Supplementary Material Comparative Proteomic Analysis of Latex from Euphorbia Kansui Laticifers at Different Development Stages
Total Page：16
File Type：pdf, Size：1020Kb
Load more
Recommended publications
-
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. -
Functional Assignments in the Enolase Superfamily: Investigations of Two Divergent Groups of D-Galacturonate Dehydratases and Galactarate Dehydratase-Iii
FUNCTIONAL ASSIGNMENTS IN THE ENOLASE SUPERFAMILY: INVESTIGATIONS OF TWO DIVERGENT GROUPS OF D-GALACTURONATE DEHYDRATASES AND GALACTARATE DEHYDRATASE-III BY FIONA PATRICIA GRONINGER-POE i DISSERTATION Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Biochemistry in the Graduate College of the University of Illinois at Urbana-Champaign, 2014 Urbana, Illinois Doctoral Committee: Professor John A. Gerlt, Chair Professor John E. Cronan, Jr. Associate Professor Rutilo Fratti Associate Professor Raven H. Huang ABSTRACT More than a decade after the genomic age, full genome sequencing is cost-effective and fast, allowing for the deposit of an ever increasing number of DNA sequences. New fields have arisen from this availability of genomic information, and the way we think about biochemistry and enzymology has been transformed. Unfortunately, there is no robust method for accurately determining the functions of enzymes encoded by these sequences that matches the speed in which genomes are deposited into public databases. Functional assignment of enzymes remains of utmost importance in understanding microbial metabolism and has applications in agriculture by examining bacterial plant pathogen metabolism and additionally in human health by providing metabolic context to the human gut microbiome. To aid in the functional identification of proteins, enzymes can be grouped into superfamilies which share common structural motifs as well as mechanistic features. To this end, the enolase superfamily is an excellent model system for functional assignment because more than half of the members still lack functional identification. Structurally, these enzymes contain substrate specificity residues in the N-terminal capping domain and catalytic residues in the C-terminal barrel domain. -
Download Article (PDF)
Enzymatic Biosynthesis of Vomilenine, a Key Intermediate of the Ajmaline Pathway, Catalyzed by a Novel Cytochrome P 450-Dependent Enzyme from Plant Cell Cultures of Rauwolfia serpentina Heike Falkenhagen and Joachim Stöckigt Lehrstuhl für Pharmazeutische Biologie der Johannes Gutenberg-Universität Mainz, Institut für Pharmazie, Staudinger Weg 5, D-55099 Mainz, Bundesrepublik Deutschland Z. Naturforsch. 50c, 45-53 (1995); received September 26, 1994 Vomilenine, Vinorine, Vinorine Hydroxylase, Cytochrome P450, Rauwolfia serpentina Microsomal preparations from Rauwolfia serpentina Benth. cell suspension cultures cata lyze a key step in the biosynthesis of ajmaline - the enzymatic hydroxylation of the indole alkaloid vinorine at the allylic C-21 resulting in vomilenine. Vomilenine is an important branch-point intermediate, leading not only to ajmaline but also to several side reactions of the biosynthetic pathway to ajmaline. The investigation of the taxonomical distribution of the enzyme indicated that vinorine hydroxylase is exclusively present in ajmaline-producing plant cells. The novel enzyme is strictly dependent on NADPH2 and 0 2 and can be inhibited by typical cytochrome P450 inhibitors such as cytochrome c, ketoconazole and carbon mon oxide (the effect of CO is reversible with light of 450 nm). This suggests that vinorine hy droxylase is a cytochrome P450-dependent monooxygenase. A pH optimum of 8.3 and a temperature optimum of 40 °C were found. The Km value was 3 for NADPH2 and 26 [i,M for vinorine. The optimum enzyme activity could be determined at day 4 after inoculation of the cell cultures in AP I medium. Vinorine hydroxylase could be stored with 20% sucrose at -28 °C without significant loss of activity. -
Changes in the Sclerotinia Sclerotiorum Transcriptome During Infection of Brassica Napus
Seifbarghi et al. BMC Genomics (2017) 18:266 DOI 10.1186/s12864-017-3642-5 RESEARCHARTICLE Open Access Changes in the Sclerotinia sclerotiorum transcriptome during infection of Brassica napus Shirin Seifbarghi1,2, M. Hossein Borhan1, Yangdou Wei2, Cathy Coutu1, Stephen J. Robinson1 and Dwayne D. Hegedus1,3* Abstract Background: Sclerotinia sclerotiorum causes stem rot in Brassica napus, which leads to lodging and severe yield losses. Although recent studies have explored significant progress in the characterization of individual S. sclerotiorum pathogenicity factors, a gap exists in profiling gene expression throughout the course of S. sclerotiorum infection on a host plant. In this study, RNA-Seq analysis was performed with focus on the events occurring through the early (1 h) to the middle (48 h) stages of infection. Results: Transcript analysis revealed the temporal pattern and amplitude of the deployment of genes associated with aspects of pathogenicity or virulence during the course of S. sclerotiorum infection on Brassica napus. These genes were categorized into eight functional groups: hydrolytic enzymes, secondary metabolites, detoxification, signaling, development, secreted effectors, oxalic acid and reactive oxygen species production. The induction patterns of nearly all of these genes agreed with their predicted functions. Principal component analysis delineated gene expression patterns that signified transitions between pathogenic phases, namely host penetration, ramification and necrotic stages, and provided evidence for the occurrence of a brief biotrophic phase soon after host penetration. Conclusions: The current observations support the notion that S. sclerotiorum deploys an array of factors and complex strategies to facilitate host colonization and mitigate host defenses. This investigation provides a broad overview of the sequential expression of virulence/pathogenicity-associated genes during infection of B. -
Comparative Analysis of Temporal Transcriptome Reveals The
bioRxiv preprint doi: https://doi.org/10.1101/2020.10.02.323402; this version posted October 3, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. This article is a US Government work. It is not subject to copyright under 17 USC 105 and is also made available for use under a CC0 license. 1 Comparative analysis of temporal transcriptome reveals the 2 relationship between pectin degradation and pathogenicity of 3 defoliating Verticillium dahliae to Upland cotton (Gossypium 4 hirsutum) 5 6 Fan Zhang1,2,#a, Jiayi Zhang1; Wanqing Chen3; Xinran Liu3; Cheng Li1; Yuefen Cao1; Tianlun 7 Zhao1; Donglin Lu1; Yixuan Hui1; Yi Zhang1; Jinhong Chen1; Jingze Zhang3; Alan E. 8 Pepper2*,#a; John Z. Yu4*; Shuijin Zhu1* 9 10 1 Institute of Crop Science, College of Agriculture & Biotechnology, Zhejiang University, 11 Hangzhou, Zhejiang, China 12 2 Department of Biology, College of Science, Texas A&M University, College Station, Texas, 13 United States of America 14 3 Institute of Biotechnology, College of Agriculture & Biotechnology, Zhejiang University, 15 Hangzhou, Zhejiang, China 16 4 United States Department of Agriculture-Agricultural Research Service (USDA-ARS), 17 Southern Plains Agricultural Research Center, College Station, Texas, United States of 18 America 19 20 #a Current Address: Department of Biology, College of Science, Texas A&M University, 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.10.02.323402; this version posted October 3, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. This article is a US Government work. -
Evolutionary Routes to Biochemical Innovation Revealed by Integrative
RESEARCH ARTICLE Evolutionary routes to biochemical innovation revealed by integrative analysis of a plant-defense related specialized metabolic pathway Gaurav D Moghe1†, Bryan J Leong1,2, Steven M Hurney1,3, A Daniel Jones1,3, Robert L Last1,2* 1Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, United States; 2Department of Plant Biology, Michigan State University, East Lansing, United States; 3Department of Chemistry, Michigan State University, East Lansing, United States Abstract The diversity of life on Earth is a result of continual innovations in molecular networks influencing morphology and physiology. Plant specialized metabolism produces hundreds of thousands of compounds, offering striking examples of these innovations. To understand how this novelty is generated, we investigated the evolution of the Solanaceae family-specific, trichome- localized acylsugar biosynthetic pathway using a combination of mass spectrometry, RNA-seq, enzyme assays, RNAi and phylogenomics in different non-model species. Our results reveal hundreds of acylsugars produced across the Solanaceae family and even within a single plant, built on simple sugar cores. The relatively short biosynthetic pathway experienced repeated cycles of *For correspondence: [email protected] innovation over the last 100 million years that include gene duplication and divergence, gene loss, evolution of substrate preference and promiscuity. This study provides mechanistic insights into the † Present address: Section of emergence of plant chemical novelty, and offers a template for investigating the ~300,000 non- Plant Biology, School of model plant species that remain underexplored. Integrative Plant Sciences, DOI: https://doi.org/10.7554/eLife.28468.001 Cornell University, Ithaca, United States Competing interests: The authors declare that no Introduction competing interests exist. -
Structural Studies of Three Enzymes: Telomerase, the Methyltransferase Cobj and Pectate Lyase
Structural studies of three enzymes: Telomerase, the methyltransferase CobJ and Pectate lyase Teng Teng To Thesis submitted to the University of London for the Degree of Doctor of Philosophy 1 Abstract This thesis investigates the structure and function of three enzymes of biotechnological and biomedical interest: telomerase from Caenorhabtidis elegans , pectate lyase from Bacillus subtilis and the methyltransferase CobJ from Rhodobacter capsulatus . Telomerase is a ribonucleoprotein found in all eukaryotes and its function is to maintain telomere length, sustain chromosome integrity and circumvent the end-replication problem. The protein requires two subunits to function, telomerase reverse transcriptase (TERT), the catalytic component, and an intrinsic RNA template (TR). The TR makes telomerase a unique reverse transcriptase using the template in the synthesis of short iterative sequences which cap the ends of telomeres. This work reports the successful cloning of a small and therefore potentially crystallisable TERT from C. elegans and expression trials of this catalytic component. Cobalamin (vitamin B 12 ) is an intricate small molecule belonging to a group of compounds called cyclic tetrapyrroles. Its biosynthesis is achieved through a complex pathway encompassing over thirty different enzyme-mediated reactions. Within this pathway there are seven methyltransferases which add eight S-adenosyl-methionine (SAM) derived methyl groups to the macrocycle. CobJ catalyses the methylation of C17 and ring contraction at C20, this reaction which exudes C20 from the tetrapyrrole ring is unprecedented in nature. In this thesis I report the crystallisation of native CobJ and refinement and validation of a high resolution structure along side co-crystallisation and soaking experiments aimed at capturing an enzyme-tetrapyrrole complex. -
3D-Structure of Vinorine Synthase from Rauvolfia Serpentina in Complex with Its Ligand Acetyl-Coa
3D-Structure of Vinorine Synthase from Rauvolfia serpentina in Complex with its Ligand Acetyl-CoA M. Hill, S. Panjikar1, X. Ma, J. Stöckigt Department of Pharmaceutical Biology, Institute of Pharmacy, Johannes Gutenberg-University Mainz, Staudingerweg 5, D-55099 Mainz, Germany 1EMBL Hamburg outstation DESY, Notkestraße 85, D-22607 Hamburg, Germany Vinorine synthase (VS, EC 2.3.1.160) is an acetyl transferase that occupies a central role in the biosynthesis of the antiarrhythmic monoterpenoid indole alkaloid ajmaline in the Indian medicinal plant Rauvolfia serpentina. The enzyme catalyzes the reversible acetyl-CoA dependent formation of the ajmalan-type alkaloid vinorine from the sarpagine-type alkaloid 16-epi-vellosimine (Fig. 1) [1]. VS belongs to the BAHD (benzylalcohol acetyl-, anthocyanin-O-hydroxy-cinnamoyl, anthranilate-N-hydroxy-cinnamoyl/benzoyl-, deacetylvindoline acetyltransferase) enzyme superfamily of acetyl transferases, which members are involved in biosynthesis of several important drugs (morphine, taxol, vincaleucoblastine and vincristine) and other products of secondary metabolism in plants. The synthase consists of 412 amino acids and has a molecular weight of 46.8 kDa. All conserved residues typical for the BAHD family are found in VS. Prominent features of this family are the HxxxD motif in the active site and the DFGWG motif near the C-terminus. The typical low overall sequence identity (25-34%) to other BAHD members might indicate a divergent evolution of the family from one ancestral gene [2]. O H C H OAc 16 AcCoA CoA N N N H H VS N H AcCoA CoA 16-epi- Vinorin Figure 1: Reaction catalyzed by vinorine synthase (VS) Vinorine synthase from R. -
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 -
Properties of Vinorine Synthase — the Rauwolfia Enzyme Involved in the Formation of the Ajmaline Skeleton
Properties of Vinorine Synthase — the Rauwolfia Enzyme Involved in the Formation of the Ajmaline Skeleton Artur Pfitzner, Leo Polz, and Joachim Stöckigt Institut für Pharmazeutische Biologie der Ludwig Maximilians Universität München, Karlstr. 29, D-8000 München 2, Bundesrepublik Deutschland Z. Naturforsch. 41c, 103—114 (1986); received July 3. 1985 Dedicated to Professor Hans Grisebach on the occasion of his 60th birthday Rauwolfia serpentina Benth., Cell Suspension Cultures, Vinorine Synthase, Ajmaline Skeleton Vinorine synthase, a key enzyme in the formation of the Rauwolfia alkaloid ajmaline and its derivatives, has been isolated from Rauwolfia serpentina cell suspension cultures. The new enzy me has been 160-fold purified and characterized in detail. The synthase catalyses a single step in the biosynthesis of ajmalan alkaloids by the acetyl-coenzyme A and 16-epi-vellosimine dependent formation of vinorine, which shows the basic ajmaline skeleton. Besides a characteristic substrate specificity the major properties of the enzyme are a relatively high pH optimum (pH 8.5), a temperature optimum of 35 °C, an isoelectric point of pH 4.4, and a relative molecular weight of 31000 ± 8%. The apparent K m values for 16-epi-vellosimine and acetyl-coenzyme A were 19.4 [xm and 64 |xm resp. for the formation of vinorine. Kinetic data of the catalysed reaction indicate that 17-deacetylvinorine is not involved as a free intermediate during the vinorine biosyn thesis. Vinorine was proved by in vivo feeding experiments to be the biosynthetic precursor of the alkaloids in the final stages of the ajmaline pathway, vomilenine (21-hydroxyvinorine), 17-0- acetylnorajmaline and 17-O-acetylajmaline. -
Thesematthieuvillegente2013annexes
Supplemental table 1: list of the proteins identifed from the total protein fraction of Amborella trichopoda isolated embryo by shot gun Proteins have been analyzed by mono-dimensional electrophoresis and identified by mass spectrometry LC/MS-MS. The protein spots were analysed by LC-MS/MS on the PAPPSO plateform (Benoit Valot, Thierry Balliau, Michel Zivy, INRA Moulon, France; http://pappso.inra.fr). Based on the spectrum generated, proteins were identified using the X-Tandem software. "NCBI accession number" is the accession number in NCBI database. "Protein name" . "Organism" relates to the organism from which the identied protein comes from for functional analysis - efforts were focus on Arabidopsis thaliana as a plant model. " "AGI" . "Function category" and "Function description" relate to the functional categories defined according to the ontological classification of Bevan et al . [Bevan et al . (1998) Nature 391:485-488]. "log(Evalue) identification" reflects the statistical power of the identification by BLAST (performed on TAIR or BLAST). "Identity" indicates in % the recovery of the Amborella protein sequence against the identified protein. "Compartement" indicates if the identification is found in the embryo (emb.), the endosperm (end.) or both (emb./end.). "Description" was taken from the Amborella EVM 27 Predicted Proteins (http://www.amborella.org). The "log (E value)" is a statistical parameter that represents the number of peptides present at random in the database. It was calculated by the product of the Evalue of unique peptides identified in the protein spot (Valot et al., 2011). "Coverage" refers to the recovery rate of the protein by the identified peptides, expressed in %. -
Identification and Characterization of Piperine Synthase from Black
ARTICLE https://doi.org/10.1038/s42003-021-01967-9 OPEN Identification and characterization of piperine synthase from black pepper, Piper nigrum L. Arianne Schnabel 1, Benedikt Athmer1, Kerstin Manke1, Frank Schumacher2, Fernando Cotinguiba 3 & ✉ Thomas Vogt 1 Black pepper (Piper nigrum L.) is the world’s most popular spice and is also used as an ingredient in traditional medicine. Its pungent perception is due to the interaction of its major compound, piperine (1-piperoyl-piperidine) with the human TRPV-1 or vanilloid receptor. We now identify the hitherto concealed enzymatic formation of piperine from piperoyl coenzyme A and piperidine based on a differential RNA-Seq approach from developing black pepper 1234567890():,; fruits. This enzyme is described as piperine synthase (piperoyl-CoA:piperidine piperoyl transferase) and is a member of the BAHD-type of acyltransferases encoded by a gene that is preferentially expressed in immature fruits. A second BAHD-type enzyme, also highly expressed in immature black pepper fruits, has a rather promiscuous substrate specificity, combining diverse CoA-esters with aliphatic and aromatic amines with similar efficiencies, and was termed piperamide synthase. Recombinant piperine and piperamide synthases are members of a small gene family in black pepper. They can be used to facilitate the microbial production of a broad range of medicinally relevant aliphatic and aromatic piperamides based on a wide array of CoA-donors and amine-derived acceptors, offering widespread applications. 1 Leibniz Institute of Plant Biochemistry, Dept. Cell and Metabolic Biology, Halle (Saale), Germany. 2 Core Facility Vienna Botanical Gardens, Vienna, Austria. ✉ 3 Instituto de Pesquisas de Produtos Naturais (IPPN), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro/RJ, Brasil.