DOCSLIB.ORG

SUPLEMENTARY MATERIAL 1) Comparative Analysis of The

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
SUPLEMENTARY MATERIAL 1) Comparative Analysis of The 1 SUPLEMENTARY MATERIAL 2 1) Comparative analysis of the different differential expression methods applied to the 3 transcriptome of Vanilla planifolia Jacks. 4 5 6 7 8 9 10 11 12 13 14 2dpi 10dpi 15 16 Supplemental Figure S1. Venn diagram showing the comparison of the differentially 17 expressed unigenes obtained with the methods DESeq2, EdgeR, NOISeq, and DESeq. At the 18 center of the diagram we observed that the EdgeR method comprises the great majority of 19 genes determined by the other methods. The right panel corresponds to 2 dpi, while the left 20 panel corresponds to 10 dpi. 21 22 23 24 25 26 2) Global expression profiles in response to infection caused by Fusarium 27 oxysporum f. sp. vanillae in vanilla. 28 . 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 2dpi 10dpi 51 Supplemental Figure S2. Heat map that contrasts the global vanilla response to 52 Fusarium oxysporum f. sp. vanillae. On the right we observe the early response 53 (2dpi); while in the left panel it presents the response to 10dpi. All differentially 54 expressed unigenes are included. 55 56 3) Expression profiles related to biotic stress, in the late response (10dpi) of 57 vanilla to Fusarium oxysporum f. sp. vanillae 58 59 60 61 62 63 64 65 66 67 68 69 70 71 Supplemental Figure S3. Heat map indicating the expression profiles of the annotated DEG 72 unigenes, corresponding to 10dpi. The numbers in the figure correspond to different 73 categories of gene ontology, as described below: 25 C1-metabolism, 11 lipid metabolism, 3 74 minor CHO metabolism, 13 amino acid metabolism, 16 secondary metabolism, 26 misc, 17 75 hormone metabolism, 30 signalling, 31 cell, 23 nucleotide metabolism, 27 RNA, 28 DNA, 76 33 development, 24 Biodegradation of Xenobiotics, 18 Co-factor and vitamine metabolism, 77 35 not assigned, 34 transport, 29 protein, 20 stress, 2 major CHO metabolism, 10 cell wall. 78 79 80 81 4) Expression profiles related to biotic stress, in the late response (10dpi) of 82 vanilla to Fusarium. 83 84 85 86 87 88 89 90 91 92 93 94 95 96 Supplemental Figure S4. In the present figure, generated with the Mapman software, the 97 expression profiles of the annotated unigenes related to biotic stress in the plants (plant- 98 pathogen interaction), in the late response, to the 10dpi, of vanilla before Fusarium. 99 100 101 102 103 104 105 5) STRING network of genes differentially expressed at 10 dpi in the vanilla 106 response to Fusarium. 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 Supplemental Figure S5. Protein-protein interactions were plotted in STRING by entering 125 the TAIR codes of all genes differentially expressed in the vanilla transcriptome in response 126 to Fusarium at 10 dpi. The colored bubbles correspond to different proteins present in 127 Arabidopsis. The thickness of the edge corresponds positively to the confidence of the 128 interactio 129 130 1) Main categories of gene ontology corresponding to the transcripts of the early 131 response (2 dpi) of vanilla before Fusarium. GO term Ontology Description Number Reference p-value FDR GO:0006412 P translation 74 1445 2.90E-41 2.10E-38 GO:0034645 P Celular macromolecule biosynthetic process 93 3661 6.50E-29 1.90E-26 GO:0009058 P biosynthetic process 110 5118 7.90E-29 1.90E-26 GO:0009059 P macromolecule biosynthetic process 93 3685 1.00E-28 1.90E-26 GO:0044249 P cellular biosynthetic process 107 4925 2.80E-28 4.00E-26 GO:0019538 P protein metabolic process 94 4009 1.10E-26 1.30E-24 GO:0010467 P gene expression 90 3962 1.80E-24 1.90E-22 GO:0044267 P cellular protein metabolic process 84 3487 2.70E-24 2.40E-22 GO:0044238 P primary metabolic process 140 8995 4.00E-24 3.20E-22 GO:0043170 P macromolecule metabolic process 117 7127 6.60E-21 4.70E-19 GO:0008152 P metabolic process 147 10614 1.40E-20 9.10E-19 GO:0044260 P cellular macromolecule metabolic process 107 6447 4.40E-19 2.60E-17 GO:0044237 P cellular metabolic process 124 8722 3.40E-17 1.90E-15 GO:0009987 P cellular process 147 11684 1.60E-16 8.30E-15 GO:0042254 P ribosome biogenesis 21 241 2.70E-16 1.30E-14 GO:0022613 P ribonucleoprotein complex biogenesis 21 253 6.60E-16 3.00E-14 GO:0044085 P cellular component biogenesis 23 571 4.40E-11 1.80E-09 GO:0003735 F structural constituent of ribosome 63 494 4.20E-57 1.40E-54 GO:0005198 F structural molecule activity 63 659 5.20E-50 8.30E-48 GO:0008135 F translation factor activity, nucleic acid 11 181 1.20E-07 1.30E-05 binding GO:0003746 F translation elongation factor activity 6 38 6.10E-07 4.90E-05 GO:0022626 C cytosolic ribosome 62 336 4.60E-65 1.00E-62 GO:0044445 C cytosolic part 58 360 1.00E-57 1.10E-55 GO:0033279 C ribosomal subunit 58 389 5.50E-56 4.10E-54 GO:0005840 C ribosome 63 524 1.20E-55 6.50E-54 GO:0030529 C ribonucleoprotein complex 63 703 2.00E-48 8.80E-47 GO:0043232 C intracellular non-membrane-bounded 69 1040 3.70E-45 1.20E-43 organelle GO:0043228 C non-membrane-bounded organelle 69 1040 3.70E-45 1.20E-43 GO:0005829 C cytosol 64 912 3.90E-43 1.10E-41 GO:0022625 C cytosolic large ribosomal subunit 36 162 3.20E-40 7.70E-39 GO:0015934 C large ribosomal subunit 36 225 1.10E-35 2.40E-34 GO:0044422 C organelle part 80 2562 3.30E-30 6.00E-29 GO:0044446 C intracellular organelle part 80 2561 3.20E-30 6.00E-29 GO:0032991 C macromolecular complex 70 2180 7.00E-27 1.20E-25 GO:0022627 C cytosolic small ribosomal subunit 22 130 1.20E-22 1.80E-21 GO:0015935 C small ribosomal subunit 22 164 1.10E-20 1.60E-19 GO:0044444 C cytoplasmic part 106 6289 2.30E-19 3.20E-18 GO:0005737 C cytoplasm 109 6822 2.80E-18 3.70E-17 GO:0005730 C nucleolus 20 209 2.70E-16 3.20E-15 GO:0043229 C intracellular organelle 112 8149 4.40E-14 4.90E-13 GO:0005622 C intracellular 125 9671 4.40E-14 4.90E-13 GO:0043226 C organelle 112 8155 4.70E-14 4.90E-13 GO:0031981 C nuclear lumen 22 374 1.00E-13 1.00E-12 GO:0044424 C intracellular part 120 9302 2.70E-13 2.60E-12 GO:0043233 C organelle lumen 24 539 2.20E-12 1.90E-11 GO:0070013 C intracellular organelle lumen 24 539 2.20E-12 1.90E-11 GO:0044428 C nuclear part 24 543 2.50E-12 2.10E-11 GO:0031974 C membrane-enclosed lumen 24 546 2.80E-12 2.30E-11 GO:0044464 C cell part 152 15217 1.80E-08 1.30E-07 GO:0005623 C cell 152 15217 1.80E-08 1.30E-07 GO:0016020 C membrane 56 4068 7.70E-07 5.60E-06 132 Supplemental Table 1. List of the main functional categories, determined with the 133 AgriGO 2.0 software, to which the annotated transcripts belong, which show 134 differential expression at 2 dpi, in the vanilla transcriptome in response to Fusarium 2) Top 100 list of transcripts expressed (up-regulated) at 2 dpi in the vanilla transcriptome, in response to Fusarium. Name logFc TRINITY_DN89410_c0_g1_i1|CDS1,AT1G64550.1,"AT1G64550.1 | ATGCN3, GCN3 | general control non- 12.7703632 repressible 3 TRINITY_DN104321_c0_g1_i1|CDS1 AT5G36950.1 AT5G36950.1|DegP10|DegPprotease10 11.1087838 TRINITY_DN83426_c0_g1_i1|CDS1,AT1G18610.1,AT1G18610.1 | Galactose oxidase/kelch repeat superfamily 10.4627113 protein TRINITY_DN54807_c0_g2_i1|CDS1,AT5G60390.3,AT5G60390.3 | GTP binding Elongation factor Tu family 10.1980704 protein TRINITY_DN6978_c0_g1_i1|CDS1,AT1G69100.1,AT1G69100.1 | Eukaryotic aspartyl protease family protein 10.1743963 TRINITY_DN63794_c0_g1_i3|CDS1, AT3G22590.1,"AT3G22590.1 | PHP, CDC73 | PLANT HOMOLOGOUS 10.014206 TO PARAFIBROMIN TRINITY_DN75904_c0_g1_i1|CDS1,AT4G00680.1,AT4G00680.1 | ADF8 | actin depolymerizing factor 8 9.88375811 TRINITY_DN91577_c0_g1_i1|CDS1,AT5G66720.1,AT5G66720.1 | Protein phosphatase 2C family protein 9.82955438 TRINITY_DN29703_c0_g1_i2|CDS1 AT4G00900.1 AT4G00900.1|ECA2,ATECA2|ER-typeCa2+-ATPase2 9.64577056 TRINITY_DN66086_c0_g1_i2|CDS1,AT1G10760.1,"AT1G10760.1 | SEX1, SOP1, SOP, GWD1, GWD | 9.57132483 Pyruvate phosphate dikinase, PEP/pyruvate binding domain TRINITY_DN65143_c0_g1_i1|CDS1,AT4G01210.1,AT4G01210.1 | glycosyl transferase family 1 protein 9.34292421 TRINITY_DN90514_c0_g1_i1|CDS1,AT3G02260.1,"AT3G02260.1 | BIG, DOC1, TIR3, UMB1, ASA1, LPR1, 9.30763592 CRM1 | auxin transport protein (BIG) TRINITY_DN65916_c0_g1_i2|CDS1,AT1G10095.1,AT1G10095.1 | Protein prenylyltransferase superfamily 9.28687646 protein TRINITY_DN18150_c0_g1_i1|CDS1 AT3G15720.1 AT3G15720.1|Pectinlyase-likesuperfamilyprotein 9.21071873 TRINITY_DN45207_c1_g1_i1|CDS1 AT5G58420.1 AT5G58420.1|RibosomalproteinS4(RPS4A)familyprotein 9.13507978 TRINITY_DN74463_c0_g1_i1|CDS1,AT4G16370.1,"AT4G16370.1 | ATOPT3, OPT3 | oligopeptide transporter 9.11594149 TRINITY_DN10093_c0_g2_i1|CDS1 AT1G06080.1 AT1G06080.1|ADS1|delta9desaturase1 9.10695891 TRINITY_DN89649_c0_g1_i1|CDS1,AT4G35840.1,AT4G35840.1 | RING/U-box superfamily protein 9.07751021 TRINITY_DN97412_c0_g1_i1|CDS1,AT1G18610.1,AT1G18610.1 | Galactose oxidase/kelch repeat superfamily 9.02973479 protein TRINITY_DN64271_c0_g1_i1|CDS1,AT2G24820.1,AT2G24820.1 | TIC55-II | translocon at the inner envelope 9.0048794 membrane of chloroplasts 55-II TRINITY_DN89945_c0_g1_i1|CDS1,AT3G04400.1,AT3G04400.1 | emb2171 | Ribosomal protein L14p/L23e 8.93054813 family protein TRINITY_DN41912_c0_g2_i1|CDS1 AT1G13950.1 AT1G13950.1|EIF-5A,ELF5A-1,ATELF5A- 8.91277437 1,EIF5A|eukaryoticelongationfactor5A-1 TRINITY_DN97075_c0_g1_i1|CDS1,AT5G02960.1,AT5G02960.1 | Ribosomal protein S12/S23 family protein 8.88831654 TRINITY_DN47565_c0_g2_i1|CDS1 AT3G60245.1 AT3G60245.1|Zinc-bindingribosomalproteinfamilyprotein 8.83080173 TRINITY_DN69294_c0_g1_i1|CDS1,AT5G15520.1,AT5G15520.1 | Ribosomal protein S19e family protein 8.74353089 TRINITY_DN66456_c0_g1_i5|CDS1,AT2G34780.1,"AT2G34780.1 | EMB1611, MEE22 | maternal effect 8.71800884 embryo
Load more

Recommended publications
  • Intrinsically Disordered Proteins As Crucial Constituents of Cellular Aqueous Two Phase Systems and Coacervates ⇑ Vladimir N
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector FEBS Letters 589 (2015) 15–22 journal homepage: www.FEBSLetters.org Hypothesis Intrinsically disordered proteins as crucial constituents of cellular aqueous two phase systems and coacervates ⇑ Vladimir N. Uversky a,b,c,d, , Irina M. Kuznetsova d,e, Konstantin K. Turoverov d,e, Boris Zaslavsky f a Department of Molecular Medicine and USF Health Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA b Institute for Biological Instrumentation, Russian Academy of Sciences, Pushchino, Moscow Region, Russian Federation c Biology Department, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia d Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russian Federation e St. Petersburg State Polytechnical University, St. Petersburg, Russian Federation f AnalizaDx Inc., 3615 Superior Ave., Suite 4407B, Cleveland, OH 44114, USA article info abstract Article history: Here, we hypothesize that intrinsically disordered proteins (IDPs) serve as important drivers of the Received 17 August 2014 intracellular liquid–liquid phase separations that generate various membrane-less organelles. This Revised 10 October 2014 hypothesis is supported by the overwhelming abundance of IDPs in these organelles. Assembly and Accepted 19 November 2014 disassembly of these organelles are controlled by changes in the concentrations of IDPs, their post- Available online 29 November 2014 translational modifications, binding of specific partners, and changes in the pH and/or temperature Edited by A. Valencia of the solution.
    [Show full text]
  • Dissertation Inês Silva ITQB.Pdf
    The Role of Small RNAs and Ribonucleases in the Control of Gene Expression in Salmonella Typhimurium Inês de Jesus de Almeida e Silva Insert here an image with rounded corners Dissertation presented to obtain the Ph.D degree in Biology Instituto de Tecnologia Química e Biológica | Universidade Nova de Lisboa Oeiras, December, 2012 The Role of Small RNAs and Ribonucleases in the Control of Gene Expression in Salmonella Typhimurium Inês de Jesus de Almeida e Silva Dissertation presented to obtain the Ph.D degree in Biology Instituto de Tecnologia Química e Biológica Universidade Nova de Lisboa Oeiras, December, 2012 Financial Support from Fundação para a Ciência e Tecnologia (FCT) – Ph.D: grant - SFRH / BD / 43211 / 2008. Work performed at: Control of Gene Expression Laboratory Instituto de Tecnologia Química e Biológica Av. da República (EAN) 2781-901 Oeiras – Portugal Tel: +351-21-4469548 Fax: +351-21-4469549 Supervisor : Professora Doutora Cecília Maria Pais de Faria de Andrade Arraiano – Investigadora Coordenadora, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa. (Head of the Laboratory of Control of Gene Expression, where the work of this Dissertation was performed) Co-supervisor : Doutora Sandra Cristina de Oliveira Viegas – Investigadora Pós-Doutorada, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa. (Post-doc Fellow in the Laboratory of Control of Gene Expression, where the work of this Dissertation was performed) President of the Jury : Doutora Claudina Amélia Marques Rodrigues Pousada – Professora Catedrática Convidada do Instituto de Tecnologia Química e Biológica da Universidade Nova de Lisboa, por delegação; iii Examiners: Professor Doutor Iñigo Lasa Uzcudun – Head of Microbial Biofilm Research Group, Instituto de Agrobiotecnología, Pamplona (Principal Examiner).
    [Show full text]
  • 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_005222025Cyc: Escherichia coli 121 Cellular Overview Connections between pathways are omitted for legibility. pro a dicarboxylate a dicarboxylate an amino putrescine putrescine thiosulfate a hexose 6- glycine betaine glycine succinate γ-butyrobetaine L-ascorbate acid a dipeptide a dipeptide a dipeptide poly-β-1,6- 1-(β-D O-acetyl-L-serine O-acetyl-L-serine spermidine spermidine D-mannitol galactitol sulfate phosphate phosphate phosphate betaine Fe 3+ an amino an amino D-cellobiose an aromatic an aromatic a dipeptide 6 phosphate phosphate N-acetyl-D- thiamine cys cys spermidine spermidine protoheme 2+ citrate N -(D-fructosyl)-L-lysine L-proline betaine glutamate L-proline betaine L-carnitine acid an amino acid an amino an amino an amino an amino a tripeptide a tripeptide a tripeptide amino acid amino acid ribofuranosyl) (R)- putrescine Fe N-acetyl-D- molybdate phosphate a hydroxamate 3+ 3+ arbutin shikimate enterobactin 2-oxoglutarate N 6 -(D-psicosyl)-L-lysine D-sorbitol D-glucosamine D-mannitol galactitol N-acetylneuraminate N-acetylneuraminate sulfate sulfate sulfate glycine betaine
    [Show full text]
  • Ribonuclease E Organizes the Protein Interactions in the Escherichia Coli RNA Degradosome
    Downloaded from genesdev.cshlp.org on September 26, 2021 - Published by Cold Spring Harbor Laboratory Press Ribonuclease E organizes the protein interactions in the Escherichia coli RNA degradosome Nathalie F. Vanzo,1 Yeun Shan Li,2 Be´atrice Py,2,3 Erwin Blum,2 Christopher F. Higgins,2,4 Lelia C. Raynal,1 Henry M. Krisch,1 and Agamemnon J. Carpousis1,5 1Laboratoire de Microbiologie et Ge´ne´tique Mole´culaire, UPR 9007, Centre National de la Recherche Scientifique (CNRS), 31062 Toulouse Cedex, France; 2Nuffield Department of Clinical Biochemistry and Imperial Cancer Research Fund Laboratories, Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK The Escherichia coli RNA degradosome is the prototype of a recently discovered family of multiprotein machines involved in the processing and degradation of RNA. The interactions between the various protein components of the RNA degradosome were investigated by Far Western blotting, the yeast two-hybrid assay, and coimmunopurification experiments. Our results demonstrate that the carboxy-terminal half (CTH) of ribonuclease E (RNase E) contains the binding sites for the three other major degradosomal components, the DEAD-box RNA helicase RhlB, enolase, and polynucleotide phosphorylase (PNPase). The CTH of RNase E acts as the scaffold of the complex upon which the other degradosomal components are assembled. Regions for oligomerization were detected in the amino-terminal and central regions of RNase E. Furthermore, polypeptides derived from the highly charged region of RNase E, containing the RhlB binding site, stimulate RhlB activity at least 15-fold, saturating at one polypeptide per RhlB molecule. A model for the regulation of the RhlB RNA helicase activity is presented.
    [Show full text]
  • Rnase E Activity Is Conferred by a Single Polypeptide
    Proc. Natl. Acad. Sci. USA Vol. 90, pp. 9006-9010, October 1993 Biochemustry RNase E activity is conferred by a single polypeptide: Overexpression, purification, and properties of the ams/rne/hmpl gene product (endoribonuclease/RNA processing) R. S. CORMACK, J. L. GENEREAUX, AND G. A. MACKIE* Department of Biochemistry, University of Western Ontario, London, Ontario, Canada N6A 5C1 Communicated by Myron K. Brakke, June 29, 1993 (receivedfor review May 10, 1993) ABSTRACT Ribonuclease E, an enzyme that processes encoding a high molecular mass protein hypothesized to be pre-SS rRNA from Its precursor, is now believed to be the involved in nucleoid partitioning or cell wall invagination major endoribonuclease participating in mRNA turnover in during division (16). The revised DNA sequence, coterminal Escherichia coli. The product of the ams/rne/hmpl gene, with the 5' end of the two previous sequences, encodes a which is required for RNase E activity, was overexpressed, protein of 1025 amino acid residues whose predicted relative purified to near homogeneity by electroelution from an molecular mass would be 114,000. This polypeptide displays SDS/polyacrylamide gel, and renatured. The purified poly- anomalous electrophoretic mobility in SDS/polyacrylamide peptide possesses nucleolytic activity in vitro with a specificity gels, however, and migrates with an apparent size of 180 kDa identical to that observed for crude RNase E preparations. In (16). It has not been proven that the polypeptide encoded by addition, both UV crosslinking and RNA-protein blotting the ams/rne/hmpl gene is, in fact, a ribonuclease or is unambiguously showed that the Ams/Rne/Hmpl polypeptide intimately associated with the cleavage ofRNA either in vitro has a high affnity for RNA.
    [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]
  • Supplementary Information
    Electronic Supplementary Material (ESI) for ChemComm. This journal is © The Royal Society of Chemistry 2020 Supplementary Information Electrical tension-triggered conversion of anaerobic to aerobic respiration of Shewanella putrefaciens CN32 while promoting biofilm growth in microbial fuel cells Xiu He a, Xiaoshuai Wu c,Yan Qiao a*,Tianbao Hu a, Deng Wang a, Xiao Han a and Changt Ming Li a ,b ,c ,d* a Institute for Clean Energy & Advanced Materials, Faculty of Materials & Energy, Southwest University, No. 2 T iansheng Road, Chongqing 400715, P. R. China. b Chongqing Engineering Research Center for Rapid Diagnosis of Dread Disease, Southwest University, Chongqin g 400715, P. R. China. c Institute of Materials Science and Devices, Suzhou University of Science and Technology, Suzhou 215011, P. R. China. d Institute of Advanced Crossfield Science, Qingdao University, Qingdao 266071, P. R. China. * Corresponding author. E-mail: yanqiao@ swu.edu.cn; [email protected] Experimental section: Bacteria culture A single colony of S. putrefaciens CN32 (ATCC, BBA-1097) was cultured aerobically in 100 ml LB at 30 °C overnight1 and the cells were harvested and inoculated into fresh LB. After grown at 30 °C for 6 hours, the cells were by centrifuging at 4 °C (6000 rpm, 5 min) for MFC half-cell operation2. Before every test, nitrogen was purged into the suspension for 30 min to remove oxygen from the cell. MFC half-cell operation For the anodic half-cell analysis, a piece of 1 cm∗1cm a NiO nanowire decelerated carbon cloth was used as working electrode, saturated calomel electrode (SCE) was used as the reference electrode and titanium plate as the counter electrode3.
    [Show full text]
  • Specificity of Escherichia Coli Endoribonuclease Rnase E: in Vivo and in Vitro Analysis of Mutants in a Bacteriophage T4 Mrna Processing Site
    Downloaded from genesdev.cshlp.org on October 6, 2021 - Published by Cold Spring Harbor Laboratory Press specificity of Escherichia coli endoribonuclease RNase E: in vivo and in vitro analysis of mutants in a bacteriophage T4 mRNA processing site Claude P. Ehretsmann/ Agamemnon J. Carpousis,^ and Henry M. Krisch^ Department of Molecular Biology, University of Geneva, 1211 Geneva 4, Switzerland Endoribonuclease RNase £ has an important role in the processing and degradation of bacteriophage T4 and Escherichia coli mRNAs. We have undertaken a mutational analysis of the -71 RNase E processing site of T4 gene 32. A Series of mutations were introduced into a synthetic T4 sequence cloned on a plasmid, and their effects on processing were analyzed in vivo. The same mutations were transferred into T4 by homologous recombination. In both the plasmid and the phage contexts the processing of the transcripts was similarly affected by the mutations. Partially purified RNase E has also been used to ascertain the effect of these mutations on RNase E processing in vitro. The hierarchy of the efficiency of processing of the various mutant transcripts was the same in vivo and in vitro. These results and an analysis of all of the known putative RNase E sites suggest a consensus sequence RAUUW (R = A or G; W ^ A or U) at the cleavage site. Modifications of the stem-loop structure downstream of the -71 site indicate that a secondary structure is required for RNase E processing. Processing by RNase E was apparently inhibited by sequences that sequester the site in secondary structure. [Key Words: Bacteriophage T4 gene 32; mRNA degradation; RNA processing; ribonuclease E] Received August 29, 1991; revised version accepted November 14, 1991.
    [Show full text]
  • Rnase E Activity Is Conferred by a Single Polypeptide: Overexpression
    Proc. Natl. Acad. Sci. USA Vol. 90, pp. 9006-9010, October 1993 Biochemustry RNase E activity is conferred by a single polypeptide: Overexpression, purification, and properties of the ams/rne/hmpl gene product (endoribonuclease/RNA processing) R. S. CORMACK, J. L. GENEREAUX, AND G. A. MACKIE* Department of Biochemistry, University of Western Ontario, London, Ontario, Canada N6A 5C1 Communicated by Myron K. Brakke, June 29, 1993 (receivedfor review May 10, 1993) ABSTRACT Ribonuclease E, an enzyme that processes encoding a high molecular mass protein hypothesized to be pre-SS rRNA from Its precursor, is now believed to be the involved in nucleoid partitioning or cell wall invagination major endoribonuclease participating in mRNA turnover in during division (16). The revised DNA sequence, coterminal Escherichia coli. The product of the ams/rne/hmpl gene, with the 5' end of the two previous sequences, encodes a which is required for RNase E activity, was overexpressed, protein of 1025 amino acid residues whose predicted relative purified to near homogeneity by electroelution from an molecular mass would be 114,000. This polypeptide displays SDS/polyacrylamide gel, and renatured. The purified poly- anomalous electrophoretic mobility in SDS/polyacrylamide peptide possesses nucleolytic activity in vitro with a specificity gels, however, and migrates with an apparent size of 180 kDa identical to that observed for crude RNase E preparations. In (16). It has not been proven that the polypeptide encoded by addition, both UV crosslinking and RNA-protein blotting the ams/rne/hmpl gene is, in fact, a ribonuclease or is unambiguously showed that the Ams/Rne/Hmpl polypeptide intimately associated with the cleavage ofRNA either in vitro has a high affnity for RNA.
    [Show full text]
  • Asca (Yeca) Is a Molecular Chaperone Involved in Sec-Dependent Protein Translocation
    bioRxiv preprint doi: https://doi.org/10.1101/2020.07.21.215244; this version posted July 22, 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-ND 4.0 International license. 1 1 AscA (YecA) is a molecular chaperone involved in Sec-dependent protein translocation 2 in Escherichia coli 3 4 Running title: AscA is a Sec chaperone 5 6 Tamar Cranford Smith1, Max Wynne1, Cailean Carter, Chen Jiang, Mohammed Jamshad, 7 Mathew T. Milner, Yousra Djouider, Emily Hutchinson, Peter A. Lund, Ian Henderson2 and 8 Damon Huber* 9 10 Institute for Microbiology and Infection; University of Birmingham; Edgbaston, 11 Birmingham, UK 12 13 1These authors contributed equally to this work 14 15 2Current address: Institute for Molecular Bioscience; University of Queensland; Brisbane, 16 Australia 17 18 *To whom correspondence should be addressed: [email protected] 19 20 Keywords: protein translocation, Sec pathway, molecular chaperone, SecB, metal binding 21 domain 22 23 ABSTRACT. 24 Proteins that are translocated across the cytoplasmic membrane by Sec 25 machinery must be in an unfolded conformation in order to pass through the protein- bioRxiv preprint doi: https://doi.org/10.1101/2020.07.21.215244; this version posted July 22, 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-ND 4.0 International license.
    [Show full text]
  • Mechanism of Ribonuclease III Catalytic Regulation by Serine
    www.nature.com/scientificreports OPEN Mechanism of Ribonuclease III Catalytic Regulation by Serine Phosphorylation Received: 08 January 2016 Swapna Gone1,*,†, Mercedes Alfonso-Prieto2,‡,*, Samridhdi Paudyal3,$ & Allen W. Nicholson1,3 Accepted: 15 April 2016 Ribonuclease III (RNase III) is a conserved, gene-regulatory bacterial endonuclease that cleaves double- Published: 06 May 2016 helical structures in diverse coding and noncoding RNAs. RNase III is subject to multiple levels of control, reflective of its global regulatory functions.Escherichia coli (Ec) RNase III catalytic activity is known to increase during bacteriophage T7 infection, reflecting the expression of the phage-encoded protein kinase, T7PK. However, the mechanism of catalytic enhancement is unknown. This study shows that Ec-RNase III is phosphorylated on serine in vitro by purified T7PK, and identifies the targets as Ser33 and Ser34 in the N-terminal catalytic domain. Kinetic experiments reveal a 5-fold increase in kcat and a 1.4-fold decrease in Km following phosphorylation, providing a 7.4–fold increase in catalytic efficiency. Phosphorylation does not change the rate of substrate cleavage under single-turnover conditions, indicating that phosphorylation enhances product release, which also is the rate-limiting step in the steady-state. Molecular dynamics simulations provide a mechanism for facilitated product release, in which the Ser33 phosphomonoester forms a salt bridge with the Arg95 guanidinium group, thereby weakening RNase III engagement of product. The simulations also show why glutamic acid substitution at either serine does not confer enhancement, thus underscoring the specific requirement for a phosphomonoester. RNA maturation and decay pathways are fundamentally involved in gene expression and regulation in bacterial cells, and are defined by the coordinated action of endoribonucleases and exoribonucleases.
    [Show full text]
  • Generate Metabolic Map Poster
    Authors: Pallavi Subhraveti Peter D Karp Ingrid Keseler 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. Anamika Kothari Periplasmic (where appropriate) and extracellular reactions and proteins may also be shown. Pathways are colored according to their cellular function. Gcf_000980815Cyc: Corynebacterium camporealensis DSM 44610 Cellular Overview Connections between pathways are omitted for legibility. Ron Caspi phosphate phosphate (S)-lactate phosphate ammonium predicted ABC RS04760 RS02955 RS06425 RS10630 transporter of phosphate phosphate (S)-lactate phosphate ammonium phosphate Amine and Tetrapyrrole Biosynthesis Amino Acid Degradation glutaminyl-tRNA gln Aminoacyl-tRNA Charging Polyamine a ring-opened 7- a DNA containing (1S,2R)-1- a [ThiI sulfur- biosynthesis via transamidation Biosynthesis an apo [peptidyl- all-trans- an L-asparaginyl- an L-cysteinyl- Polyprenyl Biosynthesis siroheme biosynthesis TCA cycle TCA cycle IV (2-oxoglutarate decarboxylase) L-valine degradation I L-asparagine methylguanine coenzyme A an apurinic/ ser C-(indol-3- carrier protein]- cys a [glutamine- L-isoleucine degradation I L-leucine degradation I L-threonine carrier protein] ATP retinyl palmitate [tRNA Asn ] [tRNA Cys ] dGDP spermidine degradation I in DNA apyrimidinic site yl)glycerol L-cysteine synthetase]-
    [Show full text]