Polyamines in Microalgae: Something Borrowed, Something New
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Polyamines Protect Escherichia Coli Cells from the Toxic Effect of Oxygen
Polyamines protect Escherichia coli cells from the toxic effect of oxygen Manas K. Chattopadhyay, Celia White Tabor, and Herbert Tabor* Laboratory of Biochemistry and Genetics, Building 8, Room 223, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892 Contributed by Herbert Tabor, December 31, 2002 Wild-type Escherichia coli cells grow normally in 95% O2͞5% CO2. aliquots were diluted into VB medium and spread on LB plates In contrast, cells that cannot make polyamines because of muta- for viable cell counts. tions in the biosynthetic pathway are rapidly killed by incubation For the experiments studying the toxicity of hydrogen perox- in 95% O2͞5% CO2. Addition of polyamines prevents the toxic ide, the deprived cells were incubated overnight in limiting Ϫ effect of oxygen, permitting cell survival and optimal growth. glucose with and without the addition of putrescine (10 4 M) and Ϫ5 Oxygen toxicity can also be prevented if the growth medium spermidine (10 M) to an OD600 of 0.15–0.2. Additional glucose contains an amino acid mixture or if the polyamine-deficient cells (0.4%) was then added to each culture, and after a further contain a manganese-superoxide dismutase (Mn-SOD) plasmid. incubation for 2 h, the cells were harvested by centrifugation and Partial protection is afforded by the addition of 0.4 M sucrose or 0.4 washed twice with 100 mM potassium phosphate (pH 7) to M sorbitol to the growth medium. We also report that concentra- remove extracellular amines that might react directly with the tions of H2O2 that are nontoxic to wild-type cells or to mutant cells hydrogen peroxide. -
Table 2. Significant
Table 2. Significant (Q < 0.05 and |d | > 0.5) transcripts from the meta-analysis Gene Chr Mb Gene Name Affy ProbeSet cDNA_IDs d HAP/LAP d HAP/LAP d d IS Average d Ztest P values Q-value Symbol ID (study #5) 1 2 STS B2m 2 122 beta-2 microglobulin 1452428_a_at AI848245 1.75334941 4 3.2 4 3.2316485 1.07398E-09 5.69E-08 Man2b1 8 84.4 mannosidase 2, alpha B1 1416340_a_at H4049B01 3.75722111 3.87309653 2.1 1.6 2.84852656 5.32443E-07 1.58E-05 1110032A03Rik 9 50.9 RIKEN cDNA 1110032A03 gene 1417211_a_at H4035E05 4 1.66015788 4 1.7 2.82772795 2.94266E-05 0.000527 NA 9 48.5 --- 1456111_at 3.43701477 1.85785922 4 2 2.8237185 9.97969E-08 3.48E-06 Scn4b 9 45.3 Sodium channel, type IV, beta 1434008_at AI844796 3.79536664 1.63774235 3.3 2.3 2.75319499 1.48057E-08 6.21E-07 polypeptide Gadd45gip1 8 84.1 RIKEN cDNA 2310040G17 gene 1417619_at 4 3.38875643 1.4 2 2.69163229 8.84279E-06 0.0001904 BC056474 15 12.1 Mus musculus cDNA clone 1424117_at H3030A06 3.95752801 2.42838452 1.9 2.2 2.62132809 1.3344E-08 5.66E-07 MGC:67360 IMAGE:6823629, complete cds NA 4 153 guanine nucleotide binding protein, 1454696_at -3.46081884 -4 -1.3 -1.6 -2.6026947 8.58458E-05 0.0012617 beta 1 Gnb1 4 153 guanine nucleotide binding protein, 1417432_a_at H3094D02 -3.13334396 -4 -1.6 -1.7 -2.5946297 1.04542E-05 0.0002202 beta 1 Gadd45gip1 8 84.1 RAD23a homolog (S. -
The Role of Polyamine Uptake Transporters on Growth and Development of Arabidopsis Thaliana
THE ROLE OF POLYAMINE UPTAKE TRANSPORTERS ON GROWTH AND DEVELOPMENT OF ARABIDOPSIS THALIANA Jigarkumar Patel A Dissertation Submitted to the Graduate College of Bowling Green State University in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY May 2015 Committee: Paul Morris, Advisor Wendy D Manning Graduate Faculty Representative Vipaporn Phuntumart Scott Rogers Ray Larsen © 2015 Jigarkumar Patel All Rights Reserved iii ABSTRACT Paul Morris, Advisor Transgenic manipulation of polyamine levels has provided compelling evidence that polyamines enable plants to respond to environmental cues by activation of stress and developmental pathways. Here we show that the chloroplasts of A. thaliana and soybeans contain both an arginine decarboxylase, and an arginase/agmatinase. These two enzymes combine to synthesize putrescine from arginine. Since the sequences of plant arginases show conservation of key residues and the predicted 3D structures of plant agmatinases overlap the crystal structure of the enzyme from Deinococcus radiodurans, we suggest that these enzymes can synthesize putrescine, whenever they have access to the substrate agmatine. Finally, we show that synthesis of putrescine by ornithine decarboxylase takes place in the ER. Thus A. thaliana has two, and soybeans have three separate pathways for the synthesis of putrescine. This study also describes key changes in plant phenotypes in response to altered transport of polyamines. iv Dedicated to my father, Jayantilal Haribhai Patel v ACKNOWLEDGMENTS I would like to thank my advisor, Dr. Paul F. Morris, for helping me learn and grow during my Ph.D. Dr. Morris has an open door policy, and he was always available to answer my questions and provide helpful suggestions. -
Generated by SRI International Pathway Tools Version 25.0, Authors S
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. Periplasmic (where appropriate) and extracellular reactions and proteins may also be shown. Pathways are colored according to their cellular function. Gcf_000238675-HmpCyc: Bacillus smithii 7_3_47FAA Cellular Overview Connections between pathways are omitted for legibility. -
The Histone Deacetylase HDA15 Interacts with MAC3A and MAC3B to Regulate Intron
bioRxiv preprint doi: https://doi.org/10.1101/2020.11.17.386672; this version posted November 17, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 The histone deacetylase HDA15 interacts with MAC3A and MAC3B to regulate intron 2 retention of ABA-responsive genes 3 4 Yi-Tsung Tu1#, Chia-Yang Chen1#, Yi-Sui Huang1, Ming-Ren Yen2, Jo-Wei Allison Hsieh2,3, 5 Pao-Yang Chen2,3*and Keqiang Wu1* 6 7 1Institute of Plant Biology, National Taiwan University, Taipei 10617, Taiwan 8 2 Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan 9 3 Genome and Systems Biology Degree Program, Academia Sinica and National Taiwan 10 University, Taipei, Taiwan 11 12 # These authors contributed equally to this work. 13 * Corresponding authors: Keqiang Wu ([email protected], +886-2-3366-4546) and Pao-Yang 14 Chen ([email protected], +886-2-2787-1140) 15 16 Short title: HDA15 and MAC3A/MAC3B coregulate intron retention 17 One sentence summary: HDA15 and MAC3A/MAC3B coregulate intron retention and reduce 18 the histone acetylation level of the genomic regions near ABA-responsive retained introns. 19 20 The author responsible for distribution of materials integral to the findings presented in this 21 article in accordance with the policy described in the Instructions for Authors (www.plantcell.org) 22 is: Keqiang Wu ([email protected]) 23 24 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.11.17.386672; this version posted November 17, 2020. -
Supplementary Table S1. Table 1. List of Bacterial Strains Used in This Study Suppl
Supplementary Material Supplementary Tables: Supplementary Table S1. Table 1. List of bacterial strains used in this study Supplementary Table S2. List of plasmids used in this study Supplementary Table 3. List of primers used for mutagenesis of P. intermedia Supplementary Table 4. List of primers used for qRT-PCR analysis in P. intermedia Supplementary Table 5. List of the most highly upregulated genes in P. intermedia OxyR mutant Supplementary Table 6. List of the most highly downregulated genes in P. intermedia OxyR mutant Supplementary Table 7. List of the most highly upregulated genes in P. intermedia grown in iron-deplete conditions Supplementary Table 8. List of the most highly downregulated genes in P. intermedia grown in iron-deplete conditions Supplementary Figures: Supplementary Figure 1. Comparison of the genomic loci encoding OxyR in Prevotella species. Supplementary Figure 2. Distribution of SOD and glutathione peroxidase genes within the genus Prevotella. Supplementary Table S1. Bacterial strains Strain Description Source or reference P. intermedia V3147 Wild type OMA14 isolated from the (1) periodontal pocket of a Japanese patient with periodontitis V3203 OMA14 PIOMA14_I_0073(oxyR)::ermF This study E. coli XL-1 Blue Host strain for cloning Stratagene S17-1 RP-4-2-Tc::Mu aph::Tn7 recA, Smr (2) 1 Supplementary Table S2. Plasmids Plasmid Relevant property Source or reference pUC118 Takara pBSSK pNDR-Dual Clonetech pTCB Apr Tcr, E. coli-Bacteroides shuttle vector (3) plasmid pKD954 Contains the Porpyromonas gulae catalase (4) -
Natural Products That Target the Arginase in Leishmania Parasites Hold Therapeutic Promise
microorganisms Review Natural Products That Target the Arginase in Leishmania Parasites Hold Therapeutic Promise Nicola S. Carter, Brendan D. Stamper , Fawzy Elbarbry , Vince Nguyen, Samuel Lopez, Yumena Kawasaki , Reyhaneh Poormohamadian and Sigrid C. Roberts * School of Pharmacy, Pacific University, Hillsboro, OR 97123, USA; cartern@pacificu.edu (N.S.C.); stamperb@pacificu.edu (B.D.S.); fawzy.elbarbry@pacificu.edu (F.E.); nguy6477@pacificu.edu (V.N.); lope3056@pacificu.edu (S.L.); kawa4755@pacificu.edu (Y.K.); poor1405@pacificu.edu (R.P.) * Correspondence: sroberts@pacificu.edu; Tel.: +1-503-352-7289 Abstract: Parasites of the genus Leishmania cause a variety of devastating and often fatal diseases in humans worldwide. Because a vaccine is not available and the currently small number of existing drugs are less than ideal due to lack of specificity and emerging drug resistance, the need for new therapeutic strategies is urgent. Natural products and their derivatives are being used and explored as therapeutics and interest in developing such products as antileishmanials is high. The enzyme arginase, the first enzyme of the polyamine biosynthetic pathway in Leishmania, has emerged as a potential therapeutic target. The flavonols quercetin and fisetin, green tea flavanols such as catechin (C), epicatechin (EC), epicatechin gallate (ECG), and epigallocatechin-3-gallate (EGCG), and cinnamic acid derivates such as caffeic acid inhibit the leishmanial enzyme and modulate the host’s immune response toward parasite defense while showing little toxicity to the host. Quercetin, EGCG, gallic acid, caffeic acid, and rosmarinic acid have proven to be effective against Leishmania Citation: Carter, N.S.; Stamper, B.D.; in rodent infectivity studies. -
Polyamine and Ethylene Biosynthesis in Relation to Somatic Embryogenesis in Carrot (Daucus Carota L.) Cell Cultures
Polyamines and Ethylene: Biochemistry, Physiology, and Interactions, HE Flores, RN Arteca, JC Shannon, eds, Copyright 1990, American Society of Plant Physiologists Polyamine and Ethylene Biosynthesis in Relation to Somatic Embryogenesis in Carrot (Daucus carota L.) Cell Cultures Subhash C. Minocha, Cheryl A. Roble, Akhtar J. Khan, Nancy S. Papa, Andrew I. Samuelsen, and Rakesh Minocha Department of Plant Biology, University of New Hampshire, Durham, New Hampshire 03824 (S.C.M., C.A.R., A.J.K., N.S.P., A.I.S.); and USDA Forest Service, Northeast Forest Experiment Station, Durham, New Hampshire 03824 (R.M.) INTRODUCTION Carrot cell cultures provide a model experimental system for the analysis of biochemical and molecular events associated with morphogenesis in plants (3, 4, 5, 14). Among the biochemical changes accompanying somatic embryogenesis in this tissue is an increased biosynthesis ofpolyamines (1, 2, 7, 10, 11, 13). A variety of inhibitors of polyamine biosynthetic enzymes have been used to analyze the role of polyamines in somatic embryogenesis. A summary of our work on the effects of DFMO, DFMA, MGBG and CHAP on somatic embryogenesis, cellular polyamine levels, and activities of ADC, ODC, AdoMet decarboxylase, and AdoMet-synthetase in carrot cell cultures is reported here. Details of materials and methods and results are published elsewhere (6, 8, 9, 12, 13). The results obtained so far support our working hypothesis (7,13) that (a) ethylene is a major suppressor of embryogenesis, and its production is promoted by auxin; and (b) promotion of polyamine biosynthesis through increased utilization of S-adenosylmethionine may adversely affect ACC and ethylene syntheses, which could, in turn, promote somatic embryogenesis. -
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 -
Transcriptomic and Proteomic Profiling Provides Insight Into
BASIC RESEARCH www.jasn.org Transcriptomic and Proteomic Profiling Provides Insight into Mesangial Cell Function in IgA Nephropathy † † ‡ Peidi Liu,* Emelie Lassén,* Viji Nair, Celine C. Berthier, Miyuki Suguro, Carina Sihlbom,§ † | † Matthias Kretzler, Christer Betsholtz, ¶ Börje Haraldsson,* Wenjun Ju, Kerstin Ebefors,* and Jenny Nyström* *Department of Physiology, Institute of Neuroscience and Physiology, §Proteomics Core Facility at University of Gothenburg, University of Gothenburg, Gothenburg, Sweden; †Division of Nephrology, Department of Internal Medicine and Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan; ‡Division of Molecular Medicine, Aichi Cancer Center Research Institute, Nagoya, Japan; |Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden; and ¶Integrated Cardio Metabolic Centre, Karolinska Institutet Novum, Huddinge, Sweden ABSTRACT IgA nephropathy (IgAN), the most common GN worldwide, is characterized by circulating galactose-deficient IgA (gd-IgA) that forms immune complexes. The immune complexes are deposited in the glomerular mesangium, leading to inflammation and loss of renal function, but the complete pathophysiology of the disease is not understood. Using an integrated global transcriptomic and proteomic profiling approach, we investigated the role of the mesangium in the onset and progression of IgAN. Global gene expression was investigated by microarray analysis of the glomerular compartment of renal biopsy specimens from patients with IgAN (n=19) and controls (n=22). Using curated glomerular cell type–specific genes from the published literature, we found differential expression of a much higher percentage of mesangial cell–positive standard genes than podocyte-positive standard genes in IgAN. Principal coordinate analysis of expression data revealed clear separation of patient and control samples on the basis of mesangial but not podocyte cell–positive standard genes. -
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Food & Function Accepted Manuscript This is an Accepted Manuscript, which has been through the Royal Society of Chemistry peer review process and has been accepted for publication. Accepted Manuscripts are published online shortly after acceptance, before technical editing, formatting and proof reading. Using this free service, authors can make their results available to the community, in citable form, before we publish the edited article. We will replace this Accepted Manuscript with the edited and formatted Advance Article as soon as it is available. You can find more information about Accepted Manuscripts in the Information for Authors. Please note that technical editing may introduce minor changes to the text and/or graphics, which may alter content. The journal’s standard Terms & Conditions and the Ethical guidelines still apply. In no event shall the Royal Society of Chemistry be held responsible for any errors or omissions in this Accepted Manuscript or any consequences arising from the use of any information it contains. www.rsc.org/foodfunction Page 1 of 16 PleaseFood do not & Functionadjust margins Food&Function REVIEW ARTICLE Interactions between acrylamide, microorganisms, and food components – a review. Received 00th January 20xx, a† a a a a Accepted 00th January 20xx A. Duda-Chodak , Ł. Wajda , T. Tarko , P. Sroka , and P. Satora DOI: 10.1039/x0xx00000x Acrylamide (AA) and its metabolites have been recognised as potential carcinogens, but also they can cause other negative symptoms in human or animal organisms so this chemical compounds still attract a lot of attention. Those substances are www.rsc.org/ usually formed during heating asparagine in the presence of compounds that have α-hydroxycarbonyl groups, α,β,γ,δ- diunsaturated carbonyl groups or α-dicarbonyl groups. -
Supplementary Table 1. the List of 1,675 All Stages of AD-Related Upregulated Genes
Supplementary Table 1. The list of 1,675 all stages of AD-related upregulated genes Gene ID Gene symbol Gene name 51146 A4GNT ALPHA-1,4-N-ACETYLGLUCOSAMINYLTRANSFERASE 9625 AATK APOPTOSIS-ASSOCIATED TYROSINE KINASE 19 ABCA1 ATP-BINDING CASSETTE, SUB-FAMILY A (ABC1), MEMBER 1 20 ABCA2 ATP-BINDING CASSETTE, SUB-FAMILY A (ABC1), MEMBER 2 10058 ABCB6 ATP-BINDING CASSETTE, SUB-FAMILY B (MDR/TAP), MEMBER 6 89845 ABCC10 ATP-BINDING CASSETTE, SUB-FAMILY C (CFTR/MRP), MEMBER 10 5826 ABCD4 ATP-BINDING CASSETTE, SUB-FAMILY D (ALD), MEMBER 4 25 ABL1 V-ABL ABELSON MURINE LEUKEMIA VIRAL ONCOGENE HOMOLOG 1 3983 ABLIM1 ACTIN BINDING LIM PROTEIN 1 30 ACAA1 ACETYL-COENZYME A ACYLTRANSFERASE 1 (PEROXISOMAL 3-OXOACYL-COENZYME A THIOLASE) 35 ACADS ACYL-COENZYME A DEHYDROGENASE, C-2 TO C-3 SHORT CHAIN 8310 ACOX3 ACYL-COENZYME A OXIDASE 3, PRISTANOYL 56 ACRV1 ACROSOMAL VESICLE PROTEIN 1 2180 ACSL1 ACYL-COA SYNTHETASE LONG-CHAIN FAMILY MEMBER 1 86 ACTL6A ACTIN-LIKE 6A 93973 ACTR8 ACTIN-RELATED PROTEIN 8 91 ACVR1B ACTIVIN A RECEPTOR, TYPE IB 8747 ADAM21 ADAM METALLOPEPTIDASE DOMAIN 21 27299 ADAMDEC1 ADAM-LIKE, DECYSIN 1 56999 ADAMTS9 ADAM METALLOPEPTIDASE WITH THROMBOSPONDIN TYPE 1 MOTIF, 9 105 ADARB2 ADENOSINE DEAMINASE, RNA-SPECIFIC, B2 (RED2 HOMOLOG RAT) 109 ADCY3 ADENYLATE CYCLASE 3 113 ADCY7 ADENYLATE CYCLASE 7 120 ADD3 ADDUCIN 3 (GAMMA) 125 ADH1C ALCOHOL DEHYDROGENASE 1A (CLASS I), ALPHA POLYPEPTIDE 9370 ADIPOQ ADIPONECTIN, C1Q AND COLLAGEN DOMAIN CONTAINING 165 AEBP1 AE BINDING PROTEIN 1 4299 AFF1 AF4/FMR2 FAMILY, MEMBER 1 173 AFM AFAMIN 79814 AGMAT AGMATINE