DOCSLIB.ORG

Vegetative Cell and Spore Proteomes of Clostridioides Difficile Show Finite Differences and Reveal Potential Protein Markers

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Vegetative Cell and Spore Proteomes of Clostridioides Difficile Show Finite Differences and Reveal Potential Protein Markers Supporting Information Vegetative Cell and Spore Proteomes of Clostridioides difficile show finite differences and reveal potential protein markers. Wishwas R. Abhyankar1, 2, Linli Zheng1, 2, Stanley Brul1*, Chris G. de Koster2†, Leo J. de Koning2 1Department of Molecular Biology and Microbial Food Safety, University of Amsterdam, Amsterdam, the Netherlands; 2Department of Mass Spectrometry of Bio-Macromolecules,University of Amsterdam, Amsterdam, the Netherlands. † Deceased August 5th, 2019. *Corresponding author E-mail: [email protected] Table of Contents Supplementary Figure S1. Cellular overview of quantified proteins from spores and vegetative cells of C. difficile 630. Supplementary Figure S2. Pathways and proteins shared by the vegetative cells and spores of C. difficile 630. Supplementary Figure S1. Cellular overview of quantified proteins from spores and vegetative cells of C. difficile 630. The overview is generated using the BioCyc pathway analysis tool. The quantified proteins that are spore-predominant (red), commonly shared yet spore-enriched, commonly shared but cell-enriched (grey) and cell-predominant proteins (purple) are represented with the pathways to which they belong. Refer to Supplementary Table S1 and Supplementary Figure S2 for more details. os o os p o o l-hist1dme b10synthes1S os o o L·homosenneand L·meth1onuie b1osynthesis superpathway of L·tyrosine b1osynthes1s o superpathwayof L-meth1ornne ATP b1osynthes1s (transsutfurat1on) l D-erythr e PAPP ph ph enol as xal acetate pyruv 4-p phate xal acetate chorismate oxal acetate osaspartate kinase I: dapG aspartate aspartate l phospho-2- aspartale bifunclionaJ I aspartokinase: ysC aminotranslerase: ammotransferase: aspC os phosphoribosyltrans1erase:o � aspC hisG dehydro-3- aminotransrerase: chorismate r os deoxyheptonate a,pC aspartate l mutasel L-aspartyl-4-ph phate aspartate aldolase:aroF aminotranslerase: aspB prephenate aspartale dehydratase: aminotranslerase: t-(5-ph ph - aminotransrerase: aspartate am!notransferase· aspB � j pheA aspartate-semiatdehyde -D- ib yl) phospho-2- asps CD630_25l50 dehydro-3· s sl dehydrogenase:asd aspartate deoxyheptonate p aspartate aminotrans!erase: ::; aldolase: aroF aspartate CD630_28280 prephenate aminotrans!erase: o aminotranslerase: !i� CD630_25t50 E oso L-a partate- emialdehyde r.� CD630_25150 phosphoribosyl·ATP., o as l bltuocllonat l 3-d xy- aspartate pyrophosphatase: aspartate chorismate homo,enne aminotranslerase: hisl D-arabin ­ aminolranslerase: mutase/ p aspartate kmase L dapG j dehydrogenase:hom1 CD630_26260 D�7iifo��1f.�'M�- heptul nate CD630_28280 l prephenate 7-ph phate s l aspartokinase:os ysC dehydratase: homoserine o o pheA o os dehydrogenase:hom2 asp 1 3·dehydroquinate l lo as p p l I synthase:aroB l-a partyl-4-ph phate a,partate I l kmase brluncbonal a,pa,tate 2- x -3- L-h m erine :dapG phosphonbosyl kinase henyl anoate j 3-dehydrl quinate l:dapG aspartate-semlaldehyde homoserine 0- j dehydrogenase:asd p aspartokinase: ��:sp�i�;���� l s o os r "-- succiny translerase: metA s lysC 3-dehydroquinate aspartokinase: j pyrophosphatase: rosh s os dehydratase:aroD lysC hIsI p p L-aspartate-semialdehyde he l-a partyl- m cy -L-h m erine 3-d <,a� + 4-phosphate J;\�;fif1-(5 ph ph @ D-nbosyl)- L-a partyl- homo,ertne � ;if�'��' s o � 4- hos hate j dehydrogenase: hom1 8spMate­ a,partate­ homoserine l semialdehyde �: o os dehydrogenase:hom2 dehydrogenase· semialdehyde L-cy tathi nine s r a,o l dehydrogenase: l s a,d ] I bilunctional cystathionine dehy���i�nase: L-h m erine s beta-lyaselmaltose l-a pa tate- methylldeneamino] regulon repressor: ma!Y sem;aldehy im!dazole-4- L-a partate- homoserine 0- :: r carboxamide sem;aldehy s "-- succinyltranslerase:o os metA mo,eooe os o os or isomeraseo : hisA hikimate :: dehydrogenase: os mo,e.,ne dehydrogenase: homl shikimate homocysteine S­ l hom1 cy -L-h m erine methyltranslerase: kmase: i j homoserine ph ph ribul ylf mimin ­ s aroK � CD630_35960 dehydrogenase: AICAA-ph phate os j homoserine s o o s r h0m2 dehydrogenase: o o hom2 hikimate 3- lmldazole ph phate L-cy tathi nine glycerol l l-h mo e ine phosphate l 3-phosphoshikimate 1- L-h m serine blfunctional cystathionine synthase: o carboxyvinyllranslerase:o l beta-Iyase1maItose homoserfne os o hIsHhisF o aroA kinase: thrB o homoserineo regu on repressor: malY o os o kinase:thrB l o os superpathway of branched chamamino acid b1osynthes1s 5-en lp ruv yl­ O-ph ph ­ -erythr - l l shikimate 3- l-h m erine AICAA O-ph sph ­ pyruvate lmid � -� 1 er l- phos hate homocysteine S­ thr � �� � � L-h m erine l l uueonloe chorismate methyltransferase: acetolactate lmidazo eglycero synthase: l threonioe CD630_35960 l ­ synthase: synthase large o threonineo o sl thrC o ophosphate a,OC synlhase: o subunit:ilvB dehydratase dehydratase: hisB thrC 11:tdcB osI (2Z)-2-amin but-2-en ate tht lmidaz le acet l- ch ri mate {S)-2-acet lactate 1 thr l ph pha1e o o olhreomne bifunct�oal l ketot-a,� o histidinol-phosphate chorismate reducto.isomerase:ro dehydratase l 11:tdcB aminotranslerase: mutase/ o ,I,c hisC l prephenate 2-imin butan ate (22)-2-amin but- dehydratase: 1 I o (2A)-2,3-dihyd xy­ 2-en ate histidino -phosphate r pheA s o !3-methylbutanl ate aminotranslerase: s hisC dihydroxy-acid dehydratase: ilvD 2-oxobutan ate p ephenate 2-iminobutanoate l-hi tidin l­ 1 pho phate 1 acetolactate 1 prephenate IMNMiH synthase large os o o o o dehydrogenase: subunit:ilvB histidinol­ o ty,C p ro o phosphatase: hiSK l 2- xobutan ate 3-ph ph - (S)-2-acet -2- l histidinol 4-hydr xyphenylpyruvate D-glycerate _ _ so o hyd xybutan ate phosphatase/ o o 0 3 1 acetola""" hydrolase: phosphog ycerate l ketol-acid synthase s o 1 l dehydrogenase: serA reductoisomerase:ro CD630_10690 arge. _ a,part:.: a,pa,agine (2S)-2-i pr pylmalate o l l o flvC subunIt:Ilv8 -ammonia synthetase: o o 3-ph sph - ligase: asnA asnB tyr hydrox rruvate 3-isopropytmalate hi tidin l so ro dehydratase: (A)-2,3-dihyd xy- l os o asparagine asparagine {S)-2-acet -2- r euc leuD 3-methylpentanl ate sy synthetase: l synthetase: hydr xybutan ate s histidinol asnB asnB dihydroxy-acid dehydrogenase: 2-i p pylmaleate o o o ketol-acld 1 l dehydratase: ilvD l hisD 3-ph ph ­ asparagine reductoisome ase: o l- erine syn!hetase: ilvC so ro3-isopropylmalate o hi tidinat asnB dehydratase: l l asn euC leuD (S)-3-methyl-2- x pentan ate (A)-2,3-dihydr xy- histidinol 3-methy!pentan ate s dehydrogenase: (2A,3S)-3-i lp pylmalate hisD l dihydroxy-acid asn l so 3-o isopropylmatate dehydratase: o os dehydrogenase: ilvD hi serinel l ile p teuB hydroxymethyltranslerase:g yA senne (2S)-2-i pr pyl- (S)-3-methyl-2· hydroxymethy translerase: g yA 3- x uccinate1 oxo e noate o o o r gly 4-methyl-2- x pentan ate l#;i#iffiHe 1MI I os os leu D-rib e 5- Scale representing the ph lphate Log (14N/15N) ratios nbose-phospha\e 2 pyrophosphokmase: prs PAPP superpathway of purine nucleondes de novo b1osynthests I superpathway of pynmidine nbonucleot1des de novo b10synthesis superpathway ot punne nucleotides de novo brosynthests II PRPP PAPP gin hydrogencarbonate amidophosphont>Osyltranslerase:purF am;dopMsp,o,;bOsy,oans<,,asec P"'' carbamoy1-phosphate ! l synthase· carB1 carA carbamoyl-phosphate o gly synthase: carB2 carA J:ff�t:i� ·jl· o gty phospnor,oosy1amine­ J3ctf.�g:0��- - carbamoyl ph phate asp ·glycme ligase: purD phosphon�osylamine­ ·glycme hgase pu,o aspartate � carbamoyltranslerase py1B GAR GAR phosphoribOsylglycinam!de l rormyltrans1erase:purN N-carbamoyl-L·aspartate FGAR 1 d1hydroorotase:pyre FGAA priospnorib0sy1lormy1g1ycinam1dlne dihydroorotase: synthase: purL phosphor1bosyllormylglycinamid1ne CD630_36430 1 synthase: purL l FGAM 1 (S)-dihydroorotate FGAM phosphoribosyllormylglycinamldine cyclo-ligase: purG phosphoribosyllormylglycinamidine l cyclo-ligase:purG RPP 1 o,otat AIR 1 AIR orotate A;R Y-phosphonbosyltranslerase· carbOxylase: pyrE l C0630_0l950 carboxy1ase: C0630_01950 N5·CAIR orotidine 5'·phosphate A;R asp NCA;R m"<a,ec carboxylase: C0630 01950 purE orotidine 5'-phosphate decarboxylase: pyrF 5-carn:xyamlnolmldazore l nbonucleotJde mutase:pure l CAI UMP j "" uridylate kinase: pyrH i CAIR phosphorlbosylaminoimidazolesucclnocarboxamide synlhase:purC UDP pnospnorit>OsyramJnolmidazoiesuccinocarbOxamide syntnase:purC phosphonbosylam,noimlaa:rolesucc,nocarboxam,de synlhase: C0630_04890 phosphoribosyraminoimidazotesuccinocarboxamide synthase: C0630_04890 SAICAA SAICAAl gin adenylosucc1nate UTP adenylosuccJnate lyase:purB '-- lyase: purB 1 AICAA 1 CTP AICAA o;t"="ona, """nc,;ona, phosphoribOsytamlnolmlda:roleca,bOxamide phosphoribosylamJnolmlda:roteca1boxamlde lormyltransferas@IIMP cycrohydrOLas@: purH lormyltransleras&IIMP cyclohydrolase:purH 5-aminoimidazore- 5-am,noimidazole- 4-carboxamlde 4-carboxamide nbonucleotlde nbonucleollde translormylase translormylase: CD630_08410 C0630_064 10 l l FAICAR FAICAA bilunc1ional bllunclional phosphorlbosylaminolmldazolecarboxamide phosphonbosylamlnolmlda:rorecarbOxamlde lormyltranslerase/lMP cyclohydrolase: purH lormyltranslerase/lMP cyclohydrolase: purH asp IMPl IMP asp j superpathway of adenosme adenylosucclnate nucleotides de novo b1osynthesis I Jnosine 5- inosine 5- synthetase. purA monophosphate monophosphale denyarogenase: aenyarogenase: guaB guaB adenylo-succinate adenylo-succinate adeny,os"cdna<e adeny<os"cdaa<e 1yase: pure l XMP lyase:pu1B l adenylo·succinate XMP GMP AMP adeny,os=c,na<e syntnase· AMP guaA lyase: purB GMP adeny<a<e synthas@: adenylate l 9"aA kmase:adk kmase· adk l l GMPl l AMP GMP ADP adeny<a<e kmase: gmk kinase:adk g"any<a<e l •"··,···· l kinase:gmk ribonucleoside-
Load more

Recommended publications
  • The Regulation of Carbamoyl Phosphate Synthetase-Aspartate Transcarbamoylase-Dihydroorotase (Cad) by Phosphorylation and Protein-Protein Interactions
    THE REGULATION OF CARBAMOYL PHOSPHATE SYNTHETASE-ASPARTATE TRANSCARBAMOYLASE-DIHYDROOROTASE (CAD) BY PHOSPHORYLATION AND PROTEIN-PROTEIN INTERACTIONS Eric M. Wauson A dissertation submitted to the faculty of the University of North Carolina at Chapel Hill in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Department of Pharmacology. Chapel Hill 2007 Approved by: Lee M. Graves, Ph.D. T. Kendall Harden, Ph.D. Gary L. Johnson, Ph.D. Aziz Sancar M.D., Ph.D. Beverly S. Mitchell, M.D. 2007 Eric M. Wauson ALL RIGHTS RESERVED ii ABSTRACT Eric M. Wauson: The Regulation of Carbamoyl Phosphate Synthetase-Aspartate Transcarbamoylase-Dihydroorotase (CAD) by Phosphorylation and Protein-Protein Interactions (Under the direction of Lee M. Graves, Ph.D.) Pyrimidines have many important roles in cellular physiology, as they are used in the formation of DNA, RNA, phospholipids, and pyrimidine sugars. The first rate- limiting step in the de novo pyrimidine synthesis pathway is catalyzed by the carbamoyl phosphate synthetase II (CPSase II) part of the multienzymatic complex Carbamoyl phosphate synthetase, Aspartate transcarbamoylase, Dihydroorotase (CAD). CAD gene induction is highly correlated to cell proliferation. Additionally, CAD is allosterically inhibited or activated by uridine triphosphate (UTP) or phosphoribosyl pyrophosphate (PRPP), respectively. The phosphorylation of CAD by PKA and ERK has been reported to modulate the response of CAD to allosteric modulators. While there has been much speculation on the identity of CAD phosphorylation sites, no definitive identification of in vivo CAD phosphorylation sites has been performed. Therefore, we sought to determine the specific CAD residues phosphorylated by ERK and PKA in intact cells.
    [Show full text]
  • Developmental Outcomes with Early Orthotopic Liver Transplantation For
    Developmental Outcomes With Early Orthotopic Liver Transplantation for Infants With Neonatal-Onset Urea Cycle Defects and a Female Patient With Late-Onset Ornithine Transcarbamylase Deficiency Kim L. McBride, MD*; Geoffrey Miller, MD‡; Susan Carter, BSN*࿣; Saul Karpen, MD, PhD‡; John Goss, MD§; and Brendan Lee, MD, PhD*࿣ ABSTRACT. Urea cycle defects (UCDs) typically nherited disorders of the urea cycle are character- present with hyperammonemia, the duration and peak ized by high ammonia levels and altered amino levels of which are directly related to the neurologic acid metabolism. There are 6 well-characterized outcome. Liver transplantation can cure the underlying I urea cycle defects (UCDs), ie, N-acetylyglutamate defect for some conditions, but the preexisting neuro- synthase, carbamoyl phosphate synthase (CPS), X- logic status is a major factor in the final outcome. Mul- linked ornithine transcarbamylase (OTC), arginosuc- ticenter data indicate that most of the children who re- cinate synthase, arginosuccinate lyase, and arginase ceive transplants remain significantly neurologically deficiencies. Arginase deficiency is not typical of the impaired. We wanted to determine whether aggressive other UCDs, because it presents not with hyperam- metabolic management of ammonia levels after early monemia but with spastic diplegia. Presentation of referral/transfer to a metabolism center and early liver transplantation would result in better neurologic out- the other UCDs can be quite variable, from cata- comes. We report on 5 children with UCDs, ie, 2 male strophic neonatal illness and acute episodic enceph- patients with X-linked ornithine transcarbamylase defi- alopathy in childhood or adulthood to chronic neu- 1 ciency and 2 male patients with carbamoyl phosphate rologic disorders.
    [Show full text]
  • Carbamoyl Phosphate Synthetase I Deficiency
    Carbamoyl phosphate synthetase I deficiency Description Carbamoyl phosphate synthetase I deficiency is an inherited disorder that causes ammonia to accumulate in the blood (hyperammonemia). Ammonia, which is formed when proteins are broken down in the body, is toxic if the levels become too high. The brain is especially sensitive to the effects of excess ammonia. In the first few days of life, infants with carbamoyl phosphate synthetase I deficiency typically exhibit the effects of hyperammonemia, which may include unusual sleepiness, poorly regulated breathing rate or body temperature, unwillingness to feed, vomiting after feeding, unusual body movements, seizures, or coma. Affected individuals who survive the newborn period may experience recurrence of these symptoms if diet is not carefully managed or if they experience infections or other stressors. They may also have delayed development and intellectual disability. In some people with carbamoyl phosphate synthetase I deficiency, signs and symptoms may be less severe and appear later in life. Frequency Carbamoyl phosphate synthetase I deficiency is a rare disorder; its overall incidence is unknown. Researchers in Japan have estimated that it occurs in 1 in 800,000 newborns in that country. Causes Mutations in the CPS1 gene cause carbamoyl phosphate synthetase I deficiency. The CPS1 gene provides instructions for making the enzyme carbamoyl phosphate synthetase I. This enzyme participates in the urea cycle, which is a sequence of biochemical reactions that occurs in liver cells. The urea cycle processes excess nitrogen, generated when protein is broken down by the body, to make a compound called urea that is excreted by the kidneys. The specific role of the carbamoyl phosphate synthetase I enzyme is to control the first step of the urea cycle, a reaction in which excess nitrogen compounds are incorporated into the cycle to be processed.
    [Show full text]
  • Decreased Concentration of Xanthine Dehydrogenase (EC 1.1.1.204) in Rat Hepatomas1
    [CANCER RESEARCH 46, 3838-3841, August 1986] Decreased Concentration of Xanthine Dehydrogenase (EC 1.1.1.204) in Rat Hepatomas1 Tadashi Ikegami, Yutaka Natsumeda, and George Weber2 Laboratory for Experimental Oncology, Indiana University School of Medicine, Indianapolis, Indiana 46223 ABSTRACT Immunodiffusion disc was from Miles Laboratories, Inc., Naperville, IL. All other chemicals were also of analytical grade. Xanthine dehydrogenase (EC 1.1.1.204), the rate-limiting enzyme of Tissues. Chemically induced transplantable hepatomas were main purine degradation, was purified 642-fold to homogeneity from liver of tained as described previously (9). Hepatoma 20 was transplanted in male Wistar rats. Antibody was generated to the purified enzyme in white male Buffalo strain rats, and hepatoma 3924A was carried in male rabbits and was partially purified. For the immunotitration a radioassay ACI/N rats. Livers from Buffalo and ACI/N rats were used as controls. of high sensitivity was developed to determine low enzyme activities. Hepatoma 3924A was homogenized with 3.3 volumes and hepatoma Titration curves with the antibody showed that the xanthine dehydrogen 20 and the livers were homogenized with 5 volumes of SOHIMpotassium ase enzyme protein amounts in slowly growing hepatoma 20 and rapidly phosphate buffer, pH 7.4, containing 0.25 M sucrose and 0.3 mM growing hepatoma 3924A were 34 and 4% of those of normal liver, which EDTA, respectively. The homogenates were centrifuged at 100,000 x was in good agreement with the decrease in the activity of the enzyme to g for 30 min, and the clear supernatants were used for the enzyme 33 and 2%, respectively.
    [Show full text]
  • Cell and Gene Therapy for Carbamoyl Phosphate Synthetase 1 Deficiency
    Journal of Pediatrics and Neonatal Care Cell and Gene Therapy for Carbamoyl Phosphate Synthetase 1 Deficiency Abstract Review Article Volume 7 Issue 1 - 2017 Carbamoyl phosphate synthetase 1 (CPS1) is the first and rate-limiting enzyme in the urea cycle. CPS1 deficiency is a devastating condition, which is clinically characterized by periodic episodes of life-threatening hyperammonemia. Currently, 1Associate at Department of Genetic Medicine, Children’s there is no cure for CPS1 deficiency except for liver transplantation, which is limited Research Institute, Children’s National Health System, USA on the progress to date, cell-based therapies—including hepatocyte or stem cell 2 by a severe shortage of donors and significant risk of mortality and morbidity. Based Washington Institute for Health Sciences, Department of transplantation—and new approaches for gene therapy have become the promising Biochemistry and Molecular & Cellular Biology, Georgetown University Medical Center, USA curative treatments for CPS1 deficiency. This review outlines the current progress and *Corresponding author: Bin Li, MD, Washington Institute Keywords:challenges of cell and gene therapies for CPS1 deficiency. for Health Sciences, 4601 N Fairfax Drive, Arlington, VA therapy; Gene therapy 22203; Georgetown University Medical Center, 4000 Urea cycle defects; Carbamoyl phosphate synthetase 1 deficiency; Cell Reservoir Road, N.W., Washington D.C. 20057, United States. Tel: 202-687-6484, Fax: (202) 687-1800, Email: Abbreviations: AAVs: Adeno-Associated Viruses;
    [Show full text]
  • Nucleotide Metabolism II
    Nucleotide Metabolism II • Biosynthesis of deoxynucleotides • Salvage Pathway • Catabolism: Purines • Catabolism: Pyrimidines • Feedback inhibition in purine nucleotide biosynthesis CPS II • Cytosolic CPS II uses glutamine as the nitrogen donor to carbamoyl phosphate Regulation of pyrimidine synthesis •CPSII is allosterically regulated: PRPP and IMP are activators Several pyrimidines are inhibitors • Aspartate transcarbamoylase (ATCase) Important regulatory point in prokaryotes Catalyzes the first committed pathway step Allosteric regulators: CTP (-), CTP + UTP (-), ATP (+) • Regulation of pyrimidine nucleotide synthesis in E. coli Biosynthesis of deoxynucleotides • Uses diphosphates (ribo) • Ribonucleotide reducatase • 2 sub-units • R1- reduces, active and two allosteric sites (activity and specificity site) • R2- tyrosine radical carries electrons • removes 2' OH to H Ribonucleotide reductase reaction • removes 2' OH to H • Thioredoxin and NADPH used to regenerate sulfhydryl groups Thymidylate synthesis • UDP ------> dUMP • dUMP --------> dTMP • required THF • methylates uracil Regulation THF • Mammals cannot conjugate rings or synthesize PABA. • So must get in diet. • Sulfonamides effective in bacteria due to competitive inhibition of the incorporation of PABA Cancer Drugs • fluorouracil-- suicide inhibitor of Thy synthase • aminopterin • Methotrexate -- inhibits DHF reductase Salvage of Purines and Pyrimidines • During cellular metabolism or digestion, nucleic acids are degraded to heterocyclic bases • These bases can be salvaged
    [Show full text]
  • Amino Acid Catabolism: Urea Cycle the Urea Bi-Cycle Two Issues
    BI/CH 422/622 OUTLINE: OUTLINE: Protein Degradation (Catabolism) Digestion Amino-Acid Degradation Inside of cells Urea Cycle – dealing with the nitrogen Protein turnover Ubiquitin Feeding the Urea Cycle Activation-E1 Glucose-Alanine Cycle Conjugation-E2 Free Ammonia Ligation-E3 Proteosome Glutamine Amino-Acid Degradation Glutamate dehydrogenase Ammonia Overall energetics free Dealing with the carbon transamination-mechanism to know Seven Families Urea Cycle – dealing with the nitrogen 1. ADENQ 5 Steps 2. RPH Carbamoyl-phosphate synthetase oxidase Ornithine transcarbamylase one-carbon metabolism Arginino-succinate synthetase THF Arginino-succinase SAM Arginase 3. GSC Energetics PLP uses Urea Bi-cycle 4. MT – one carbon metabolism 5. FY – oxidases Amino Acid Catabolism: Urea Cycle The Urea Bi-Cycle Two issues: 1) What to do with the fumarate? 2) What are the sources of the free ammonia? a-ketoglutarate a-amino acid Aspartate transaminase transaminase a-keto acid Glutamate 1 Amino Acid Catabolism: Urea Cycle The Glucose-Alanine Cycle • Vigorously working muscles operate nearly anaerobically and rely on glycolysis for energy. a-Keto acids • Glycolysis yields pyruvate. – If not eliminated (converted to acetyl- CoA), lactic acid will build up. • If amino acids have become a fuel source, this lactate is converted back to pyruvate, then converted to alanine for transport into the liver. Excess Glutamate is Metabolized in the Mitochondria of Hepatocytes Amino Acid Catabolism: Urea Cycle Excess glutamine is processed in the intestines, kidneys, and liver. (deaminating) (N,Q,H,S,T,G,M,W) OAA à Asp Glutamine Synthetase This costs another ATP, bringing it closer to 5 (N,Q,H,S,T,G,M,W) 29 N 2 Amino Acid Catabolism: Urea Cycle Excess glutamine is processed in the intestines, kidneys, and liver.
    [Show full text]
  • Nitrogen-Stimulated Orotic Acid Synthesis and Nucleotide Imbalance1
    [CANCER RESEARCH (SUPPL.) 52. 2082s-2084s. April I. 1992] Nitrogen-stimulated Orotic Acid Synthesis and Nucleotide Imbalance1 Willard J. Visek2 University of Illinois, College of Medicine, Urbana, Illinois 61801 Abstract bound to the inner mitochondria! membrane. The cytoplasmic enzymes reside in two separate multifunctional complexes. One Orotic acid, first discovered in ruminant milk, is an intermediate in contains carbamoyl phosphate synthetase II, aspartate trans- the pyrimidine biosynthesis pathway of animal cells. Its synthesis is carbamylase, and dihydroorotase, whereas the other includes initiated by the formation of carbamoyl phosphate (CP) in the cytoplasm, orotate phosphoribosyl transferase and orotodine-5"-phosphate with ammonia derived from glutamine. Ureotelic species also form CP in the first step of urea synthesis in liver mitochondria. For that, ammonia decarboxylase (2, 3). A deficiency of the latter two enzyme is derived from tissue fluid. When there is insufficient capacity for activities results in accumulation of orotate and a profound rise detoxifying the load of ammonia presented for urea synthesis, CP leaves in its excretion in the urine, a condition known as hereditary the mitochondria and enters the pyrimidine pathway, where orotic acid orotic aciduria (4). This bifunctional protein complex with its biosynthesis is stimulated, orotic acid excretion in urine then increases. two enzyme activities is also referred to as UMP synthase. Orotic acid synthesis is abnormally high with hereditary deficiencies of A severe deficiency of UMP synthase elevates urinary orotic urea-cycle enzymes or uridine monophosphate synthase. It is also ele acid excretion in humans to 1500 mg/day, compared with the vated by ammonia intoxication and during feeding of diets high in protein, usual 2.5 mg/day.
    [Show full text]
  • Nucleo'de)Metabolism) (Chapter)23)) INTRODUCTION)TO)NUCLEIC)ACIDS)
    BIOCH 765: Biochemistry II Spring 2014 Nucleo'de)Metabolism) (Chapter)23)) Jianhan)Chen) Office)Hour:)MF)1:30B2:30PM,)Chalmers)034) Email:)[email protected]) Office:)785B2518) INTRODUCTION)TO)NUCLEIC)ACIDS) (c))Jianhan)Chen) 2) Eukaryo'c)cell) 3 Genome)is)believed)to)define)a)species) 4 Nucleic)Acids) • Polymer(of( nucleotides:(highly( flexible((compared( to(peptides)( • Nucleic(acids(are( universal(in(living( things,(as(they(are( found(in(all(cells( and(viruses.( • Nucleic(acids(were( first(discovered(by( Friedrich(Miescher( in(1871.( (c))Jianhan)Chen) 5 Building)Blocks)of)Nucleo'des) • Phosphate(group(+(pentose(carbohydrate(+( base((nitrogenGcontaining(heterocyclic(ring)( • Deoxyribonucleic(acid((DNA):(A/G/C/T( • Ribonuclei(acid((RNA):(A/G/C/U( Nucleotide nucleobase 6 Nucleo'des)have)many)roles) • Building(blocks(of(the(nucleic(acid(polymers(RNA(and( DNA.( • Energy(transfer(or(energy(coupling(to(drive(biosynthesis( and(other(processes((muscle(contraction,(transport,(etc).( • Oxidation(reduction(reactions.( • Intracellular(signaling.( ATP 7 Pentose)sugars) Base Phosphate sugar • The(pentose(sugar(in(the(nucloetide(is(either(ribose(or( deoxyribose.( ( – The(base(is(added(at(the(1(position(and(phosphates(are(added(at( the(5(position.( – Most(nucleotides,(including(those(incorporated(into(RNA,(contain( ribose.( – 2’GOH(reduced(to(–H(in(deoxynucleotides( – 3’GOH(participates(in(forming(phosphodiester(linkage( – Deoxynucleotides(are(exclusively(used(for(DNA(synthesis.( 8 Nucleo'de)forma'on) O ║ H N The base is added at the 1 6 N position and phosphates
    [Show full text]
  • Critical Care and Resuscitation
    CASE REPORTS Late-onset ornithine transcarbamylase deficiency: a potentially fatal yet treatable cause of coma David C Crosbie, Hariharan Sugumar, Marion A Simpson, Susan P Walker, Helen M Dewey and Michael C Reade Coma is a common presentation to hospital. In most cases, ABSTRACT routine history or investigations reveal the diagnosis. Rarely, a patientCrit Care remains Resusc comatose ISSN: 1441-2772 for no obvious 7 Septem- reason. Here we Hyperammonaemia due to ornithine transcarbamylase describeber 2009 such 11 3a 222-227case, where thinking beyond the usual (OTC) deficiency is a well-described cause of coma in ©Crit Care Resusc 2009 diagnosticwww.jficm.anzca.edu. possibilities andau/aaccm/journal/publi- extrapolating therapeutic prin- neonates. Rarely, adults with this disorder may also present ciplescations.htm from other areas of medicine prevented rapid pro- with coma. Here we describe the first reported case, to our gressionCase toReports death. knowledge, in a pregnant woman. She was successfully treated with metabolic therapy and, contrary to usual paediatric practice, renal replacement therapy. We review Clinical record the biochemistry of OTC deficiency and other urea cycle A 39-year-old woman who was 12 weeks’ pregnant was disorders, and discuss the physiological rationale and admitted to the neurology ward to investigate a 1-day evidence base for treatment of this condition. We highlight history of confusion and fluctuating level of consciousness. the need to consider hyperammonaemia in the differential She had experienced daily hyperemesis over the previous 3 diagnosis of coma. weeks, but there had been no associated headache, fever Crit Care Resusc 2009; 11: 222–227 or other constitutional symptoms.
    [Show full text]
  • Carbamoyl-Phosphate Synthetases (CPS) in Lactic Acid Bacteria and Other Gram-Positive Bacteria Hervé Nicoloff, Jean-Claude Hubert, Françoise Bringel
    Carbamoyl-phosphate synthetases (CPS) in lactic acid bacteria and other Gram-positive bacteria Hervé Nicoloff, Jean-Claude Hubert, Françoise Bringel To cite this version: Hervé Nicoloff, Jean-Claude Hubert, Françoise Bringel. Carbamoyl-phosphate synthetases (CPS)in lactic acid bacteria and other Gram-positive bacteria. Le Lait, INRA Editions, 2001, 81 (1-2), pp.151- 159. 10.1051/lait:2001119. hal-00895468 HAL Id: hal-00895468 https://hal.archives-ouvertes.fr/hal-00895468 Submitted on 1 Jan 2001 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Lait 81 (2001) 151–159 151 © INRA, EDP Sciences, 2001 Physiology, metabolism Carbamoyl-phosphate synthetases (CPS) in lactic acid bacteria and other Gram-positive bacteria Hervé NICOLOFF, Jean-Claude HUBERT, Françoise BRINGEL* Laboratoire de Microbiologie et de Génétique UPRES A-CNRS 7010, Université Louis-Pasteur Strasbourg-I, 28 rue Goethe, 67083 Strasbourg Cedex, France Abstract — Carbamoyl-phosphate synthetases (CPS) catalyze carbamoyl phosphate (CP) biosynthesis from glutamine, bicarbonate and ATP. CPS are formed of two subunits, a small glutaminase subunit and a large synthetase subunit. CP is a common intermediate of arginine and pyrimidine biosynthe- sis. CPS in prokaryotes are either arginine-regulated (CPS-A), pyrimidine-regulated (CPS-P) or reg- ulated by both components.
    [Show full text]
  • The Structure of Carbamoyl Phosphate Synthetase Determined to 2.1 A
    research papers Acta Crystallographica Section D Biological The structure of carbamoyl phosphate synthetase Crystallography determined to 2.1 AÊ resolution ISSN 0907-4449 James B. Thoden,a Frank M. Carbamoyl phosphate synthetase catalyzes the formation of Received 10 March 1998 Raushel,b Matthew M. Benning,a carbamoyl phosphate from one molecule of bicarbonate, two Accepted 29 April 1998 2+ Ivan Raymenta and Hazel M. molecules of Mg ATP and one molecule of glutamine or a ammonia depending upon the particular form of the enzyme PDB Reference: carbamoyl Holden * phosphate synthetase, 1jdb. under investigation. As isolated from Escherichia coli, the enzyme is an , -heterodimer consisting of a small subunit aInstitute for Enzyme Research, The Graduate that hydrolyzes glutamine and a large subunit that catalyzes School, and Department of Biochemistry, the two required phosphorylation events. Here the three- College of Agricultural and Life Sciences, University of Wisconsin±Madison, 1710 dimensional structure of carbamoyl phosphate synthetase University Avenue, Madison, Wisconsin 53705, from E. coli re®ned to 2.1 AÊ resolution with an R factor of USA, and bDepartment of Chemistry, Texas 17.9% is described. The small subunit is distinctly bilobal with A&M University, College Station, Texas 77843, a catalytic triad (Cys269, His353 and Glu355) situated USA between the two structural domains. As observed in those enzymes belonging to the = -hydrolase family, the active-site Correspondence e-mail: nucleophile, Cys269, is perched at the top of a tight turn. The [email protected] large subunit consists of four structural units: the carboxypho- sphate synthetic component, the oligomerization domain, the carbamoyl phosphate synthetic component and the allosteric domain.
    [Show full text]