DOCSLIB.ORG

( 12 ) Patent Application Publication ( 10 ) Pub . No .: US 2020/0407740 A1 CUI Et Al

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
( 12 ) Patent Application Publication ( 10 ) Pub . No .: US 2020/0407740 A1 CUI Et Al US 20200407740A1 IN ( 19 ) United States ( 12 ) Patent Application Publication ( 10 ) Pub . No .: US 2020/0407740 A1 CUI et al. ( 43 ) Pub . Date : Dec. 31 , 2020 ( 54 ) MATERIALS AND METHODS FOR Publication Classification CONTROLLING BUNDLE SHEATH CELL ( 51 ) Int. CI . FATE AND FUNCTION IN PLANTS C12N 15/82 ( 2006.01 ) ( 71 ) Applicant: FLORIDA STATE UNIVERSITY ( 52 ) U.S. CI . RESEARCH FOUNDATION , INC . , CPC C12N 15/8225 ( 2013.01 ) ; C12N 15/8269 Tallahassee, FL ( US ) ( 2013.01 ) ; C12N 15/8261 ( 2013.01 ) ( 57 ) ABSTRACT ( 72 ) Inventors : HONGCHANG CUI , The subject invention concerns materials and methods for TALLAHASSEE , FL (US ); DANYU increasing and / or improving photosynthetic efficiency in KONG , BLACKSBURG , VA (US ); plants, and in particular, C3 plants. In particular, the subject YUELING HAO , TALLAHASSEE , FL invention provides for means to increase the number of ( US ) bundle sheath ( BS ) cells in plants , to improve the efficiency of photosynthesis in BS cells , and to increase channels between BS and mesophyll ( M ) cells . In one embodiment, a ( 21 ) Appl . No .: 17 / 007,043 method of the invention concerns altering the expression level or pattern of one or more of SHR , SCR , and / or SCL23 in a plant. The subject invention also pertains to genetically ( 22 ) Filed : Aug. 31 , 2020 modified plants , and in particular, C3 plants, that exhibit increased expression of one or more of SHR , SCR , and / or SCL23 . Transformed and transgenic plants are contemplated Related U.S. Application Data within the scope of the invention . The subject invention also ( 62 ) Division of application No. 14 / 898,046 , filed on Dec. concerns methods for increasing expression of photosyn 11 , 2015 , filed as application No. PCT US2014/ / thetically important genes in a plant, wherein one or more 041975 on Jun . 11 , 2014 . genes of interest are operably linked with a plant SHR , SCR ( 60 ) Provisional application No. 61 / 833,771 , filed on Jun . or SCL23 promoter sequence and expressed in a plant. 11 , 2013 . Specification includes a Sequence Listing . Patent Application Publication Dec. 31 , 2020 Sheet 1 of 10 US 2020/0407740 A1 FIG . 1A FIG . 1C FIG . 1E BS BS 29 BS X BS p 14 p 22 : 4 um 40 + 10 um 22 + 5um FIG . 1A - 1 FIG . 1C - 1 FIG . 1E - 1 Patent Application Publication Dec. 31 , 2020 Sheet 2 of 10 US 2020/0407740 A1 FIG . 1B FIG . 1D FIG . 1F BS V BS X X 21+ 8 um 35 + 10 um 40 + 12 um FIG . 1B - 1 FIG . 1D - 1 FIG . 1F - 1 Patent Application Publication Dec. 31 , 2020 Sheet 3 of 10 US 2020/0407740 A1 FIG . 2A FIG . 2B FIG . 2C BS BS BS V X p < 1 ? FIG . 2D FIG . 2E FIG . 2F X X 13p H P FIG . 2G FIG . 2H Patent Application Publication Dec. 31 , 2020 Sheet 4 of 10 US 2020/0407740 A1 I QSCR E FIG.3C 0.37 3DFIG. € ou 0 A L 0 23-2SC/ FIG.3B FIG3E. scr1- 3AFIG. Patent Application Publication Dec. 31 , 2020 Sheet 5 of 10 US 2020/0407740 A1 23-2scScr-1 4BFIG. Col sc/23-2 FIG.4D WsSCP-1 GlucoseFructoseSucrose 5 3 2 1 ColShr-2 FIG.4A FIG.4C SM SCI1- 23-2SC/ scl23-2 Patent Application Publication Dec. 31 , 2020 Sheet 6 of 10 US 2020/0407740 A1 23-2sc!SCP1- FIG.4E Sc/23-2 Patent Application Publication Dec. 31 , 2020 Sheet 7 of 10 US 2020/0407740 A1 FIG . 5A 1 2 1218 bp D o o B 120.0 % 100.0 % 80.0 % 60.0 % 40.0 % 20.0 % 0.0 % sc /23 1 , sc123 1 , sc123 2 , sc.23 2 , # 1 # 2 # 1 # 2 FIG . 5B Patent Application Publication Dec. 31 , 2020 Sheet 8 of 10 US 2020/0407740 A1 FIG . 6A FIG . 6C A C 03:33 B D cao FIG . 6B FIG . 6D Patent Application Publication Dec. 31 , 2020 Sheet 9 of 10 US 2020/0407740 A1 a b FIG . 7A FIG . 7B Patent Application Publication Dec. 31 , 2020 Sheet 10 of 10 US 2020/0407740 A1 SCR targets 26 w 24 1877 SHR targets SCL23 targets Lists contain 2539 unique elements FIG . 8 US 2020/0407740 A1 Dec. 31 , 2020 1 MATERIALS AND METHODS FOR with the active transport system , CO2 is effectively concen CONTROLLING BUNDLE SHEATH CELL trated in the bundle sheath cells , which in turn leads to the FATE AND FUNCTION IN PLANTS repression of the oxygenase activity of RUBISCO . Last but not least , each bundle sheath cell layer is associated with a CROSS - REFERENCE TO RELATED central cylinder of vascular tissue , which provides water and APPLICATIONS inorganic nutrients, and is surrounded by a single layer of [ 0001] The present application is a divisional of U.S. mesophyll cells , a feature characteristic of C4 plants called application Ser. No. 14 / 898,046 , filed Dec. 11 , 2015 , which the Kranz anatomy ( Wang et al . ( 2011 ) ) . is the National Stage of International Application Number [ 0005 ] Attempts to increase yield by expressing PEP car PCT /US2014 /041975 , filed Jun . 11 , 2014 , which claims the boxylase in both mesophyll and bundle sheath cells rice benefit ofU.S. Provisional Application No. 61 / 833,771 , filed have failed ( Taniguchi et al . ( 2008 ) ) , suggesting that the Jun . 11 , 2013 , each of which is hereby incorporated by mesophyll and bundle sheath cells must be engineered reference herein in its entirety, including any figures, tables , separately ( Kajala et al . ( 2011 ) ) . nucleic acid sequences , amino acid sequences , or drawings . [ 0006 ] Despite the pivotal role of bundle sheath cells in C4 photosynthesis, the mechanisms that determine their cell identity and patterning are still unknown. Extensive mutant SEQUENCE LISTING screening efforts in the past decades have identified several [ 0002 ] The Sequence Listing for this application is labeled maize and Arabidopsis mutants defective in chloroplast “ 2QK2480.TXT" which was created on Sep. 17 , 2020 and development in the bundle sheath cells ( Nelson ( 2011 ) ; is 187 KB . The entire contents of the sequence listing is Brutnell et al . ( 1999 ) ; Hall et al . ( 1998 ) ; Kinsman and Pyke incorporated herein by reference in its entirety. ( 1998 ) ; Petricka et al . ( 2008 ) ; Rossini et al . ( 2001 ) ) , but none of these mutants affects bundle sheath cell identity. BACKGROUND OF THE INVENTION [ 0007 ] Bundle sheath cells are a leaf cell type that forms [ 0003 ] With a rapidly growing world population and a single cell layer between the mesophyll cells and the dwindling natural resources , we are facing an enormous central vascular tissue . In C3 plants, both the mesophyll challenge of increasing crop yields while simultaneously cells and BS cells are photosynthetic, but the BS cells are improving the efficiency of resource utilization . In C3 small with fewer chloroplasts. In contrast, the BS cells are plants, a 3 - carbon molecule is the first product of carbon the major sites of photosynthesis in most C4 plants, whereas fixation , whereas in C4 plants, a 4 -carbon molecule is the the mesophyll cells are involved in CO2 fixation only . first product. Because C4 plants are much more efficient than Accordingly , the BS cells are much larger in size . The spatial C3 plants in photosynthesis as well as water and nitrogen separation of the two phases of photosynthesis into meso usage , particularly in hot climates ( Langdale ( 2011 ) ) , tre phyll and BS cells is one of the features that make C4 plants mendous efforts are being taken to introduce C4 photosyn significantly more efficient photosynthetically. Another fea thesis into economically important C3 crops ( Sage and Zhu ture that improves the photosynthetic efficiency in C4 plants ( 2011 ) ) , such as rice ( Hibberd et al . ( 2008 ) ) . It is estimated is the Kranz anatomy, characterized by an approximately 1 : 1 that yields can be increased by 50 % if rice is transformed ratio between mesophyll and BS cells . The close association into a C4 plant ( Hibberd et al . ( 2008 ) ) . between the two cell types facilitates metabolite transport, [ 0004 ] Evidence indicates that C4 plants have evolved which is critical for the C4 mechanism . In C3 plants , this multiple times from C3 plants ( Brown et al . ( 2011 ) ) , but all ratio is greater than 2 : 1 . C4 plants share some common features that make them [ 0008 ] Many important crops , such as rice ( Oryza sativa ) perform better . A critical innovation is the deployment of and wheat ( Triticum aestivum ) , are C3 plants. To meet the phosphoenolpyruvate ( PEP ) carboxylase as the enzyme for needs for food of a rapidly growing population, tremendous the initial fixation of CO2 in C4 plants. Unlike RUBISCO , efforts are being undertaken to introduce the C4 mechanism the enzyme used for the initial fixation of CO2 in C3 plants, into C3 crops ( Langdale, 2011 ) . For example , millions of PEP carboxylase does not have an oxygenase activity and dollars have been invested at the C4 rice consortium to therefore can maintain a high rate of photosynthesis even convert this important crop into a C4 plant ( von Caemmerer under conditions of low CO2 ( stomates partially closed ) and et al . , 2012 ) . Although the input is huge and the risk is high , high temperature (RUBISCO's oxygenase activity is stimu the potential reward is enormous. It is estimated that a 10 % lated at high temperatures ( Spreitzer et al . ( 2002 ) ) . Another increase in the photosynthetic efficiency would increase the critical feature of C4 plants is the separation of the two yield by 50 % ( Langdale , 2011 ) . However, to achieve C4 phases of photosynthesis , namely Co , fixation and carbo photosynthesis in C3 plants requires engineering of the BS hydrate biosynthesis, into the mesophyll and bundle sheath and mesophyll cells at many levels , including an increase in cells , respectively . To sustain a high rate of photosynthesis, the density of BS cells and modification of the physiology in C4 plants also have numerous plasmodesmata and various the BS and mesophyll cells .
Load more

Recommended publications
  • Grapes for the Desert: Salt Stress Signaling in Vitis
    Grapes for the Desert: Salt Stress Signaling in Vitis Zur Erlangung des akademischen Grades eines DOKTORS DER NATURWISSENSCHAFTEN (Dr. rer. Nat.) der Fakultät für Chemie und Biowissenschaften des Karlsruher Instituts für Technologie (KIT) genehmigte DISSERTATION von Ahmed Abd Alkarim Mohammed Ismail aus Damanhour, Ägypten Die vorliegende Dissertation wurde in der Abteilung Molekulare Zellbiologie, am Botanischen Institut des Karlsruher Instituts für Technologie (KIT) im Zeitraum von April 2010 bis Juli 2013 angefertigt. Dekan: Prof. Dr. M. Bastmeyer Referent: Prof. Dr. P. Nick Korreferent: Prof. Dr. H. Puchta Prof. Dr. Natalia Requena Dr. Christoph Basse Tag der mündlichen Prüfung: 19. Juli 2013 Hiermit erkläre ich, dass ich die vorliegende Dissertation, abgesehen von der Benutzung der angegebenen Hilfsmittel, selbstständig verfasst habe. Alle Stellen, die gemäß Wortlaut oder Inhalt aus anderen Arbeiten entnommen sind, wurden durch Angabe der Quelle als Entlehnungen kenntlich gemacht. Diese Dissertation liegt in gleicher oder ähnlicher Form keiner anderen Prüfungsbehörde vor. Karlsruhe, den 19. Juli 2013 Ahmed Abd Alkarim Mohammed Ismail Table of Contents Table of Contents Abbreviations ........................................................................... IV Summary / Zusammenfassung ............................................... XI 1 Introduction ............................................................................. 1 1.1 What does stress mean for a plant? .............................................. 1 1.2 Environmental
    [Show full text]
  • Carnitine Metabolism to Trimethylamine by an Unusual Rieske-Type Oxygenase from Human Microbiota
    Carnitine metabolism to trimethylamine by an unusual Rieske-type oxygenase from human microbiota Yijun Zhua,1, Eleanor Jamesona,1, Marialuisa Crosattib,1, Hendrik Schäfera, Kumar Rajakumarb, Timothy D. H. Buggc, and Yin Chena,2 aSchool of Life Sciences and cDepartment of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom; and bDepartment of Infection, Immunity, and Inflammation, University of Leicester, Leicester LE1 9HN, United Kingdom Edited by David W. Russell, University of Texas Southwestern Medical Center, Dallas, TX, and approved January 29, 2014 (received for review September 5, 2013) Dietary intake of L-carnitine can promote cardiovascular diseases in (14, 15). Assigning functions encoded in the human microbiome humans through microbial production of trimethylamine (TMA) using existing databases can be problematic. For example, the and its subsequent oxidation to trimethylamine N-oxide by hepatic Pfam protein database currently contains over 25% of protein flavin-containing monooxygenases. Although our microbiota are re- families with no assigned functions (release 26.0) (19). sponsible for TMA formation from carnitine, the underpinning mo- Lack of functional characterization of key microbial functions lecular and biochemical mechanisms remain unclear. In this study, in our microbiota is exemplified by very recent studies on car- using bioinformatics approaches, we first identified a two-component diovascular diseases (20–23). These studies have shown that the Rieske-type oxygenase/reductase (CntAB) and associated gene human microbiota is responsible for the production of trime- cluster proposed to be involved in carnitine metabolism in repre- thylamine N-oxide (TMAO), which is believed to promote ath- sentative genomes of the human microbiota. CntA belongs to a erogenesis through its interaction with macrophages and lipid group of previously uncharacterized Rieske-type proteins and has metabolism (20–23).
    [Show full text]
  • Thermophilic Bacteria Are Potential Sources of Novel Rieske Non-Heme
    Chakraborty et al. AMB Expr (2017) 7:17 DOI 10.1186/s13568-016-0318-5 ORIGINAL ARTICLE Open Access Thermophilic bacteria are potential sources of novel Rieske non‑heme iron oxygenases Joydeep Chakraborty, Chiho Suzuki‑Minakuchi, Kazunori Okada and Hideaki Nojiri* Abstract Rieske non-heme iron oxygenases, which have a Rieske-type [2Fe–2S] cluster and a non-heme catalytic iron center, are an important family of oxidoreductases involved mainly in regio- and stereoselective transformation of a wide array of aromatic hydrocarbons. Though present in all domains of life, the most widely studied Rieske non-heme iron oxygenases are found in mesophilic bacteria. The present study explores the potential for isolating novel Rieske non- heme iron oxygenases from thermophilic sources. Browsing the entire bacterial genome database led to the identifi‑ cation of 45 homologs from thermophilic bacteria distributed mainly among Chloroflexi, Deinococcus–Thermus and Firmicutes. Thermostability, measured according to the aliphatic index, showed higher values for certain homologs compared with their mesophilic relatives. Prediction of substrate preferences indicated that a wide array of aromatic hydrocarbons could be transformed by most of the identified oxygenase homologs. Further identification of putative genes encoding components of a functional oxygenase system opens up the possibility of reconstituting functional thermophilic Rieske non-heme iron oxygenase systems with novel properties. Keywords: Rieske non-heme iron oxygenase, Oxidoreductase, Thermophiles, Aromatic hydrocarbons, Biotransformation Introduction of a wide array of agrochemically and pharmaceutically Rieske non-heme iron oxygenases (ROs) constitute a important compounds (Ensley et al. 1983; Wackett et al. large family of oxidoreductase enzymes involved primar- 1988; Hudlicky et al.
    [Show full text]
  • Downloaded in February 2021) (Boeckmann Et Al., 2003)
    bioRxiv preprint doi: https://doi.org/10.1101/2021.08.16.456528; this version posted August 17, 2021. 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. Deciphering Rubber Tree Growth Using Network-Based Multi Omics Approaches Felipe Roberto Francisco1†, Alexandre Hild Aono 1†, Carla Cristina da Silva1, Paulo de Souza Gonçalves2, Erivaldo José Scaloppi Junior2, Vincent Le Guen3, Roberto Fritsche Neto4, Livia Moura Souza1,5, Anete Pereira de Souza1,6* 1Molecular Biology and Genetic Engineering Center (CBMEG), University of Campinas (UNICAMP), Campinas, Brazil 2Center of Rubber Tree and Agroforestry Systems, Agronomic Institute (IAC), Votuporanga, Brazil 3Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), UMR AGAP, Montpellier, France 4Department of Genetics, Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo (USP), Piracicaba, São Paulo, Brazil 5São Francisco University (USF), Itatiba, Brazil 6Department of Plant Biology, Biology Institute, University of Campinas (UNICAMP), Campinas, Brazil †These authors have contributed equally to this work * Correspondence: Anete Pereira de Souza [email protected] Number of Words: 8909 Number of Figures: 7 Number of Tables: 1 Keywords: GBS, GWAS, Hevea brasiliensis, linkage disequilibrium, metabolic networks, QTL, RNA-Seq, WGCNA Abstract Hevea brasiliensis (rubber tree) is a large tree species of the Euphorbiaceae family with inestimable economic importance. Rubber tree breeding programs currently aim to improve growth and production, and the use of early genotype selection technologies can accelerate such processes, mainly with the incorporation of genomic tools, such as marker-assisted selection (MAS).
    [Show full text]
  • Role in Plant Stress Physiology and Regulation of Gene Expression
    Characterisation of selected Arabidopsis aldehyde dehydrogenase genes: role in plant stress physiology and regulation of gene expression Dissertation Zur Erlangung des Doktorgrades (Dr. rer. nat.) der Mathematisch-Naturwissenschaftlichen Fakultät der Rheinischen Friedrich-Wilhelms-Universität Bonn vorgelegt von Tagnon Dègbédji MISSIHOUN aus Cotonou, Benin Bonn, November 2010 Angefertigt mit Genehmigung der Mathematisch- Naturwissenschaftlichen Fakultät der Rheinischen Friedrich-Wilhelms-Universität Bonn Gedruckt mit Unterstützung des Deutschen Akademischen Austauschdienstes 1. Referentin: Prof. Dr. Dorothea Bartels 2. Koreferent: Priv. Doz. Dr. Hans-Hubert Kirch Tag der Promotion: 22. Februar 2011 Erscheinungsjahr: 2011 II DECLARATION I hereby declare that the whole PhD thesis is my own work, except where explicitly stated otherwise in the text or in the bibliography. Bonn, November 2010 ------------------------------------ Tagnon D. MISSIHOUN III DEDICATION To My wife: Fabienne TOSSOU-MISSIHOUN and our kids Floriane S. Jennifer and Sègnon Anges- Anis My parents: Lucrèce KOTOMALE and Dadjo MISSIHOUN My sister and brothers: Mariette, Marius, Ricardo, Renaud, Ulrich And my dearest aunts and uncles: Hoho, Rebecca, Cyriaque, Dominique, Alphonsine IV CONTENTS ABBREVIATIONS ...............................................................................................................................................X FIGURES AND TABLES ...............................................................................................................................XIII
    [Show full text]
  • Characterization of the CRM Gene Family and Elucidating the Function of Oscfm2 in Rice
    biomolecules Article Characterization of the CRM Gene Family and Elucidating the Function of OsCFM2 in Rice Qiang Zhang y , Lan Shen y, Deyong Ren, Jiang Hu, Li Zhu, Zhenyu Gao, Guangheng Zhang , Longbiao Guo, Dali Zeng and Qian Qian * State Key Laboratory of Rice Biology/China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China; [email protected] (Q.Z.); [email protected] (L.S.); [email protected] (D.R.); [email protected] (J.H.); [email protected] (L.Z.); [email protected] (Z.G.); [email protected] (G.Z.); [email protected] (L.G.); [email protected] (D.Z.) * Correspondence: [email protected]; Tel.: +86-571-6337-0483 These authors contributed equally to this work. y Received: 10 January 2020; Accepted: 17 February 2020; Published: 18 February 2020 Abstract: The chloroplast RNA splicing and ribosome maturation (CRM) domain-containing proteins regulate the expression of chloroplast or mitochondrial genes that influence plant growth and development. Although 14 CRM domain proteins have previously been identified in rice, there are few studies of these gene expression patterns in various tissues and under abiotic stress. In our study, we found that 14 CRM domain-containing proteins have a conservative motif1. Under salt stress, the expression levels of 14 CRM genes were downregulated. However, under drought and cold stress, the expression level of some CRM genes was increased. The analysis of gene expression patterns showed that 14 CRM genes were expressed in all tissues but especially highly expressed in leaves. In addition, we analyzed the functions of OsCFM2 and found that this protein influences chloroplast development by regulating the splicing of a group I and five group II introns.
    [Show full text]
  • The Role of the Salvage Pathway in Nucleotide Sugar Biosynthesis
    THE ROLE OF THE SALVAGE PATHWAY IN NUCLEOTIDE SUGAR BIOSYNTHESIS: IDENTIFICATION OF SUGAR KINASES AND NDP-SUGAR PYROPHOSPHORYLASES by TING YANG (Under the Direction of Maor Bar-Peled) ABSTRACT The synthesis of polysaccharides, glycoproteins, glycolipids, glycosylated secondary metabolites and hormones requires a large number of glycosyltransferases and a constant supply of nucleotide sugars. In plants, photosynthesis and the NDP-sugar inter-conversion pathway are the major entry points to form NDP-sugars. In addition to these pathways is the salvage pathway, a less understood metabolism that provides the flux of NDP-sugars. This latter pathway involves the hydrolysis of glycans to free sugars, sugar transport, sugar phosphorylation and nucleotidylation. The balance between glycan synthesis and recycling as well as its regulation at various plant developmental stages remains elusive as many of the molecular components are unknown. To understand how the salvage pathway contributes to the sugar flux and cell wall biosynthesis, my research focused on the functional identification of salvage pathway sugar kinases and NDP-sugar pyrophosphorylases. This research led to the first identification and enzymatic characterization of galacturonic acid kinase (GalA kinase), galactokinase (GalK), a broad UDP-sugar pyrophosphorylase (sloppy), two promiscuous UDP-GlcNAc pyrophosphorylases (GlcNAc-1-P uridylyltransferases), as well as UDP-sugar pyrophosphorylase paralogs from Trypanosoma cruzi and Leishmania major. To evaluate the salvage pathway in plant biology, we further investigated a sugar kinase mutant: galacturonic acid kinase mutant (galak) and determined if and how galak KO mutant affects the synthesis of glycans in Arabidopsis. Feeding galacturonic acid to the seedlings exhibited a 40-fold accumulation of free GalA in galak mutant, while the wild type (WT) plant readily metabolizes the fed-sugar.
    [Show full text]
  • Relating Metatranscriptomic Profiles to the Micropollutant
    1 Relating Metatranscriptomic Profiles to the 2 Micropollutant Biotransformation Potential of 3 Complex Microbial Communities 4 5 Supporting Information 6 7 Stefan Achermann,1,2 Cresten B. Mansfeldt,1 Marcel Müller,1,3 David R. Johnson,1 Kathrin 8 Fenner*,1,2,4 9 1Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, 10 Switzerland. 2Institute of Biogeochemistry and Pollutant Dynamics, ETH Zürich, 8092 11 Zürich, Switzerland. 3Institute of Atmospheric and Climate Science, ETH Zürich, 8092 12 Zürich, Switzerland. 4Department of Chemistry, University of Zürich, 8057 Zürich, 13 Switzerland. 14 *Corresponding author (email: [email protected] ) 15 S.A and C.B.M contributed equally to this work. 16 17 18 19 20 21 This supporting information (SI) is organized in 4 sections (S1-S4) with a total of 10 pages and 22 comprises 7 figures (Figure S1-S7) and 4 tables (Table S1-S4). 23 24 25 S1 26 S1 Data normalization 27 28 29 30 Figure S1. Relative fractions of gene transcripts originating from eukaryotes and bacteria. 31 32 33 Table S1. Relative standard deviation (RSD) for commonly used reference genes across all 34 samples (n=12). EC number mean fraction bacteria (%) RSD (%) RSD bacteria (%) RSD eukaryotes (%) 2.7.7.6 (RNAP) 80 16 6 nda 5.99.1.2 (DNA topoisomerase) 90 11 9 nda 5.99.1.3 (DNA gyrase) 92 16 10 nda 1.2.1.12 (GAPDH) 37 39 6 32 35 and indicates not determined. 36 37 38 39 S2 40 S2 Nitrile hydration 41 42 43 44 Figure S2: Pearson correlation coefficients r for rate constants of bromoxynil and acetamiprid with 45 gene transcripts of ECs describing nucleophilic reactions of water with nitriles.
    [Show full text]
  • The CRM Domain: an RNA Binding Module Derived from an Ancient Ribosome-Associated Protein
    JOBNAME: RNA 13#1 2007 PAGE: 1 OUTPUT: Thursday December 7 00:09:11 2006 csh/RNA/127813/rna1396 Downloaded from rnajournal.cshlp.org on September 28, 2021 - Published by Cold Spring Harbor Laboratory Press The CRM domain: An RNA binding module derived from an ancient ribosome-associated protein ALICE BARKAN,1 LARIK KLIPCAN,2 OREN OSTERSETZER,2 TETSUYA KAWAMURA,1,3 YUKARI ASAKURA,1 and KENNETH P. WATKINS1 1Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403-1229, USA 2Agricultural Research Organization, Volcani Center, Bet Dagan 50250, Israel ABSTRACT The CRS1–YhbY domain (also called the CRM domain) is represented as a stand-alone protein in Archaea and Bacteria, and in a family of single- and multidomain proteins in plants. The function of this domain is unknown, but structural data and the presence of the domain in several proteins known to interact with RNA have led to the proposal that it binds RNA. Here we describe a phylogenetic analysis of the domain, its incorporation into diverse proteins in plants, and biochemical properties of a prokaryotic and eukaryotic representative of the domain family. We show that a bacterial member of the family, Escherichia coli YhbY, is associated with pre-50S ribosomal subunits, suggesting that YhbY functions in ribosome assembly. GFP fused to a single-domain CRM protein from maize localizes to the nucleolus, suggesting that an analogous activity may have been retained in plants. We show further that an isolated maize CRM domain has RNA binding activity in vitro, and that a small motif shared with KH RNA binding domains, a conserved ‘‘GxxG’’ loop, contributes to its RNA binding activity.
    [Show full text]
  • The Mitochondrial Pentatricopeptide Repeat Protein PPR18 Is Required for the Cis-Splicing of Nad4 Intron 1 and Essential to Seed Development in Maize
    International Journal of Molecular Sciences Article The Mitochondrial Pentatricopeptide Repeat Protein PPR18 Is Required for the cis-Splicing of nad4 Intron 1 and Essential to Seed Development in Maize Rui Liu 1, Shi-Kai Cao 1 , Aqib Sayyed 1, Chunhui Xu 1, Feng Sun 1, Xiaomin Wang 2 and Bao-Cai Tan 1,* 1 Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China; [email protected] (R.L.); [email protected] (S.-K.C.); [email protected] (A.S.); [email protected] (C.X.); [email protected] (F.S.) 2 Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou 730000, China; [email protected] * Correspondence: [email protected] Received: 10 May 2020; Accepted: 2 June 2020; Published: 5 June 2020 Abstract: Pentatricopeptide repeat (PPR) protein comprises a large family, participating in various aspects of organellar RNA metabolism in land plants. There are approximately 600 PPR proteins in maize, but the functions of many PPR proteins remain unknown. In this study, we defined the function of PPR18 in the cis-splicing of nad4 intron 1 in mitochondria and seed development in maize. Loss function of PPR18 seriously impairs embryo and endosperm development, resulting in the empty pericarp (emp) phenotype in maize. PPR18 encodes a mitochondrion-targeted P-type PPR protein with 18 PPR motifs. Transcripts analysis indicated that the splicing of nad4 intron 1 is impaired in the ppr18 mutant, resulting in the absence of nad4 transcript, leading to severely reduced assembly and activity of mitochondrial complex I and dramatically reduced respiration rate.
    [Show full text]
  • Metabolomics and Molecular Approaches Reveal Drought Stress Tolerance in Plants
    International Journal of Molecular Sciences Review Metabolomics and Molecular Approaches Reveal Drought Stress Tolerance in Plants Manoj Kumar 1,* , Manish Kumar Patel 2 , Navin Kumar 3 , Atal Bihari Bajpai 4 and Kadambot H. M. Siddique 5,* 1 Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon LeZion 7505101, Israel 2 Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, Volcani Center, Rishon LeZion 7505101, Israel; [email protected] 3 Department of Life Sciences, Ben-Gurion University, Be’er Sheva 84105, Israel; [email protected] 4 Department of Botany, D.B.S. (PG) College, Dehradun 248001, Uttarakhand, India; [email protected] 5 The UWA Institute of Agriculture, and UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA 6001, Australia * Correspondence: [email protected] (M.K.); [email protected] (K.H.M.S.) Abstract: Metabolic regulation is the key mechanism implicated in plants maintaining cell osmotic potential under drought stress. Understanding drought stress tolerance in plants will have a signif- icant impact on food security in the face of increasingly harsh climatic conditions. Plant primary and secondary metabolites and metabolic genes are key factors in drought tolerance through their involvement in diverse metabolic pathways. Physio-biochemical and molecular strategies involved in plant tolerance mechanisms could be exploited to increase plant survival under drought stress. This review summarizes the most updated findings on primary and secondary metabolites involved in drought stress. We also examine the application of useful metabolic genes and their molecular Citation: Kumar, M.; Kumar Patel, responses to drought tolerance in plants and discuss possible strategies to help plants to counteract M.; Kumar, N.; Bajpai, A.B.; Siddique, unfavorable drought periods.
    [Show full text]
  • Proteome-Wide Characterization of Sugarbeet Seed Vigor and Its Tissue Specific Expression
    Proteome-wide characterization of sugarbeet seed vigor and its tissue specific expression Julie Catusse*†, Jean-Marc Strub†‡, Claudette Job*, Alain Van Dorsselaer†, and Dominique Job*§ *Centre National de la Recherche Scientifique-Universite´Claude Bernard Lyon 1, Institut National des Sciences Applique´es–Bayer CropScience Joint Laboratory, Unite´Mixte de Recherche 5240, Bayer CropScience, 14-20 rue Pierre Baizet, F69263 Lyon Cedex 9, France; and ‡Laboratoire de Spectrome´trie de Masse Bio-Organique, De´partement des Sciences Analytiques, Institut Pluridisciplinaire Hubert Curien, Unite´Mixte de Recherche 7178, Centre National de la Recherche Scientifique-Universite´Louis Pasteur, Ecole Europe´enne de Chimie, Mate´riaux et Polyme`res, 25 rue Becquerel, F67087 Strasbourg Cedex 2, France Edited by Roland Douce, Universite´de Grenoble, Grenoble, France, and approved April 11, 2008 (received for review January 19, 2008) Proteomic analysis of mature sugarbeet seeds led to the identifi- The use of metabolic inhibitors (␣-amanitin and cyclohexi- cation of 759 proteins and their specific tissue expression in root, mide) showed that transcription is not required for the comple- cotyledons, and perisperm. In particular, the proteome of the tion of germination in Arabidopsis, implying that the potential of perispermic storage tissue found in many seeds of the Caryophyl- germination is largely programmed during seed maturation on lales is described here. The data allowed us to reconstruct in detail the mother plant (4). Therefore, in this work, we have charac- the metabolism of the seeds toward recapitulating facets of seed terized sugarbeet seed¶ vigor by proteomics. This was challeng- development and provided insights into complex behaviors such as ing, however, because there are virtually no genomics data germination.
    [Show full text]