Laccases Arogenate PHYTOSTEROLS (n.a.) (1.14.13.-) (2.1.1.68) coumaro ylsh ikimate o r coumaro ylquin ate est ers Tryptophanyl ε dehydratase L-Phenyl- MONOTERPENES (4.-.-.-) L-Tyrosyl tRNA Cinnamyl alcohol Cinnamoyl-CoA alanine synthetase dehydrogenase reductase Adenosine-5’- tRNA (6.1.1.2) (1.1.1.195) (1.2.1.44) Phytyl triphosphate Adenosine SESQUITERPENES Arogenate diphosphate LIGNINS kinase (2.7.4.3) Adenosine-5’- DNA monophosphate Homogentisate RNA Prephenate Arogenate p-Hydroxyphenyl- Geranylgeranyl Inosine aminotransferase dehydrogenase L-Tyrosine p-Hydrox yphenyl- reductase Adenylo- Tyrosine pyruvate monophosphate (n.a.) (1.3.1.12) pyruv ate (n.a.) Xanthosine dehydrogenase Adenylo- succinate aminotransferase dioxygenase 5’-phosphate (1.1.1.200) succinate lyase (2.6.1.5) (1.13.11.27) synthase Geranygeranyl (4.3.2.2) Phosphoribosyl (6.3.4.4) N-(5’-phospho- diphosphate anthranilate 5’-Phosphoribosyl- ribosyl)- synthase 5-amino-4-imidazole 5N-Formyl- Adenylo- Prephenate isomerase ( 2.5.1.29) Inosine anthranilate (5.3.1.24) L-Tryptophan carboxamide AICAR succinate AICAR formyl- Inosine 5’-phosphate synthase Copalyl Geranylgeranyl Farnesyl Geranyl (AICAR) transferase monophosphate (4.2.1.20) diphosphate Phosphoribulosyl- (2.1.2.3) cyclohydrolase Chorismate α-subunit diphosphate Copalyl diphosphate diphosphate Anthranilate Imidazoleglycerol- (5.3.4.10) mutase 1-(o-Carboxy- diphosphate formimino-AICAR- phosphate synthase phosphoribosyl Indolyl-3-glycerol synthase Heme (5.4.99.5) phenylamino)- β-subunit Phytoene phosphate (n.a.) transferase Ent-Kaurene (n.a.) -phosphate L-Typtophan synthase synthase Geranyl PROTEIN (2.4.2.18) 1’-deoxyribulose- Indolyl-3- Imidazole- (n.a.) (2.5.1.32) diphosphate Chlorophyll b L-Histidine NAD, NADH; 5’-phosphate glycerolphosphate synthase Phosphoribosyl glycerol DITERPENES Ferrochelatase NADP, NADPH Anthranilate Chorismate synthase (n.a.) formimino-AICAR- phosphate (4.1.1.48) (heme synthetase) phosphate isomerase L-Histdinyl Anthranilate (4.99.1.1) Chlorophyll b (3.5.4.19) t-RNA synthase synthase reductase Chlorophyll a (6.1.1.21) L-Histidinyl- (4.1.3.27) GIBBERELLINS Phytoene (n.a.) oxygenase Chorismate ent-Kaurene Polyprenyl (n.a.) tRNA synthase (plant hormone s) Phytoene Phosphoribosyl- (4.6.1.4) desaturase diphosphate s Chlorophyllase Phospho- Phospho- (1.14.99.-) (n.a.) formimino-AICAR- α-D-5-Phosphoribosyl- Isopentenyl ribosyl- ribosyl- Zeaxanthin diphosphate phosphate Phosphoribosyl- Phosphoribosyl- ATP-Phosphoribosyl- diphosphate Ribose- AMP ATP epoxidase isomerase Divinylproto- Monovinylproto- AMP cyclo- ATP-pyro- transferase 5-phosphate 3-Enolpyruvyl- (1.14.-.-) (5.3.3.2) Chlorophyll a hydrolase phosphorylase (2.11.2.17) pyrophospho- Shikimate Shikimate shikimate α-Carotene, chlorophyllide a Protochlorophyllide chlorophyllide a (3.5.4.19) (3.6.1.31) kinase 5-phosphate ABSCISIC ACID Chlorophyll Ascorbate oxidase Shikimate 3-Enolpyruv yl- β ζ reductase (2.7.6.1) 5-phosphate (plant hormone) Violaxanthin Zeaxanthin -Carotene, -Carotene Dimethylallyl Isopentenyl synthase (cell wall) kinase shikimate (n.a.) (1.18.-.-) (1.10.3.3) (2.7.1.71) 5-phosphate Violaxanthin Lutein diphosphate diphosphate Shikimate 8-Vinyl Siroheme synthase de-epoxidase dehydrogenase reductase (2.5.1.19) (n.a.) Aromatic amino (1.1.1.25) (n.a.) Ascorbate 2-Methyl-4-amino- peroxidase acids Carotenoid biosynthesis Mg-Protoporphyrin IX (cytosolic) 5-hydroxymethyl- ? (photosynthetic pigments) PHYLLOQUINONE gcpE –like protein Mg-Proto- monomethyl ester (1.11.1.11) 3-Deoxy-Darabino- pyrimidine UBIQUINONE (n.a.) Divinyl-proto- 5-Dehydro- 5-Dehydro- Proto- porphyrin IX (Mg-PME) heptulosonate 7- PYRIDOXINE porphyrin IX Mg-Proto- Mg-Proto- Mg-PME cyclase chlorophyllide a MDHA 5-Dehydroquinate quinate 5-Dehydroquinate shikimate THIAMIN DIPHOSPHATE porphyrin IX porphyrin IX (n.a.) phosphate (vitamin B6) Uroporphyrinogen III reductase Monodehydro- synthase dehydratase (vitamin B1) chelatase methyltransferase (n.a.) (4.6.1.3) (4.2.1.10) PLASTOQUINONE lytB-like protein (4.9.9.-) (PPMT) methyltransferase Ascorbic acid ascorbic acid (n.a.) Proto- (2.1.1.107) Phospho-2-keto- 5-(2-Hydroxy-ethyl)- porphyrinogen (2.1.1.11) (radical) 3-deoxyheptonate 1-Deoxy- Chemical 4-methyl-thiazole 4-(Cytidine 2-C-Methyl- oxidase (PPOX) aldolase D-xylulose (1.3.3.4) Precorrin II disproportionation 5-phosphate 2-C-Methyl- 5’-diphospho)- D-erythritol (4.1.2.15) phosphate D-erythritol Dihydroascorbate reducto- 2-C-methyl- 2,4-cyclodi- L-Galactono- isomerase 4-phosphate D-erythritol phosphate Acetoacetyl-CoA reductase cytidyltransferase 2-Phospho- Copro- Uroporpho- 1,4-lactone (GSH-dependent) Xylulo- thiJ-like protein (n.a.) 4-(Cytidine kinase synthase 1-Hydroxymethyl- (n.a.) 4-(cytidine 5’- 2-C-Methyl- Proto- dehydrogenase (n.a.) kinase D-Ribulose (n.a.) 1-Deoxy- 2-C-Methyl- (n.a.) (n.a.) Acetoacetyl-CoA porphyrinogen III bilinogen III 5’-diphospho)- porphyrinogen IX Copro- UPBG UPBG synthase bilane (1.1.3.37) (2.7.1.17) 1,5-bisphosphate D-xylulose D-erythritol diphospho)- D-erythritol thiolase (UPBG) (UPBG) Dehydro- Phosphoribulokinase 2-C-methyl- (2.3.1.9) porphyrinogen III decarboxylase (UROS) 5-phosphate 4-phosphate 2-C-methyl- 2,4-cyclo- oxidase (CPOX) (UROD) (4.2.1.75) PBG deaminase Pentose phosphate cycle (2.7.1.19) D-erythritol ascorbic acid D-erythritol diphosphate (1.3.3.3) (4.1.1.37) (PBGD) (reductive pathway) (4.1.3.8) L-Galactono- Sedoheptulose D-Ribose 1,7-bisphosphatase 1,4-lactone D-Ribulose D-Xylulose GDP- 4-Keto-6-deoxy- 5-phosphate (3.1.3.37) L-fucose | 5-phosphate Ribulose- 5-phosphate H2CO3 | GDP-D-mannose 5-phosphate- D-Sedoheptulose CO2 1-Deoxy- Photorespiration Carbonic GDP-mannose 3-epimerase Ribulose-1,5- D-xylulose Nitrite L-Galactose GDP-mannose Gluconate- 1,7-bisphosphate 3,5-epimerase- (5.1.3.1) anhydrase bisphosphate 5-phosphate Glycolate reductase Nitrate dehydrogenase 4,6-dehydratase 6-phosphate Fumarate Porphobilinogen 4-reductase (4.2.1.1) Carboxylase synthase (1.7.7.1) reductase (1.1.1.48) (4.2.1.47) dehydrogenase (GER1) (5.1.3.-) Pentose phosphate cycle (RUBISCO) (n.a.) Fumarase (PBG) (1.6.6.1) (1.1.1.44) (4.1.1.39) 2-Phospho- | Transaldolase L-Malate (4.2.1.2) Sulfur (oxidative pathway) large chain Phosphoenolpyruv ate Phosphoenolpyruv ate Citric acid NH + NO - NO - ? | (2.2.1.2) glycolate 4 2 3 assimilation L-galactose GDP- GDP- D-Sedoheptulose phosphatase carboxylase carboxykinase cycle Aminolev ulinate Sulfite PAPS D-6-Phospho- 7-phosphate small chain (n.a.) (4.1.1.31) (4.1.1.49) Succinate dehydratase reductase reductase L-galactose D-mannose dehydrogenase Carbon Malate synthase (4.2.1.24) (1.8.99.3) (1.8.99.4) gluconate (1.3.99.1) Malate (4.1.3.2) Nitrogen assimilation 3’-Phospho- Adenosine fixation dehydrogenase O-Acetyl- 2- 2- Transketolase 2-Phospho- Formyl-CoA S SO3 adenosine (1.1.1.37) 5’-phospho- GDP-mannose (2.2.1.1) hydrolase Succinate serine 5’-phospho- D-Erythrose glycolate Malate deydrogenase Formyl- sulfate (APS) pyrophos- Glucose (n.a.) 5-Amino- Serine- sulfate (PAPS) phorylase 6-phosphate 4-phosphate “malic enzyme” CoA levulinate acetylserine (2.7.7.22) dehydrogenase Glyceraldehyde- Pyruv ate dehydrogenase complex (1.1.1.40) (2.3.1.30) Succinyl-CoA ATP sulfurylase / (1.1.1.49) 3-phosphate 3-Phosphoglycerate Phosphoglycero- Oxalo- CO2 Glucose Fructose- dehydrogenase Pyruv ate Formate synthetase APS kinase 6-phosphate Pyrophosphate-dependent 1,6-bisphosphate kinase mutase Pyruv ate orthophosphate E1 (1.2.4.1) acetate + Succinate- (1.2.1.12) Oxalyl-CoA (6.2.1.5) Glutamate- Dipeptidase (2.7.7.4) α-D-Mannose isomerase phosphofructokinase aldolase (2.7.2.3) (5.4.2.1) Enolase kinase dikinase α semialdehyde cytopl. Citrate ATP-citrate H2O2 -chain 1-semialdehyde Succinate ? (Cysteine, (3.4.13.6) L-Cysteinyl- 1-phosphate (5.3.1.9) (2.7.1.90) (4.1.2.13) cytopl. cytopl. (4.2.1.11) (2.7.1.40) (2.7.9.1) E2 (2.3.1.12) decarboxylase dehydrogenase synthase lyase (4.1.1.8) (1.2.1.16) aminotransferase semialdehyde Glycine) glycine plast.
Load more

Recommended publications
  • 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]
  • (12) Patent Application Publication (10) Pub. No.: US 2014/0155567 A1 Burk Et Al
    US 2014O155567A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2014/0155567 A1 Burk et al. (43) Pub. Date: Jun. 5, 2014 (54) MICROORGANISMS AND METHODS FOR (60) Provisional application No. 61/331,812, filed on May THE BIOSYNTHESIS OF BUTADENE 5, 2010. (71) Applicant: Genomatica, Inc., San Diego, CA (US) Publication Classification (72) Inventors: Mark J. Burk, San Diego, CA (US); (51) Int. Cl. Anthony P. Burgard, Bellefonte, PA CI2P 5/02 (2006.01) (US); Jun Sun, San Diego, CA (US); CSF 36/06 (2006.01) Robin E. Osterhout, San Diego, CA CD7C II/6 (2006.01) (US); Priti Pharkya, San Diego, CA (52) U.S. Cl. (US) CPC ................. CI2P5/026 (2013.01); C07C II/I6 (2013.01); C08F 136/06 (2013.01) (73) Assignee: Genomatica, Inc., San Diego, CA (US) USPC ... 526/335; 435/252.3:435/167; 435/254.2: (21) Appl. No.: 14/059,131 435/254.11: 435/252.33: 435/254.21:585/16 (22) Filed: Oct. 21, 2013 (57) ABSTRACT O O The invention provides non-naturally occurring microbial Related U.S. Application Data organisms having a butadiene pathway. The invention addi (63) Continuation of application No. 13/101,046, filed on tionally provides methods of using Such organisms to produce May 4, 2011, now Pat. No. 8,580,543. butadiene. Patent Application Publication Jun. 5, 2014 Sheet 1 of 4 US 2014/O155567 A1 ?ueudos!SMS |?un61– Patent Application Publication Jun. 5, 2014 Sheet 2 of 4 US 2014/O155567 A1 VOJ OO O Z?un61– Patent Application Publication US 2014/O155567 A1 {}}} Hººso Patent Application Publication Jun.
    [Show full text]
  • 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
    [Show full text]
  • Pyruvate-Phosphate Dikinase of Oxymonads and Parabasalia and the Evolution of Pyrophosphate-Dependent Glycolysis in Anaerobic Eukaryotes† Claudio H
    EUKARYOTIC CELL, Jan. 2006, p. 148–154 Vol. 5, No. 1 1535-9778/06/$08.00ϩ0 doi:10.1128/EC.5.1.148–154.2006 Copyright © 2006, American Society for Microbiology. All Rights Reserved. Pyruvate-Phosphate Dikinase of Oxymonads and Parabasalia and the Evolution of Pyrophosphate-Dependent Glycolysis in Anaerobic Eukaryotes† Claudio H. Slamovits and Patrick J. Keeling* Canadian Institute for Advanced Research, Botany Department, University of British Columbia, 3529-6270 University Boulevard, Vancouver, British Columbia V6T 1Z4, Canada Received 29 September 2005/Accepted 8 November 2005 In pyrophosphate-dependent glycolysis, the ATP/ADP-dependent enzymes phosphofructokinase (PFK) and pyruvate kinase are replaced by the pyrophosphate-dependent PFK and pyruvate phosphate dikinase (PPDK), respectively. This variant of glycolysis is widespread among bacteria, but it also occurs in a few parasitic anaerobic eukaryotes such as Giardia and Entamoeba spp. We sequenced two genes for PPDK from the amitochondriate oxymonad Streblomastix strix and found evidence for PPDK in Trichomonas vaginalis and other parabasalia, where this enzyme was thought to be absent. The Streblomastix and Giardia genes may be related to one another, but those of Entamoeba and perhaps Trichomonas are distinct and more closely related to bacterial homologues. These findings suggest that pyrophosphate-dependent glycolysis is more widespread in eukaryotes than previously thought, enzymes from the pathway coexists with ATP-dependent more often than previously thought and may be spread by lateral transfer of genes for pyrophosphate-dependent enzymes from bacteria. Adaptation to anaerobic metabolism is a complex process (PPDK), respectively (for a comparison of these reactions, see involving changes to many proteins and pathways of critical reference 21).
    [Show full text]
  • Thioesterase Superfamily Member 1 Undergoes Stimulus-Coupled Conformational Reorganization to Regulate Metabolism in Mice
    ARTICLE https://doi.org/10.1038/s41467-021-23595-x OPEN Thioesterase superfamily member 1 undergoes stimulus-coupled conformational reorganization to regulate metabolism in mice Yue Li 1,2, Norihiro Imai3, Hayley T. Nicholls 3, Blaine R. Roberts 4, Samaksh Goyal 1,2, Tibor I. Krisko 3, Lay-Hong Ang 1,2, Matthew C. Tillman4, Anne M. Roberts4, Mahnoor Baqai 1,2, Eric A. Ortlund 4, ✉ ✉ David E. Cohen 3 & Susan J. Hagen 1,2 1234567890():,; In brown adipose tissue, thermogenesis is suppressed by thioesterase superfamily member 1 (Them1), a long chain fatty acyl-CoA thioesterase. Them1 is highly upregulated by cold ambient temperature, where it reduces fatty acid availability and limits thermogenesis. Here, we show that Them1 regulates metabolism by undergoing conformational changes in response to β-adrenergic stimulation that alter Them1 intracellular distribution. Them1 forms metabolically active puncta near lipid droplets and mitochondria. Upon stimulation, Them1 is phosphorylated at the N-terminus, inhibiting puncta formation and activity and resulting in a diffuse intracellular localization. We show by correlative light and electron microscopy that Them1 puncta are biomolecular condensates that are inhibited by phosphorylation. Thus, Them1 forms intracellular biomolecular condensates that limit fatty acid oxidation and sup- press thermogenesis. During a period of energy demand, the condensates are disrupted by phosphorylation to allow for maximal thermogenesis. The stimulus-coupled reorganization of Them1 provides fine-tuning of thermogenesis and energy expenditure. 1 Division of General Surgery, Department of Surgery, Beth Israel Deaconess Medical Center, Boston, MA, USA. 2 Department of Surgery, Harvard Medical School, Boston, MA, USA. 3 Division of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medical College, New York, NY, USA.
    [Show full text]
  • Characterization of a Eukaryotic Type Serine/Threonine Protein Kinase And
    Characterization of a eukaryotic type serine/threonine protein kinase and protein phosphatase of Streptococcus pneumoniae and identification of kinase substrates Linda Nova´ kova´ 1, Lenka Saskova´ 1, Petra Pallova´ 1, Jirˇı´ Janecˇek1, Jana Novotna´ 1, Alesˇ Ulrych1, Jose Echenique2, Marie-Claude Trombe3 and Pavel Branny1 1 Cell and Molecular Microbiology Division, Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic 2 Departamento de Bioquı´mica Clı´nica, Facultad de Ciencias Quı´micas, Universidad Nacional de Co´ rdoba, Medina Allende esq Haya de la Torre, Ciudad Universitaria, Co´ rdoba, Argentina 3 Centre Hospitalo-Universitaire de Rangueil, Universite´ Paul Sabatier, Toulouse, France Keywords Searching the genome sequence of Streptococcus pneumoniae revealed the phosphoglucosamine mutase; presence of a single Ser ⁄ Thr protein kinase gene stkP linked to protein phosphoproteome; protein phosphatase; phosphatase phpP. Biochemical studies performed with recombinant StkP serine ⁄ threonine protein kinase; suggest that this protein is a functional eukaryotic-type Ser ⁄ Thr protein Streptococcus pneumoniae kinase. In vitro kinase assays and Western blots of S. pneumoniae subcellu- Correspondence lar fractions revealed that StkP is a membrane protein. PhpP is a soluble P. Branny, Cell and Molecular Microbiology protein with manganese-dependent phosphatase activity in vitro against a Division, Institute of Microbiology, Czech synthetic substrate RRA(pT)VA. Mutations in the invariant aspartate resi- Academy of Sciences, Vı´denˇ ska´ 1083, dues implicated in the metal binding completely abolished PhpP activity. 142 20 Prague 4, Czech Republic Autophosphorylated form of StkP was shown to be a substrate for PhpP. Fax: +420 2 41722257 These results suggest that StkP and PhpP could operate as a functional Tel: +420 2 41062658 E-mail: [email protected] pair in vivo.
    [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]
  • Table 6. Putative Genes Involved in the Utilization of Carbohydrates in G
    Table 6. Putative genes involved in the utilization of carbohydrates in G. thermodenitrificans NG80-2 genome Carbohydrates* Enzymes Gene ID Glycerol Glycerol Kinase GT1216 Glycerol-3-phosphate dehydrogenase, aerobic GT2089 NAD(P)H-dependent glycerol-3-phosphate dehydrogenase GT2153 Enolase GT3003 2,3-bisphosphoglycerate-independentphosphoglycerate mutase GT3004 Triosephosphate isomerase GT3005 3-phosphoglycerate kinase GT3006 Glyceraldehyde-3-phosphate dehydrogenase GT3007 Phosphoglycerate mutase GT1326 Pyruvate kinase GT2663 L-Arabinose L-arabinose isomerase GT1795 L-ribulokinase GT1796 L-ribulose 5-phosphate 4-epimerase GT1797 D-Ribose Ribokinase GT3174 Transketolase GT1187 Ribose 5-phosphate epimerase GT3316 D-Xylose Xylose kinase GT1756 Xylose isomerase GT1757 D-Galactose Galactokinase GT2086 Galactose-1-phosphate uridyltransferase GT2084 UDP-glucose 4-epimerase GT2085 Carbohydrates* Enzymes Gene ID D-Fructose 1-phosphofructokinase GT1727 Fructose-1,6-bisphosphate aldolase GT1805 Fructose-1,6-bisphosphate aldolase type II GT3331 Triosephosphate isomerase GT3005 D-Mannose Mannnose-6 phospate isomelase GT3398 6-phospho-1-fructokinase GT2664 D-Mannitol Mannitol-1-phosphate dehydrogenase GT1844 N-Acetylglucosamine N-acetylglucosamine-6-phosphate deacetylase GT2205 N-acetylglucosamine-6-phosphate isomerase GT2204 D-Maltose Alpha-1,4-glucosidase GT0528, GT1643 Sucrose Sucrose phosphorylase GT3215 D-Trehalose Alpha-glucosidase GT1643 Glucose kinase GT2381 Inositol Myo-inositol catabolism protein iolC;5-dehydro-2- GT1807 deoxygluconokinase
    [Show full text]
  • Inflammatory Stimuli Induce Acyl-Coa Thioesterase 7 and Remodeling of Phospholipids Containing Unsaturated Long (C20)-Acyl Chains in Macrophages
    Supplemental Material can be found at: http://www.jlr.org/content/suppl/2017/04/17/jlr.M076489.DC1 .html Inflammatory stimuli induce acyl-CoA thioesterase 7 and remodeling of phospholipids containing unsaturated long (C20)-acyl chains in macrophages Valerie Z. Wall,*,† Shelley Barnhart,* Farah Kramer,* Jenny E. Kanter,* Anuradha Vivekanandan-Giri,§ Subramaniam Pennathur,§ Chiara Bolego,** Jessica M. Ellis,§§,*** Miguel A. Gijón,††† Michael J. Wolfgang,*** and Karin E. Bornfeldt1,*,† Department of Medicine,* Division of Metabolism, Endocrinology and Nutrition, and Department of Pathology,† UW Medicine Diabetes Institute, University of Washington, Seattle, WA; Department of Internal Medicine,§ University of Michigan, Ann Arbor, MI; Department of Pharmaceutical and Pharmacological Sciences,** University of Padova, Padova, Italy; Department of Nutrition Science,§§ Purdue University, West Lafayette, IN; Department of Biological Chemistry,*** Johns Hopkins University School of Medicine, Baltimore, MD; and Department of Pharmacology,††† University of Downloaded from Colorado Denver, Aurora, CO Abstract Acyl-CoA thioesterase 7 (ACOT7) is an intracel- containing unsaturated long (C20)-acyl chains in macro- lular enzyme that converts acyl-CoAs to FFAs. ACOT7 is in- phages, and, although ACOT7 has preferential thioesterase duced by lipopolysaccharide (LPS); thus, we investigated activity toward these lipid species, loss of ACOT7 has no ma- www.jlr.org downstream effects of LPS-induced induction of ACOT7 jor detrimental effect on macrophage inflammatory pheno- and its role in inflammatory settings in myeloid cells. Enzy- types.—Wall, V. Z., S. Barnhart, F. Kramer, J. E. Kanter, matic thioesterase activity assays in WT and ACOT7-deficient A. Vivekanandan-Giri, S. Pennathur, C. Bolego, J. M. Ellis, macrophage lysates indicated that endogenous ACOT7 con- M.
    [Show full text]
  • The Metabolic Serine Hydrolases and Their Functions in Mammalian Physiology and Disease Jonathan Z
    REVIEW pubs.acs.org/CR The Metabolic Serine Hydrolases and Their Functions in Mammalian Physiology and Disease Jonathan Z. Long* and Benjamin F. Cravatt* The Skaggs Institute for Chemical Biology and Department of Chemical Physiology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States CONTENTS 2.4. Other Phospholipases 6034 1. Introduction 6023 2.4.1. LIPG (Endothelial Lipase) 6034 2. Small-Molecule Hydrolases 6023 2.4.2. PLA1A (Phosphatidylserine-Specific 2.1. Intracellular Neutral Lipases 6023 PLA1) 6035 2.1.1. LIPE (Hormone-Sensitive Lipase) 6024 2.4.3. LIPH and LIPI (Phosphatidic Acid-Specific 2.1.2. PNPLA2 (Adipose Triglyceride Lipase) 6024 PLA1R and β) 6035 2.1.3. MGLL (Monoacylglycerol Lipase) 6025 2.4.4. PLB1 (Phospholipase B) 6035 2.1.4. DAGLA and DAGLB (Diacylglycerol Lipase 2.4.5. DDHD1 and DDHD2 (DDHD Domain R and β) 6026 Containing 1 and 2) 6035 2.1.5. CES3 (Carboxylesterase 3) 6026 2.4.6. ABHD4 (Alpha/Beta Hydrolase Domain 2.1.6. AADACL1 (Arylacetamide Deacetylase-like 1) 6026 Containing 4) 6036 2.1.7. ABHD6 (Alpha/Beta Hydrolase Domain 2.5. Small-Molecule Amidases 6036 Containing 6) 6027 2.5.1. FAAH and FAAH2 (Fatty Acid Amide 2.1.8. ABHD12 (Alpha/Beta Hydrolase Domain Hydrolase and FAAH2) 6036 Containing 12) 6027 2.5.2. AFMID (Arylformamidase) 6037 2.2. Extracellular Neutral Lipases 6027 2.6. Acyl-CoA Hydrolases 6037 2.2.1. PNLIP (Pancreatic Lipase) 6028 2.6.1. FASN (Fatty Acid Synthase) 6037 2.2.2. PNLIPRP1 and PNLIPR2 (Pancreatic 2.6.2.
    [Show full text]
  • 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.
    [Show full text]
  • Evolving a New Efficient Mode of Fructose Utilization For
    fbioe-09-669093 May 22, 2021 Time: 22:55 # 1 ORIGINAL RESEARCH published: 28 May 2021 doi: 10.3389/fbioe.2021.669093 Evolving a New Efficient Mode of Fructose Utilization for Improved Bioproduction in Corynebacterium glutamicum Irene Krahn1, Daniel Bonder2, Lucía Torregrosa-Barragán2, Dominik Stoppel1, 1 3 1 3,4 Edited by: Jens P. Krause , Natalie Rosenfeldt , Tobias M. Meiswinkel , Gerd M. Seibold , Pablo Ivan Nikel, Volker F. Wendisch1 and Steffen N. Lindner1,2* Novo Nordisk Foundation Center 1 2 for Biosustainability (DTU Biosustain), Chair of Genetics of Prokaryotes, Faculty of Biology and CeBiTec, Bielefeld University, Bielefeld, Germany, Systems 3 Denmark and Synthetic Metabolism, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany, Institute of Biochemistry, University of Cologne, Cologne, Germany, 4 Department of Biotechnology and Biomedicine, Technical Reviewed by: University of Denmark, Lyngby, Denmark Stephan Noack, Julich-Forschungszentrum, Helmholtz-Verband Deutscher Fructose utilization in Corynebacterium glutamicum starts with its uptake and Forschungszentren (HZ), Germany concomitant phosphorylation via the phosphotransferase system (PTS) to yield Fabien Létisse, UMR 5504 Laboratoire d’Ingénierie intracellular fructose 1-phosphate, which enters glycolysis upon ATP-dependent des Systèmes Biologiques et des phosphorylation to fructose 1,6-bisphosphate by 1-phosphofructokinase. This is known Procédés (LISBP), France to result in a significantly reduced oxidative pentose phosphate pathway (oxPPP) flux *Correspondence: ∼ ∼ Steffen N. Lindner on fructose ( 10%) compared to glucose ( 60%). Consequently, the biosynthesis of [email protected] NADPH demanding products, e.g., L-lysine, by C. glutamicum is largely decreased when fructose is the only carbon source. Previous works reported that fructose Specialty section: This article was submitted to is partially utilized via the glucose-specific PTS presumably generating fructose 6- Synthetic Biology, phosphate.
    [Show full text]