The 3 Require the Presence of the Hs4 Enhancer in Ig Synthesis and Class Switching Do

Total Page:16

File Type:pdf, Size:1020Kb

The 3 Require the Presence of the Hs4 Enhancer in Ig Synthesis and Class Switching Do Ig Synthesis and Class Switching Do Not Require the Presence of the hs4 Enhancer in the 3′ IgH Regulatory Region This information is current as Christelle Vincent-Fabert, Véronique Truffinet, Remi of October 1, 2021. Fiancette, Nadine Cogné, Michel Cogné and Yves Denizot J Immunol 2009; 182:6926-6932; ; doi: 10.4049/jimmunol.0900214 http://www.jimmunol.org/content/182/11/6926 Downloaded from References This article cites 25 articles, 11 of which you can access for free at: http://www.jimmunol.org/content/182/11/6926.full#ref-list-1 http://www.jimmunol.org/ Why The JI? Submit online. • Rapid Reviews! 30 days* from submission to initial decision • No Triage! Every submission reviewed by practicing scientists • Fast Publication! 4 weeks from acceptance to publication *average by guest on October 1, 2021 Subscription Information about subscribing to The Journal of Immunology is online at: http://jimmunol.org/subscription Permissions Submit copyright permission requests at: http://www.aai.org/About/Publications/JI/copyright.html Email Alerts Receive free email-alerts when new articles cite this article. Sign up at: http://jimmunol.org/alerts The Journal of Immunology is published twice each month by The American Association of Immunologists, Inc., 1451 Rockville Pike, Suite 650, Rockville, MD 20852 Copyright © 2009 by The American Association of Immunologists, Inc. All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606. The Journal of Immunology Ig Synthesis and Class Switching Do Not Require the Presence of the hs4 Enhancer in the 3؅ IgH Regulatory Region1 Christelle Vincent-Fabert,2 Ve´ronique Truffinet,2 Remi Fiancette, Nadine Cogne´, Michel Cogne´, and Yves Denizot3 Several studies have reported that regulatory elements located 3؅ of the IgH locus (namely hs3a, hs1,2, hs3b, and hs4) might play a role during class switch recombination (CSR) and Ig synthesis. While individual deletion of hs3a or hs1,2 had no effect, pairwise deletion of hs3b (an inverted copy of hs3a) and hs4 markedly affected CSR and Ig expression. Among these two elements, hs4 was tentatively presented with the master role due to its unique status within the 3؅ regulatory region: distal position outside repeated regions, early activation in pre-B cells, strong activity throughout B cell ontogeny. To clarify its role, we generated mice with a clean deletion of the hs4 after replacement with a floxed neoR cassette. Surprisingly, and as for previous deletion of hs3a or hs1,2, deletion of hs4 did not affect either in vivo CSR or the secretion level of any Ig isotype. Downloaded from In vitro CSR and Ig secretion in response to LPS and cytokines was not affected either. The only noticeable effects of the hs4 deletion were a decrease in the number of B splenocytes and a decreased membrane IgM expression. In conclusion, while dispensable for CSR and Ig transcription in plasma cells, hs4 mostly appears to contribute to Ig transcription in resting B lymphocytes. The Journal of Immunology, 2009, 182: 6926–6932. complex interplay of multiple regulatory elements is ments constitute a potent locus control region conferring position- responsible for the tissue-specific and stage-specific reg- independent and copy-dependent expression to transgenes (7). http://www.jimmunol.org/ A ulation of both transcription and rearrangement of the Studies with cell lines have suggested a role of the 3ЈRR on Ig IgH locus. Germline transcription of C␮, initiation of DJ and VDJ transcription. Thus, loss of the 3Ј IgH enhancers occurred con- rearrangement, expression of rearranged ␮ genes, and opening of comitantly with a dramatic decrease of Ig transcription in the the S␮ region to class switch recombination (CSR)4 mainly rely on LP1.2 IgA-secreting cell line (5, 8). Disruption of the 3ЈRR in the ␮ upstream regulatory elements such as VH promoters and the E 9921 cell line (which had an endogenous deletion of the E␮ ele- intronic enhancers (1, 2). In addition to upstream elements, a 3Ј ment) by inserting the neoR gene into hs1,2 abrogated IgH tran- regulatory region (3ЈRR) located downstream the locus has been scription (9). Transgenic mice bearing a bacterial artificial chro- shown to include four lymphoid-specific transcriptional enhancers: mosome that included a rearranged VDJ gene and the 3ЈRR by guest on October 1, 2021 hs3a, hs1,2, hs3b, and hs4 (3). A region of open chromatin con- showed that the 3Ј end of the IgH locus enhanced germline tran- Ј taining numerous CTCF sites is found 3 of hs4 and upstream of scription and switch recombination to the four ␥ genes (10). Fi- Ј the non-B specific gene hole, thus marking the 3 terminus of the nally, studies with IgH minilocus have highlighted the role of the IgH locus (4). The hs4 distal element is active from the pre-B cell hs3b/hs4 pair in sustaining IgH gene transcription in 9921 cells stage and throughout B cell ontogeny (5). A larger region with a (11). To elucidate the function of 3Ј IgH enhancers, mice with global “palindromic” structure encompassing the hs1,2 central en- genomic mutations were generated. Class switching and Ig syn- hancer flanked by inverted repeats including hs3a and hs3b ele- thesis were normal in mice lacking hs3a or hs1,2 (12). In contrast, ments is active at late B cell stages (6). Altogether, the four ele- joint deletion of the last two 3Ј enhancer hs3b and hs4 severely impaired germline transcription and class switching to most iso- types in mice (13). Whether these effects were due to the deletion Centre National de la Recherche Scientifique Unite´Mixte de Recherche 6101, Uni- of hs3b alone, to hs4 alone, or to both regulatory elements re- versite´de Limoges, France mained an open question. Three potent arguments argued for a role Received for publication January 21, 2009. Accepted for publication March 30, 2009. mostly carried by hs4. First, knockout deletion of hs3a (which The costs of publication of this article were defrayed in part by the payment of page shares 98% of sequence similarity with hs3b) had no effect on class charges. This article must therefore be hereby marked advertisement in accordance with 18 U.S.C. Section 1734 solely to indicate this fact. switching and Ig synthesis (12). Second, hs3b is absent in other 1 This work was supported by grants from Ligue Contre le Cancer (Comite´De´par- species than the mouse, so that humans could be considered as temental de la Haute-Vienne et de la Corre`ze), Conseil Re´gional du Limousin, and carrying a natural knockout of hs3b (14, 15). Third, the hs4 en- “Lions Club de la Corre`ze, Zone 33 District 103 Sud”. hancer was associated with active chromatin (demethylated DNA Y.D. and M.C. wrote the paper and performed and designed research. C.V.-F., V.T., and acetylated histone H3 and H4) from pro-B cells to plasma R.F., and N.C. performed research. cells, while hs3b has become associated with activated chromatin 2 C.V.-F. and V.T. contributed equally to this work. markers later in B cell differentiation (B cell and plasma cell 3 Address correspondence and reprint requests to Dr. Yves Denizot, Centre National de la Recherche Scientifique Unite´ Mixte de Recherche 6101, Laboratoire stages) (4, 16). In the present study, we have tested the hypothesis d’Immunologie, 2, rue du Dr Marcland, 87025 Limoges Cedex, France. E-mail that hs4 is of importance for CSR and Ig production. For this address: [email protected] purpose we therefore undertook gene targeting experiments where 4 Abbreviations used in this paper: CSR, class switch recombination; ES, embryonic hs4 was either replaced with a thymidine kinase (Tk)-neoR cassette stem; LCR, locus control region; 3ЈRR, 3Ј regulatory region; wt, wild type. or deleted by the cre/loxP system. Replacement of hs4 by Neo or Copyright © 2009 by The American Association of Immunologists, Inc. 0022-1767/09/$2.00 the clean deletion of hs4 from the 3ЈRR gave the surprising result www.jimmunol.org/cgi/doi/10.4049/jimmunol.0900214 The Journal of Immunology 6927 that Ig synthesis and CSR were not affected as compared with 72 h of growth, cells were incubated for 15 min at 4°C with 7-aminoacti- wild-type (wt) animals. We conclude that the suggested role of hs4 nomycin D and FITC-labeled annexin V Abs (BD Biosciences) and ana- in driving CSR and/or Ig gene transcription can be largely sup- lyzed by flow cytometry. In a separate set of experiments, splenocytes were Ј treated 24 h with various concentration of etoposide before staining with planted in vivo by the activity of the remaining 3 IgH enhancers 7-aminoactinomycin D and annexin V Abs. or other elements within the IgH locus. Proliferation assay Materials and Methods ϫ 5 Vector construction, transfection, and embryonic stem (ES) cell Splenic B cells (2 10 cells/well) were cultured (in sextuplicates) in 96-well plates, either alone or in the presence of 20 ␮g/ml LPS from Sal- screening monella typhimurium,5␮g/ml anti-CD40, or 20 ␮g/ml anti-IgM for 72 h. The studies have been reviewed and approved by Centre National de la The number of viable cells in proliferation was assessed using the CellTiter Recherche Scientifique and the Universite´de Limoges review committee. 96 One Solution cell proliferation assay (Promega) according to the man- The hs4 targeting construct was similar to the one previously used for the ufacturer’s recommendations. joint deletion of hs3b and hs4 (13). The 3Ј arm was the same while the 5Ј arm was slightly longer to include hs3b and to generate an additional Spleen cell cultures for Ig production EcoR1 site facilitating the screening of recombinant clones.
Recommended publications
  • Peroxisomal Proliferator–Activated Receptor- Upregulates
    Peroxisomal Proliferator–Activated Receptor-␥ Upregulates Glucokinase Gene Expression in ␤-Cells Ha-il Kim,1 Ji-Young Cha,1 So-Youn Kim,1 Jae-woo Kim,1 Kyung Jin Roh,2 Je-Kyung Seong,2 Nam Taek Lee,3 Kang-Yell Choi,1 Kyung-Sup Kim,1 and Yong-ho Ahn1 Thiazolidinediones, synthetic ligands of peroxisomal because of severe hyperglycemia (2,3). Adenovirus-medi- proliferator–activated receptor-␥ (PPAR-␥), improve ated expression of GLUT2 and GK in IL cells results in peripheral insulin sensitivity and glucose-stimulated gaining of glucose sensitivity (4). Thus, GLUT2 and GK are insulin secretion in pancreatic ␤-cells. To explore the important in glucose sensing of ␤-cells. However, GLUT2, role of PPAR-␥ in glucose sensing of ␤-cells, we have being a low-affinity, high-capacity glucose transporter, is ␤ ␤ dissected the -cell–specific glucokinase ( GK) pro- believed to play a more permissive role in glucose sensing, moter, which constitutes glucose-sensing apparatus in pancreatic ␤-cells, and identified a peroxisomal prolif- allowing rapid equilibration of glucose across the plasma erator response element (PPRE) in the promoter. The membrane. GK traps glucose in ␤-cells by phosphorylation GK-PPRE is located in the region between ؉47 and (5) and is the flux-controlling enzyme for glycolysis in␤ ؉68 bp. PPAR-␥/retinoid X receptor-␣ heterodimer ␤-cells (4). Thus, it serves as the gatekeeper for metabolic binds to the element and activates the ␤GK promoter. signaling, suggesting that GK rather than GLUT2 is directly The ␤GK promoter lacking or having mutations in PPRE ␥ ␥ responsible for the insulin secretion in response to in- cannot be activated by PPAR- .
    [Show full text]
  • Different Munc18 Proteins Mediate Baseline and Stimulated Airway Mucin Secretion
    Different Munc18 proteins mediate baseline and stimulated airway mucin secretion Ana M. Jaramillo, … , Michael J. Tuvim, Burton F. Dickey JCI Insight. 2019;4(6):e124815. https://doi.org/10.1172/jci.insight.124815. Research Article Cell biology Pulmonology Graphical abstract Find the latest version: https://jci.me/124815/pdf RESEARCH ARTICLE Different Munc18 proteins mediate baseline and stimulated airway mucin secretion Ana M. Jaramillo,1,2 Lucia Piccotti,1 Walter V. Velasco,1 Anna Sofia Huerta Delgado,3 Zoulikha Azzegagh,1 Felicity Chung,4 Usman Nazeer,1 Junaid Farooq,1 Josh Brenner,1 Jan Parker-Thornburg,5 Brenton L. Scott,1 Christopher M. Evans,6 Roberto Adachi,1 Alan R. Burns,7 Silvia M. Kreda,4 Michael J. Tuvim,1 and Burton F. Dickey1 1Department of Pulmonary Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas, USA. 2Institute of Bioscience and Technology, Texas A&M University Health Science Center, Houston, Texas, USA. 3Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Monterrey, Mexico. 4Marsico Lung Institute/Cystic Fibrosis Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA. 5Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, Texas, USA. 6Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado Denver School of Medicine, Aurora, Colorado, USA. 7College of Optometry, University of Houston, Houston, Texas, USA. Airway mucin secretion is necessary for ciliary clearance of inhaled particles and pathogens but can be detrimental in pathologies such as asthma and cystic fibrosis. Exocytosis in mammals requires a Munc18 scaffolding protein, and airway secretory cells express all 3 Munc18 isoforms.
    [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]
  • Signal Transduction Convergence: Phorbol Esters and Insulin Inhibit Phosphoenolpyruvate Carboxykinase Gene Transcription Through
    Proc. Natl. Acad. Sci. USA Vol. 88, pp. 6580-6584, August 1991 Biochemistry Signal transduction convergence: Phorbol esters and insulin inhibit phosphoenolpyruvate carboxykinase gene transcription through the same 10-base-pair sequence RICHARD M. O'BRIEN, MARIA T. BONOVICH, CLAUDE D. FOREST, AND DARYL K. GRANNER* Department of Molecular Physiology and Biophysics, Vanderbilt University Medical School, Nashville, TN 37232-0615 Communicated by Charles R. Park, April 29, 1991 ABSTRACT Pbosphoenolpyruvate carboxykinase describe such an element here and in so doing report an (PEPCK) governs the rate-limiting step in gluconeogenesis. example of signal transduction convergence: the inhibitory Glucocorticoids and cAMP increase PEPCK gene transcription effects of phorbol esters and insulin on the PEPCK gene, and gluconeogenesis, whereas insulin and phorbol esters have which start with the generation of unique signals, are medi- the opposite effect. Insulin and phorbol esters are dominant, ated through a common 10-base-pair (bp) sequence. since they prevent cAMP and glucocorticoid-stinulated tran- scription. Basal promoter elements and hormone response elements for cAMP, glucocorticoids, and insulin have been MATERIALS AND METHODS defined in previous studies. By using stable transfectants containing a variety of different PEPCK-chloramphenicol Plasmid Construction. The construction of a series of acetyltransferase fusion gene constructs, a phorbol ester re- reporter constructs containing 5' deletion mutations of the sponse sequence, located between positions -437 and -402 PEPCK promoter ligated to the chloramphenicol acetyltrans- relative to the transcription start site, was identified. This ferase (CAT) gene has been described (23). Plasmid TKC-VI region coincides with the insulin response sequence that has (provided by T.
    [Show full text]
  • Generate Metabolic Map Poster
    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_001591825Cyc: Bacillus vietnamensis NBRC 101237 Cellular Overview Connections between pathways are omitted for legibility. Anamika Kothari sn-glycerol phosphate phosphate pro phosphate phosphate phosphate thiamine molybdate D-xylose D-ribose glutathione 3-phosphate D-mannitol L-cystine L-djenkolate lanthionine α,β-trehalose phosphate phosphate [+ 3 more] α,α-trehalose predicted predicted ABC ABC FliY ThiT XylF RbsB RS10935 UgpC TreP PutP RS10200 PstB PstB RS10385 RS03335 RS20030 RS19075 transporter transporter of molybdate of phosphate α,β-trehalose 6-phosphate L-cystine D-xylose D-ribose sn-glycerol D-mannitol phosphate phosphate thiamine glutathione α α phosphate phosphate phosphate phosphate L-djenkolate 3-phosphate , -trehalose 6-phosphate pro 1-phosphate lanthionine molybdate phosphate [+ 3 more] Metabolic Regulator Amino Acid Degradation Amine and Polyamine Biosynthesis Macromolecule Modification tRNA-uridine 2-thiolation Degradation ATP biosynthesis a mature peptidoglycan a nascent β an N-terminal-
    [Show full text]
  • Herpes Simplex Virus Thymidine Kinase Gene Therapy in Experimental Rat BT4C Glioma Model
    © 2000 Nature America, Inc. 0929-1903/00/$15.00/ϩ0 www.nature.com/cgt Herpes simplex virus thymidine kinase gene therapy in experimental rat BT4C glioma model: Effect of the percentage of thymidine kinase-positive glioma cells on treatment effect, survival time, and tissue reactions Anu-Maaria Sandmair,1,2 Marita Turunen,1,3 Kristiina Tyynela¨,1,3 Sami Loimas,1 Pauli Vainio,4 Ritva Vanninen,4 Matti Vapalahti,2,5 Rolf Bjerkvig,6 Juhani Ja¨nne,1,5 and Seppo Yla¨-Herttuala1,5,7 1A.I. Virtanen Institute, University of Kuopio, Kuopio, Finland; Departments of 2Neurosurgery, 3Oncology, and 4Clinical Radiology, and 5Gene Therapy Unit, University Hospital of Kuopio, Kuopio, Finland; 6Department of Anatomy and Cell Biology, University of Bergen, Bergen, Norway; and 7Department of Medicine, University Hospital of Kuopio, Kuopio, Finland. Herpes simplex virus thymidine kinase (HSV-tk) gene transfer and ganciclovir (GCV) administration have been suggested for the treatment of malignant gliomas. To understand tissue responses and possible ways to improve the treatment effect, we studied tumor growth, tissue reactions, and survival time after HSV-tk/GCV treatment in a syngeneic BT4C rat glioma model by mixing various ratios of stably transfected HSV-tk-expressing BT4C-tk glioma cells with wild-type BT4C glioma cells (percentage of BT4C-tk cells: 0%, 1%, 10%, 30%, 50%, and 100%), followed by injection into BDIX rat brains (n ϭ 79). With the exception of some animals with end-stage tumors, very little astroglia or microglia reactivity was detected in the wild-type tumors as analyzed by immunocytochemistry using glial fibrillary acid protein (GFAP)-, vimentin-, human histocompatibility leukocyte antigen-DR-, OX-42-, and CD68-specific monoclonal antibodies.
    [Show full text]
  • The Effect of Glucosone on the Proliferation and Energy Metabolism of in Vitro Grown Ehrlich Ascites Tumor Cells Karl A
    The Effect of Glucosone on the Proliferation and Energy Metabolism of in vitro Grown Ehrlich Ascites Tumor Cells Karl A. Reiffen, Monika Löffler, and Friedh. Schneider Physiologisch-Chemisches Institut der Universität Marburg, Lahnberge, D-3550 Marburg Dedicated to Prof. F. Zilliken on the Occasion of His 60th Birthday Z. Naturforsch. 36 c, 255-261 (1981); received November 4/November 17, 1980 Ehrlich Ascites Tumor Cells, Proliferation, Energy Metabolism, Glucosone 1) Proliferation and energy metabolism of in vitro grown Ehrlich ascites tumor (EAT) cells in the presence of glucosone, (D-arabino-3.4.5.6-tetrahydroxy-2-oxo-hexanal) a competitive inhibitor of hexokinase, were studied. 2) Proliferation of the cells was completely inhibited by 2 m M glucosone without severely affecting viability (dye exclusion test). No phase specific arrest of cell growth was observed. 3) Incorporation of [14C]thymidine into an acid insoluble fraction of the cells decreases to 5% of the controls within 8 -1 0 h . Incorporation of [14C]leucine begins to slow down immediately after treatment with glucosone. 4) The inhibitor (2 m M ) reduces the lactate production of the cells by 60%, respiration by about 20%; the ATP/ADP ratio slows down from 4.75 to 3.5. 5) The total inhibition of cell proliferation by 2 m M glucosone cannot be explained exclusively by inhibition of hexokinase activity and impairment of energy metabolism. Because of a lack of specificity, glucosone is not a suitable inhibitor for studies on the relationship between hexo­ kinase activity and cell proliferation of tumor cells. Of all the glycolytic enzymes it may be that Rather additional effects of glucosone on cellular hexokinase is the most important in amplifying the metabolism must be taken into consideration.
    [Show full text]
  • Supplementary Information
    Supplementary information (a) (b) Figure S1. Resistant (a) and sensitive (b) gene scores plotted against subsystems involved in cell regulation. The small circles represent the individual hits and the large circles represent the mean of each subsystem. Each individual score signifies the mean of 12 trials – three biological and four technical. The p-value was calculated as a two-tailed t-test and significance was determined using the Benjamini-Hochberg procedure; false discovery rate was selected to be 0.1. Plots constructed using Pathway Tools, Omics Dashboard. Figure S2. Connectivity map displaying the predicted functional associations between the silver-resistant gene hits; disconnected gene hits not shown. The thicknesses of the lines indicate the degree of confidence prediction for the given interaction, based on fusion, co-occurrence, experimental and co-expression data. Figure produced using STRING (version 10.5) and a medium confidence score (approximate probability) of 0.4. Figure S3. Connectivity map displaying the predicted functional associations between the silver-sensitive gene hits; disconnected gene hits not shown. The thicknesses of the lines indicate the degree of confidence prediction for the given interaction, based on fusion, co-occurrence, experimental and co-expression data. Figure produced using STRING (version 10.5) and a medium confidence score (approximate probability) of 0.4. Figure S4. Metabolic overview of the pathways in Escherichia coli. The pathways involved in silver-resistance are coloured according to respective normalized score. Each individual score represents the mean of 12 trials – three biological and four technical. Amino acid – upward pointing triangle, carbohydrate – square, proteins – diamond, purines – vertical ellipse, cofactor – downward pointing triangle, tRNA – tee, and other – circle.
    [Show full text]
  • The Metabolic Building Blocks of a Minimal Cell Supplementary
    The metabolic building blocks of a minimal cell Mariana Reyes-Prieto, Rosario Gil, Mercè Llabrés, Pere Palmer and Andrés Moya Supplementary material. Table S1. List of enzymes and reactions modified from Gabaldon et. al. (2007). n.i.: non identified. E.C. Name Reaction Gil et. al. 2004 Glass et. al. 2006 number 2.7.1.69 phosphotransferase system glc + pep → g6p + pyr PTS MG041, 069, 429 5.3.1.9 glucose-6-phosphate isomerase g6p ↔ f6p PGI MG111 2.7.1.11 6-phosphofructokinase f6p + atp → fbp + adp PFK MG215 4.1.2.13 fructose-1,6-bisphosphate aldolase fbp ↔ gdp + dhp FBA MG023 5.3.1.1 triose-phosphate isomerase gdp ↔ dhp TPI MG431 glyceraldehyde-3-phosphate gdp + nad + p ↔ bpg + 1.2.1.12 GAP MG301 dehydrogenase nadh 2.7.2.3 phosphoglycerate kinase bpg + adp ↔ 3pg + atp PGK MG300 5.4.2.1 phosphoglycerate mutase 3pg ↔ 2pg GPM MG430 4.2.1.11 enolase 2pg ↔ pep ENO MG407 2.7.1.40 pyruvate kinase pep + adp → pyr + atp PYK MG216 1.1.1.27 lactate dehydrogenase pyr + nadh ↔ lac + nad LDH MG460 1.1.1.94 sn-glycerol-3-phosphate dehydrogenase dhp + nadh → g3p + nad GPS n.i. 2.3.1.15 sn-glycerol-3-phosphate acyltransferase g3p + pal → mag PLSb n.i. 2.3.1.51 1-acyl-sn-glycerol-3-phosphate mag + pal → dag PLSc MG212 acyltransferase 2.7.7.41 phosphatidate cytidyltransferase dag + ctp → cdp-dag + pp CDS MG437 cdp-dag + ser → pser + 2.7.8.8 phosphatidylserine synthase PSS n.i. cmp 4.1.1.65 phosphatidylserine decarboxylase pser → peta PSD n.i.
    [Show full text]
  • Supplementary Informations SI2. Supplementary Table 1
    Supplementary Informations SI2. Supplementary Table 1. M9, soil, and rhizosphere media composition. LB in Compound Name Exchange Reaction LB in soil LBin M9 rhizosphere H2O EX_cpd00001_e0 -15 -15 -10 O2 EX_cpd00007_e0 -15 -15 -10 Phosphate EX_cpd00009_e0 -15 -15 -10 CO2 EX_cpd00011_e0 -15 -15 0 Ammonia EX_cpd00013_e0 -7.5 -7.5 -10 L-glutamate EX_cpd00023_e0 0 -0.0283302 0 D-glucose EX_cpd00027_e0 -0.61972444 -0.04098397 0 Mn2 EX_cpd00030_e0 -15 -15 -10 Glycine EX_cpd00033_e0 -0.0068175 -0.00693094 0 Zn2 EX_cpd00034_e0 -15 -15 -10 L-alanine EX_cpd00035_e0 -0.02780553 -0.00823049 0 Succinate EX_cpd00036_e0 -0.0056245 -0.12240603 0 L-lysine EX_cpd00039_e0 0 -10 0 L-aspartate EX_cpd00041_e0 0 -0.03205557 0 Sulfate EX_cpd00048_e0 -15 -15 -10 L-arginine EX_cpd00051_e0 -0.0068175 -0.00948672 0 L-serine EX_cpd00054_e0 0 -0.01004986 0 Cu2+ EX_cpd00058_e0 -15 -15 -10 Ca2+ EX_cpd00063_e0 -15 -100 -10 L-ornithine EX_cpd00064_e0 -0.0068175 -0.00831712 0 H+ EX_cpd00067_e0 -15 -15 -10 L-tyrosine EX_cpd00069_e0 -0.0068175 -0.00233919 0 Sucrose EX_cpd00076_e0 0 -0.02049199 0 L-cysteine EX_cpd00084_e0 -0.0068175 0 0 Cl- EX_cpd00099_e0 -15 -15 -10 Glycerol EX_cpd00100_e0 0 0 -10 Biotin EX_cpd00104_e0 -15 -15 0 D-ribose EX_cpd00105_e0 -0.01862144 0 0 L-leucine EX_cpd00107_e0 -0.03596182 -0.00303228 0 D-galactose EX_cpd00108_e0 -0.25290619 -0.18317325 0 L-histidine EX_cpd00119_e0 -0.0068175 -0.00506825 0 L-proline EX_cpd00129_e0 -0.01102953 0 0 L-malate EX_cpd00130_e0 -0.03649016 -0.79413596 0 D-mannose EX_cpd00138_e0 -0.2540567 -0.05436649 0 Co2 EX_cpd00149_e0
    [Show full text]
  • Increased Cytotoxicity of Herpes Simplex Virus Thymidine Kinase Expression in Human Induced Pluripotent Stem Cells
    International Journal of Molecular Sciences Article Increased Cytotoxicity of Herpes Simplex Virus Thymidine Kinase Expression in Human Induced Pluripotent Stem Cells Chizuru Iwasawa 1, Ryota Tamura 2, Yuki Sugiura 3, Sadafumi Suzuki 4, Naoko Kuzumaki 1, Minoru Narita 1, Makoto Suematsu 3, Masaya Nakamura 5, Kazunari Yoshida 2, Masahiro Toda 2, Hideyuki Okano 4,* and Hiroyuki Miyoshi 4,* 1 Department of Pharmacology, Hoshi University School of Pharmacy and Pharmaceutical Sciences, 2-4-41, Ebara, Shinagawa-ku, Tokyo 142-8501, Japan; [email protected] (C.I.); [email protected] (N.K.); [email protected] (M.N.) 2 Department of Neurosurgery, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan; [email protected] (R.T.); [email protected] (K.Y.); [email protected] (M.T.) 3 Department of Biochemistry, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan; [email protected] (Y.S.); [email protected] (M.S.) 4 Department of Physiology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan; [email protected] 5 Department of Orthopedic Surgery, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan; [email protected] * Correspondence: [email protected] (H.O.); [email protected] (H.M.); Tel.: +81-3-5363-3747 (H.O. & H.M.); Fax: +81-3-3357-5445 (H.O. & H.M.) Received: 19 November 2018; Accepted: 11 February 2019; Published: 14 February 2019 Abstract: Human induced pluripotent stem cells (iPSCs) hold enormous promise for regenerative medicine. The major safety concern is the tumorigenicity of transplanted cells derived from iPSCs.
    [Show full text]
  • A Review of Isozymes in Cancer1
    Cancer Research VOLUME31 NOVEMBER 1971 NUMBER11 [CANCER RESEARCH 31, 1523-1542, November 1971] A Review of Isozymes in Cancer1 Wayne E. Criss Department of Obstetrics and Gynecology, University of Florida College of Medicine, Gainesville, Florida 32601 TABLE OF CONTENTS postulated role for that particular isozymic system in cellular metabolism. Summary 1523 Introduction 1523 Normal enzyme differentiation 1523 INTRODUCTION Tumor enzyme differentiation 1524 Isozymes 1524 Normal Enzyme Differentiation DNA polymerase 1524 Enzyme differentiation is the process whereby, during the Hexokinase 1525 Fructose 1,6-diphosphatase 1525 development of an organ in an animal, the organ acquires the quantitative and qualitative adult enzyme patterns (122). Key Aldolase 1526 pathway enzymes in several metabolic processes have been Pyruvate kinase 1527 found to undergo enzymatic differentiation. The enzymes Láclatedehydrogenase 1527 Isocitrate dehydrogenase 1527 involved in nitrogen metabolism, and also in urea cycle Malate dehydrogenase 1528 metabolism (180), are tyrosine aminotransferase (123, 151, Glycerol phosphate dehydrogenase 1529 330, 410), tryptophan pyrrolase (261), serine dehydratase Glutaminase 1529 (123, 410), histidine ammonia lyase (11), and aspartate Aspartate aminotransferase 1530 aminotransferase (337, 388). The enzymes involved in nucleic Adenylate kinase 1531 acid metabolism are DNA polymerase (156, 277) and RNase (52). In glycolysis the enzymes are hexokinase-glucokinase Carbamyl phosphate synthetase 1531 Lactose synthetase 1533 (98, 389), galactokinase 30, aldolase (267, 315), pyruvate Discussion 1533 kinase (73, 386), and lactate dehydrogenase (67, 69). In References 1533 mitochondrial oxidation they are NADH oxidase, succinic oxidase, a-glycero-P oxidase, ATPase, cytochrome oxidase, and flavin content (84, 296). In glycogen metabolism the SUMMARY enzymes involved are UDPG pyrophosphorylase and UDPG glucosyltransferase (19).
    [Show full text]