DOCSLIB.ORG

Generated by SRI International Pathway Tools Version 25.0, Authors S

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Generated by SRI International Pathway Tools Version 25.0, Authors S Authors: Pallavi Subhraveti Ron Caspi Peter Midford 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_000262635Cyc: Salmonella enterica enterica serovar Typhi str. UJ308A Cellular Overview Connections between pathways are omitted for legibility. Anamika Kothari sn-glycerol an amino an amino a hexose 6- 3-phosphate a dipeptide thr O-acetyl-L-serine phosphate phosphate acid acid a dipeptide O-acetyl-L-serine 1-(β-D 1-(β-D cefoperazone cefoperazone cefoperazone cefoperazone 2-dehydro- phosphate sulfate galactitol 2-dehydro- D-sorbitol 2+ phosphate phosphate an amino an amino an amino an amino an amino an amino a tripeptide a tripeptide L-homoserine cys cys ribofuranosyl) ribofuranosyl) Fe glucosyl-oleandomycin glucosyl-oleandomycin glucosyl-oleandomycin 3-deoxy-D- phosphate glutathione thiosulfate 3-deoxy-D- sn-glycerol α-L- thiamine glucosyl-oleandomycin D-fructuronate sulfate sulfate sulfate sulfate sulfate galactitol D-mannitol D-mannitol ammonium 2-oxoglutarate acid acid acid acid acid acid nicotinamide nicotinamide enterobactin cys sulfate 3-phosphate predicted rhamnopyranose gluconate gluconate predicted predicted predicted predicted predicted predicted ATP-driven predicted ABC ABC ABC ABC ABC PEP-driven transporter PEP-driven RS0102480 RS0107390 RS0116890 RS0119850 transporter transporter RS0114335 RS0119560 RS0119570 RS0113385 RS0117195 RS0121950 RS0103580 RS0100680 ThiQ RS0104585 RS0112865 RS0122375 RS0101440 RS0115795 RS0117875 MdtK RS0116300 RS0120245 RS0105495 RS0119310 transporter transporter RS0113400 RS0110045 RS0108565 RS0102410 RS0102550 transporter RS0108760 RS0112090 RS0105145 transporter RS0105525 RS0123255 GlpT of sn- RS0119480 RS0114850 RS0118295 RS0103625 transporter of an of an of phosphate of phosphate of sulfate of galactitol glycerol 3- of D-sorbitol amino acid amino acid cefoperazone cefoperazone cefoperazone cefoperazone phosphate thr O-acetyl-L-serine O-acetyl-L-serine 1-(β-D 1-(β-D Fe 2+ 2-dehydro- phosphate glutathione thiosulfate galactitol 1- 2-dehydro- D-mannitol D-mannitol α-L- glucosyl-oleandomycin glucosyl-oleandomycin glucosyl-oleandomycin glucosyl-oleandomycin D-fructuronate sulfate sulfate sn-glycerol an amino an amino an amino an amino an amino an amino a tripeptide L-homoserine cys cys thiamine ribofuranosyl) ribofuranosyl) 3-deoxy-D- phosphate phosphate sulfate sulfate sulfate phosphate 3-deoxy-D- 1-phosphate 1-phosphate ammonium 2-oxoglutarate rhamnopyranose a tripeptide enterobactin a hexose 6- cys sulfate 3-phosphate acid acid acid acid acid nicotinamide nicotinamide gluconate galactitol 1- gluconate D-sorbitol acid a dipeptide a dipeptide phosphate phosphate phosphate sulfate phosphate sn-glycerol 6-phosphate an amino an amino acid acid 3-phosphate propane-1,2,3- propane-1,2,3- TcuC tricarboxylate tricarboxylate Inorganic Nutrient Metabolism A(H2) thiosulfate Cofactor, Prosthetic Group, Electron Carrier, and Vitamin Biosynthesis Hormone Biosynthesis tetrathionate Macromolecule Modification queuosine biosynthesis 2457 2605 a protein 3-(all-trans- a ribonucleoside adenosine reductase (aminomethyl)phosphonate degradation core an E. coli phosphoenol an [HPr]- an N-modified a 23S rRNA uridine uridine DNA combined (S)-1-pyrroline- cob(II)yrinate a,c- a purine 1911/1915/1917 (S)-mandelate A tetrathionate superpathway of thiamine diphosphate biosynthesis I superpathway of pyridoxal 5'-phosphate biosynthesis and salvage superpathway of indole-3-acetate superpathway of sulfate assimilation and cysteine biosynthesis 2-aminoethylphosphonate an L-1- oligosaccharide- osmoregulated an L-1- a tRNA precursor ATP pyruvate L-histidine uridine in 23S rRNA in 23S rRNA with incorrect nonaprenyl) with exogenous 2',3'-cyclic 2',3'-cyclic a protein 5-carboxylate a protein [2Fe-2S] iron-sulfur cluster biosynthesis superpathway of adenosylcobalamin salvage from cobinamide I ubiquinol-8 biosynthesis (prokaryotic) superpathway of tetrahydrofolate biosynthesis superpathay of heme b adeninyl adenosylcobamide 2-methyladeninyl NAD salvage preQ Aldehyde Degradation ribonucleoside adenosylcobinamide CTP aminoacyl-[tRNA] diamide biosynthesis I biosynthesis VI (bacteria) 0 lipid A (E. coli periplasmic phosphoenolpyruvate- bifunctional tRNA bifunctional tRNA bifunctional tRNA disulfide bonds benzene-1,2-diol DNA to form a phosphate monophosphate mandelate racemase/ trifunctional predicted biosynthesis from demethylmenaquinol-8 biosynthesis I adenosylcobamide biosynthesis pathway IV (from Aromatic Compound Biosynthesis (aminomethyl) degradation I phosphatidylethanolamine phosphatidylethanolamine aminoacyl-tRNA thiol:disulfide interchange bifunctional 3- bifunctional 2',3'- multifunctional CCA D-alanyl-D-alanine- HslU--HslV (early cobalt insertion) biosynthesis from glutamate NADPH-dependent 7- phosphoethanolamine 5'-triphosphate bifunctional multifunctional CCA muconate lactonizing transcriptional ABC all-trans- D-erythrose phosphonate sulfate phosphoethanolamineK-12 core type) glucan (OPG) protein hydrolase: pseudouridine(32) pseudouridine(32) pseudouridine(32) protein DsbG: demethylubiquinone 3- recombinational tRNA nucleotidyl carboxypeptidase/ peptidase cob(II)inamide adenosylcobinamide-GDP from adenosylcobinamide-GDP nicotinamide riboside) cyano-7-deazaguanine aminoalkylphosphonate (2-aminoethyl) methylglyoxal degradation I transferase CptA: crossover junction cyclic-nucleotide 2'- ornithine ornithine uroporphyrinogen-III L-cysteine desulfurase 4-hydroxybenzoate octaprenyl cys 4-phosphate chorismate 1-(β-D selenate reduction L-lactaldehyde transferase CptA: adenosylcobinamide tRNA nucleotidyl phosphotransferase PtsP: STUJ308A_RS0123065 synthase/ribosomal large synthase/ribosomal large synthase/ribosomal large STUJ308A_RS0100185 junction enzyme family protein: endopeptidase AmpH: regulator/proline transporter GTP trp chorismate biosynthesis I N-acetyltransferase: phosphonate STUJ308A_RS0100165 O-methyltransferase/2- endodeoxyribonuclease phosphodiesterase/ transferase/2'3'-cyclic ATPase arg arg trp RS0112240 trp diphosphate glu 2-methyladenine ribofuranosyl) 4-hydroxyphenylpyruvate reductase QueF: sulfate adenylyltransferase: 2-aminoethylphosphonate- degradation STUJ308A_RS0100165 kinase/ transferase/2'3'-cyclic STUJ308A_RS0122645 subunit pseudouridine subunit pseudouridine subunit pseudouridine STUJ308A_RS0106625 dehydrogenase/L- of L-arginine/ uroporphyrinogen-III ATP:cob(I)alamin 4-hydroxybenzoate adenine D-erythrose- aminoacyl-tRNA bifunctional protein- octaprenyl-6-hydroxy RuvC: 3'-nucleotidase: cpdB phosphodiesterase/ STUJ308A_RS0107735 subunit: cysteine cysteine isochorismate nicotinate-nucleotide-- biosynthesis STUJ308A_RS0114060 STUJ308A_RS0107775 -pyruvate methylglyoxal phosphoethanolamine adenosylcobinamide- phosphodiesterase/ synthase RluA: synthase RluA: glutamate gamma- ornithine C-methyltransferase: octaprenyltransferase: nicotinamidetrifunctional D-erythrose (acetamidomethyl) STUJ308A_RS0109330 selenate (anaerobic) phosphoethanolamine phosphoenolpyruvate- hydrolase: synthase RluA: disulfide isomerase/ phenol methylase: STUJ308A_RS0106215 2'nucleotidase/ mandelate racemase/ [+ 3 isozymes] hslU adenosyltransferase: GTP cyclohydrolase desulfurase CsdA: nicotinate-nucleotide-- 4-phosphate synthase EntC: dimethylbenzimidazole preQ multifunctional CCA desulfurase CsdA: 1 aminotransferase: phnW lactoylglutathione lyase: transferase: phosphate 2'nucleotidase/ STUJ308A_RS0108345 STUJ308A_RS0108345 STUJ308A_RS0108345 semialdehyde STUJ308A_RS0123085 ubiA dehydrogenase: nicotinamide-nucleotide (indol-3- 4-phosphate phosphonate sulfate adenylyltransferase sulfate transferase: -protein STUJ308A_RS0121190 oxidoreductase DsbC: 2-methoxy-STUJ308A_RS0121355 phosphatase: muconate lactonizing a peptide STUJ308A_RS0114140 STUJ308A_RS0100395 3-octaprenyl-4- I FolE: an L-glutamyl- STUJ308A_RS0114140 dimethylbenzimidazole STUJ308A_RS0122380 phosphoribosyltransferase: 3-deoxy-7- Metabolic Regulator Biosynthesis phosphonoacetaldehyde (S)-lactaldehyde an E.
Load more

Recommended publications
  • C19) United States C12) Patent Application Publication C10) Pub
    1111111111111111 IIIIII IIIII 1111111111 11111 11111 111111111111111 1111111111 1111111111 11111111 US 20200081016Al c19) United States c12) Patent Application Publication c10) Pub. No.: US 2020/0081016 Al Talaat et al. (43) Pub. Date: Mar. 12, 2020 (54) BIOMARKERS FOR EARLY DIAGNOSIS Publication Classification AND DIFFERENTIATION OF (51) Int. Cl. MYCOBACTERIAL INFECTION GOIN 33/68 (2006.01) C12Q 116851 (2006.01) (71) Applicant: Wisconsin Alumni Research GOIN 33/569 (2006.01) Foundation, Madison, WI (US) (52) U.S. Cl. (72) Inventors: Adel Mohamed Talaat, Madison, WI CPC ......... GOIN 33/6854 (2013.01); GOIN 33/68 (US); Chia-wei Wu, Madison, WI (US) (2013.01); GOIN 2800/50 (2013.01); GOIN 33/5695 (2013.01); GOIN 2800/26 (2013.01); (21) Appl. No.: 16/555,819 C12Q 116851 (2013.01) (22) Filed: Aug. 29, 2019 (57) ABSTRACT Mycobacterial-specific biomarkers and methods of using Related U.S. Application Data such biomarkers for diagnosis of mycobacterial infection in (60) Provisional application No. 62/728,387, filed on Sep. a mammal are disclosed. 7, 2018. Specification includes a Sequence Listing. Patent Application Publication Mar. 12, 2020 Sheet 1 of 10 US 2020/0081016 Al FIG. 1 ·~{:: -{t i * !lpNbiNi$ 1 !lpN p~ra 111:111111 llillllll: 111!11,111llltllllll~ 11111 ■111 ~; C,,Nmnsus KR.IGINMTKX L.lC(X.AXXXXG AXXXXMPXTX RXO-GXVXXVG VKVXPWIPTX ® • ® l I I iipN lK>V(S ~Hl!lli!Wiofflij 1!11.llofJiillj mllB~lijftlt flol=fiolill ••t-il-~MM ~9 llpN p~ra HfHJoffit:torti ilffllGNillm miJllt~ttiollf ~•01:101111 llm:l:l1IA@~ iOO C,,nstmsus XXRXLXXGRS Vt IOGNT.LDP i LOt.MLSXXR XXGXOG.I...XVO ODXXXSR:AXM t2:;: i-/4~~ ! l 1 I~~~~b;:: llllil~l:1:1 llil 111111:1~:111~ 1111111::;1 1lllilllll: ~:~ C,,nimnsus XXXXXXXPGP QtHVDVXXI...X XPGPAGXIPA RHYRPXGGXX QXPt.l...VFYHG Consl:lrvat,ofl -:§;::.
    [Show full text]
  • Purification, Crystallization and Preliminary X-Ray Diffraction Analysis of Exodeoxyribonuclease III from Crenarchaeon Sulfolobus Tokodaii Strain 7
    Crystal Structure Theory and Applications, 2013, 2, 155-158 Published Online December 2013 (http://www.scirp.org/journal/csta) http://dx.doi.org/10.4236/csta.2013.24021 Purification, Crystallization and Preliminary X-Ray Diffraction Analysis of Exodeoxyribonuclease III from Crenarchaeon Sulfolobus tokodaii Strain 7 Shuichi Miyamoto1*, Chieko Naoe2, Masaru Tsunoda3, Kazuo T. Nakamura2 1Faculty of Pharmaceutical Sciences, Sojo University, Kumamoto, Japan 2School of Pharmacy, Showa University, Tokyo, Japan 3Faculty of Pharmacy, Iwaki Meisei University, Iwaki, Japan Email: *[email protected] Received October 13, 2013; revised November 12, 2013; accepted December 6, 2013 Copyright © 2013 Shuichi Miyamoto et al. This is an open access article distributed under the Creative Commons Attribution Li- cense, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. ABSTRACT Exodeoxyribonuclease III (EXOIII) acts as a 3’→5’ exonuclease and is homologous to purinic/apyrimidinic (AP) en- donuclease (APE), which plays an important role in the base excision repair pathway. To structurally investigate the reaction and substrate recognition mechanisms of EXOIII, a crystallographic study of EXOIII from Sulfolobus tokodaii strain 7 was carried out. The purified enzyme was crystallized by using the hanging-drop vapor-diffusion method. The crystals belonged to space group C2, with unit-cell parameters a = 154.2, b = 47.7, c = 92.4 Å, β = 125.8˚ and diffracted to 1.5 Å resolution. Keywords: Crenarchaeon; Crystallization; Exodeoxyribonuclease; Sulfolobus tokodaii; X-Ray Diffraction 1. Introduction formational change upon protein binding that permits complex formation and activation of attacking water, A variety of mechanisms exist to repair damaged DNA leading to incision, in the presence of Mg2+ [10,11].
    [Show full text]
  • Comparison of Strand-Specific Transcriptomes Of
    Landstorfer et al. BMC Genomics 2014, 15:353 http://www.biomedcentral.com/1471-2164/15/353 RESEARCH ARTICLE Open Access Comparison of strand-specific transcriptomes of enterohemorrhagic Escherichia coli O157:H7 EDL933 (EHEC) under eleven different environmental conditions including radish sprouts and cattle feces Richard Landstorfer1, Svenja Simon2, Steffen Schober3, Daniel Keim2, Siegfried Scherer1 and Klaus Neuhaus1* Abstract Background: Multiple infection sources for enterohemorrhagic Escherichia coli O157:H7 (EHEC) are known, including animal products, fruit and vegetables. The ecology of this pathogen outside its human host is largely unknown and one third of its annotated genes are still hypothetical. To identify genetic determinants expressed under a variety of environmental factors, we applied strand-specific RNA-sequencing, comparing the SOLiD and Illumina systems. Results: Transcriptomes of EHEC were sequenced under 11 different biotic and abiotic conditions: LB medium at pH4, pH7, pH9, or at 15°C; LB with nitrite or trimethoprim-sulfamethoxazole; LB-agar surface, M9 minimal medium, spinach leaf juice, surface of living radish sprouts, and cattle feces. Of 5379 annotated genes in strain EDL933 (genome and plasmid), a surprising minority of only 144 had null sequencing reads under all conditions. We therefore developed a statistical method to distinguish weakly transcribed genes from background transcription. We find that 96% of all genes and 91.5% of the hypothetical genes exhibit a significant transcriptional signal under at least one condition. Comparing SOLiD and Illumina systems, we find a high correlation between both approaches for fold-changes of the induced or repressed genes. The pathogenicity island LEE showed highest transcriptional activity in LB medium, minimal medium, and after treatment with antibiotics.
    [Show full text]
  • Restriction Endonucleases
    Molecular Biology Problem Solver: A Laboratory Guide. Edited by Alan S. Gerstein Copyright © 2001 by Wiley-Liss, Inc. ISBNs: 0-471-37972-7 (Paper); 0-471-22390-5 (Electronic) 9 Restriction Endonucleases Derek Robinson, Paul R. Walsh, and Joseph A. Bonventre Background Information . 226 Which Restriction Enzymes Are Commercially Available? . 226 Why Are Some Enzymes More Expensive Than Others? . 227 What Can You Do to Reduce the Cost of Working with Restriction Enzymes? . 228 If You Could Select among Several Restriction Enzymes for Your Application, What Criteria Should You Consider to Make the Most Appropriate Choice? . 229 What Are the General Properties of Restriction Endonucleases? . 232 What Insight Is Provided by a Restriction Enzyme’s Quality Control Data? . 233 How Stable Are Restriction Enzymes? . 236 How Stable Are Diluted Restriction Enzymes? . 236 Simple Digests . 236 How Should You Set up a Simple Restriction Digest? . 236 Is It Wise to Modify the Suggested Reaction Conditions? . 237 Complex Restriction Digestions . 239 How Can a Substrate Affect the Restriction Digest? . 239 Should You Alter the Reaction Volume and DNA Concentration? . 241 Double Digests: Simultaneous or Sequential? . 242 225 Genomic Digests . 244 When Preparing Genomic DNA for Southern Blotting, How Can You Determine If Complete Digestion Has Been Obtained? . 244 What Are Your Options If You Must Create Additional Rare or Unique Restriction Sites? . 247 Troubleshooting . 255 What Can Cause a Simple Restriction Digest to Fail? . 255 The Volume of Enzyme in the Vial Appears Very Low. Did Leakage Occur during Shipment? . 259 The Enzyme Shipment Sat on the Shipping Dock for Two Days.
    [Show full text]
  • The Rnase H-Like Superfamily: New Members, Comparative Structural Analysis and Evolutionary Classification Karolina A
    4160–4179 Nucleic Acids Research, 2014, Vol. 42, No. 7 Published online 23 January 2014 doi:10.1093/nar/gkt1414 The RNase H-like superfamily: new members, comparative structural analysis and evolutionary classification Karolina A. Majorek1,2,3,y, Stanislaw Dunin-Horkawicz1,y, Kamil Steczkiewicz4, Anna Muszewska4,5, Marcin Nowotny6, Krzysztof Ginalski4 and Janusz M. Bujnicki1,3,* 1Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, ul. Ks. Trojdena 4, PL-02-109 Warsaw, Poland, 2Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA USA-22908, USA, 3Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, PL-61-614 Poznan, Poland, 4Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Zwirki i Wigury 93, PL-02-089 Warsaw, Poland, 5Institute of Biochemistry and Biophysics PAS, Pawinskiego 5A, PL-02-106 Warsaw, Poland and 6Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, ul. Ks. Trojdena 4, PL-02-109 Warsaw, Poland Received September 23, 2013; Revised December 12, 2013; Accepted December 26, 2013 ABSTRACT revealed a correlation between the orientation of Ribonuclease H-like (RNHL) superfamily, also called the C-terminal helix with the exonuclease/endo- the retroviral integrase superfamily, groups together nuclease function and the architecture of the numerous enzymes involved in nucleic acid metab- active site. Our analysis provides a comprehensive olism and implicated in many biological processes, picture of sequence-structure-function relation- including replication, homologous recombination, ships in the RNHL superfamily that may guide func- DNA repair, transposition and RNA interference.
    [Show full text]
  • Supplementary Table 3 Complete List of RNA-Sequencing Analysis of Gene Expression Changed by ≥ Tenfold Between Xenograft and Cells Cultured in 10%O2
    Supplementary Table 3 Complete list of RNA-Sequencing analysis of gene expression changed by ≥ tenfold between xenograft and cells cultured in 10%O2 Expr Log2 Ratio Symbol Entrez Gene Name (culture/xenograft) -7.182 PGM5 phosphoglucomutase 5 -6.883 GPBAR1 G protein-coupled bile acid receptor 1 -6.683 CPVL carboxypeptidase, vitellogenic like -6.398 MTMR9LP myotubularin related protein 9-like, pseudogene -6.131 SCN7A sodium voltage-gated channel alpha subunit 7 -6.115 POPDC2 popeye domain containing 2 -6.014 LGI1 leucine rich glioma inactivated 1 -5.86 SCN1A sodium voltage-gated channel alpha subunit 1 -5.713 C6 complement C6 -5.365 ANGPTL1 angiopoietin like 1 -5.327 TNN tenascin N -5.228 DHRS2 dehydrogenase/reductase 2 leucine rich repeat and fibronectin type III domain -5.115 LRFN2 containing 2 -5.076 FOXO6 forkhead box O6 -5.035 ETNPPL ethanolamine-phosphate phospho-lyase -4.993 MYO15A myosin XVA -4.972 IGF1 insulin like growth factor 1 -4.956 DLG2 discs large MAGUK scaffold protein 2 -4.86 SCML4 sex comb on midleg like 4 (Drosophila) Src homology 2 domain containing transforming -4.816 SHD protein D -4.764 PLP1 proteolipid protein 1 -4.764 TSPAN32 tetraspanin 32 -4.713 N4BP3 NEDD4 binding protein 3 -4.705 MYOC myocilin -4.646 CLEC3B C-type lectin domain family 3 member B -4.646 C7 complement C7 -4.62 TGM2 transglutaminase 2 -4.562 COL9A1 collagen type IX alpha 1 chain -4.55 SOSTDC1 sclerostin domain containing 1 -4.55 OGN osteoglycin -4.505 DAPL1 death associated protein like 1 -4.491 C10orf105 chromosome 10 open reading frame 105 -4.491
    [Show full text]
  • The Impact of Genetic Diversity on Gene Essentiality Within the E. Coli Species
    bioRxiv preprint doi: https://doi.org/10.1101/2020.05.25.114553; this version posted May 25, 2020. 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-NC-ND 4.0 International license. The impact of genetic diversity on gene essentiality within the E. coli species François Rousset1,2, José Cabezas Caballero1, Florence Piastra-Facon1, Jesús Fernández-Rodríguez3, Olivier Clermont4, Erick Denamur4,5, Eduardo P.C. Rocha6 & David Bikard1,* 1- Synthetic Biology, Department of Microbiology, Institut Pasteur, Paris, France 2- Sorbonne Université, Collège Doctoral, F-75005Paris, France 3- Eligo Bioscience, Paris, France 4- Université de Paris, IAME, INSERM UMR1137, Paris, France 5- AP-HP, Laboratoire de Génétique Moléculaire, Hôpital Bichat, Paris, France 6- Microbial Evolutionary Genomics, Institut Pasteur, CNRS, UMR3525, 25-28 rue Dr Roux, Paris, 75015, France. *To whom correspondence should be addressed: [email protected] Abstract Bacteria from the same species can differ widely in their gene content. In E. coli, the set of genes shared by all strains, known as the core genome, represents about half the number of genes present in any strain. While recent advances in bacterial genomics have enabled to unravel genes required for fitness in various experimental conditions at the genome scale, most studies have focused on model strains. As a result, the impact of this genetic diversity on core processes of the bacterial cell largely remains to be investigated. Here, we developed a new CRISPR interference platform for high- throughput gene repression that is compatible with most E.
    [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]
  • A Little Sugar Goes a Long Way: the Cell Biology of O-Glcnac
    Published March 30, 2015 JCB: Review A little sugar goes a long way: The cell biology of O-GlcNAc Michelle R. Bond and John A. Hanover Unlike the complex glycans decorating the cell surface, the to nucleocytoplasmic kinases and phosphatases. In fact, there are O-linked -N-acetyl glucosamine (O-GlcNAc) modifica- many parallels between phosphorylation and O-GlcNAcylation: O-GlcNAc is added to Ser and Thr residues; the modification tion is a simple intracellular Ser/Thr-linked monosaccha- rapidly cycles on and off modified proteins at a rate faster than ride that is important for disease-relevant signaling and protein turnover; and like kinases and phosphatases, OGT and enzyme regulation. O-GlcNAcylation requires uridine OGA are phosphorylated (Fig. 1 B; Butkinaree et al., 2010; diphosphate–GlcNAc, a precursor responsive to nutrient Hanover et al., 2010). Many target proteins are modified by both status and other environmental cues. Alternative splicing O-GlcNAc and phosphate at exposed regions, suggesting the of the genes encoding the O-GlcNAc cycling enzymes presence of shared or coexisting recognition motifs. However, although the sites of protein phosphorylation can often be identified Downloaded from O-GlcNAc transferase (OGT) and O-GlcNAcase (OGA) by primary sequence alone, O-GlcNAcylation is not associated yields isoforms targeted to discrete sites in the nucleus, cy- with a clear consensus motif. toplasm, and mitochondria. OGT and OGA also partner OGT uses UDP-GlcNAc, a nucleotide sugar derived from with cellular effectors and act in tandem with other post- the nutrient-dependent hexosamine biosynthetic pathway (HBP), translational modifications. The enzymes of O-GlcNAc to catalyze O-GlcNAc addition (Fig.
    [Show full text]
  • SUPPLEMENTARY INFORMATION in Silico Signature Prediction
    SUPPLEMENTARY INFORMATION In Silico Signature Prediction Modeling in Cytolethal Distending Toxin-Producing Escherichia coli Strains Maryam Javadi, Mana Oloomi*, Saeid Bouzari Department of Molecular Biology, Pasteur Institute of Iran, Tehran 13164, Iran http://www.genominfo.org/src/sm/gni-15-69-s001.pdf Supplementary Table 6. Aalphabetic abbreviation and description of putative conserved domains Alphabetic Abbreviation Description 17 Large terminase protein 2_A_01_02 Multidrug resistance protein 2A0115 Benzoate transport; [Transport and binding proteins, Carbohydrates, organic alcohols] 52 DNA topisomerase II medium subunit; Provisional AAA_13 AAA domain; This family of domains contain a P-loop motif AAA_15 AAA ATPase domain; This family of domains contain a P-loop motif AAA_21 AAA domain AAA_23 AAA domain ABC_RecF ATP-binding cassette domain of RecF; RecF is a recombinational DNA repair ATPase ABC_SMC_barmotin ATP-binding cassette domain of barmotin, a member of the SMC protein family AcCoA-C-Actrans Acetyl-CoA acetyltransferases AHBA_syn 3-Amino-5-hydroxybenzoic acid synthase family (AHBA_syn) AidA Type V secretory pathway, adhesin AidA [Cell envelope biogenesis] Ail_Lom Enterobacterial Ail/Lom protein; This family consists of several bacterial and phage Ail_Lom proteins AIP3 Actin interacting protein 3; Aip3p/Bud6p is a regulator of cell and cytoskeletal polarity Aldose_epim_Ec_YphB Aldose 1-epimerase, similar to Escherichia coli YphB AlpA Predicted transcriptional regulator [Transcription] AntA AntA/AntB antirepressor AraC AraC-type
    [Show full text]
  • Curriculum Vitae Vern Lee Schramm
    September 2011 CURRICULUM VITAE VERN LEE SCHRAMM Department of Biochemistry Albert Einstein College of Medicine of Yeshiva University 1300 Morris Park Avenue Bronx, New York 10461 Phone: (718) 430-2813 Fax: (718) 430-8565 E-mail: [email protected] Personal Information: Date of Birth: November 9, 1941 Place of Birth: Howard, South Dakota Citizenship: U.S.A. Home Address: 68 Hampton Oval New Rochelle, NY 10805 Home Telephone: (914) 576-2578 Education: Sept 1959 – June 1963 B.S. in Bacteriology (chemistry emphasis), South Dakota State College Sept 1963 – June 1965 Masters Degree in Nutrition (biochemistry emphasis), Harvard University Research Advisor, Dr. R.P. Geyer Oct 1965 – April 1969 Ph.D. in Mechanism of Enzyme Action, Department of Biochemistry, Australian National University Research Advisor, Dr. John Morrison Postdoctoral Experience: Aug 1969 – Aug 1971 NRC-NSF Postdoctoral Research Associate at NASA Ames Research Center, Biological Adaptation Branch Appointments: July 1999 – Present University Professor of the Albert Einstein College of Medicine July 1995 – Present Ruth Merns Endowed Chair of Biochemistry Aug 1987 – Present Professor and Chairman, Department of Biochemistry, Albert Einstein College of Medicine July 1981 - July 1987 Professor of Biochemistry, Temple University School of Medicine July 1976 - June 1981 Associate Professor of Biochemistry, Temple University School of Medicine Aug 1971 - July 1976 Assistant Professor of Biochemistry, Temple University School of Medicine Vern L. Schramm 2 Fields of Interest: Enzymatic
    [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]