DOCSLIB.ORG

Plant Stress Tolerance Methods and Protocols Second Edition M E T H O D S I N M O L E C U L a R B I O L O G Y

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Plant Stress Tolerance Methods and Protocols Second Edition M E T H O D S I N M O L E C U L a R B I O L O G Y Methods in Molecular Biology 1631 Ramanjulu Sunkar Editor Plant Stress Tolerance Methods and Protocols Second Edition M ETHODS IN M OLECULAR B IOLOGY Series Editor John M. Walker School of Life and Medical Sciences University of Hertfordshire Hatfield, Hertfordshire, AL10 9AB, UK For further volumes: http://www.springer.com/series/7651 Plant Stress Tolerance Methods and Protocols Second Edition Edited by Ramanjulu Sunkar Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK, USA Editor Ramanjulu Sunkar Department of Biochemistry and Molecular Biology Oklahoma State University Stillwater, OK, USA ISSN 1064-3745 ISSN 1940-6029 (electronic) Methods in Molecular Biology ISBN 978-1-4939-7134-3 ISBN 978-1-4939-7136-7 (eBook) DOI 10.1007/978-1-4939-7136-7 Library of Congress Control Number: 2017942931 © Springer Science+Business Media LLC 2017 This work is subject to copyright. All rights are reserved by the Publisher, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilms or in any other physical way, and transmission or information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed. The use of general descriptive names, registered names, trademarks, service marks, etc. in this publication does not imply, even in the absence of a specific statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use. The publisher, the authors and the editors are safe to assume that the advice and information in this book are believed to be true and accurate at the date of publication. Neither the publisher nor the authors or the editors give a warranty, express or implied, with respect to the material contained herein or for any errors or omissions that may have been made. The publisher remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. Printed on acid-free paper This Humana Press imprint is published by Springer Nature The registered company is Springer Science+Business Media LLC The registered company address is: 233 Spring Street, New York, NY 10013, U.S.A. Preface The first edition of Plant Stress Tolerance: Methods and Protocols under the series of Methods in Molecular Biology was published in 2010. We were very gratified with its popularity. In the first edition all pertinent protocols could not be accommodated and also the fact that Plant Biology has witnessed a fast pace of molecular research over the last few years is the motivation to bring the second edition. Given the more frequent episodes of drought, increasing heat or cold as well as saline-­­ affected areas throughout the world, probing plant responses to abiotic stresses has become one of the top priority research areas now. This second edition begins with review chapters: Besides an updated review on oxidative stress responses newly emerging areas such as epi- genetics, long noncoding RNAs, and microbiome in adaptation to abiotic stresses were included. The protocols included are genetic screens, quantifying in vivo molecular interac- tions, identifying DNA methylation and histone modifications, identifying stress-responsive genes that are differentially translated, proteomics, phosphoproteomics, posttranslational redox modifications, metabolomics, and lipidomics. Additionally, the protocols on deter- mining sulfate, sulfite, thiosulfate, sulfolipids, and enzymes associated with sulfite toxicity as well as glutathione were included. The remaining methodology chapters cover a wide range of topics such as distinguishing superoxide dismutases, determining polyamines, quantifying ABA levels, silencing stress-responsive microRNAs, and identifying microbes that promote drought tolerance. I hope that this volume meets the demands of both new and established researchers who are interested in this area of plant biology research. I thank the contributors who are instrumental in bringing this volume. I also thank Prof. John Walker, who gave me the opportunity to edit the second edition. Finally I also thank Prof. John Gustafson, Head, Department of Biochemistry and Molecular Biology, Oklahoma State University, for his encouragement to take up this task. Stillwater, OK, USA Ramanjulu Sunkar v Contents Preface.......................................................... v Contributors .......................................................... xi PART I REVIEW CHAPTERS 1 Epigenetics and RNA Processing: Connections to Drought, Salt, and ABA? ................................................ 3 Min May Wong, Geeng Loo Chong, and Paul E. Verslues 2 The Fundamental Role of Reactive Oxygen Species in Plant Stress Response................................................ 23 Michael Liebthal and Karl-Josef Dietz 3 The Role of Long Noncoding RNAs in Plant Stress Tolerance............. 41 Yuepeng Song and Deqiang Zhang 4 Toward a Resilient, Functional Microbiome: Drought Tolerance-Alleviating Microbes for Sustainable Agriculture . 69 Venkatachalam Lakshmanan, Prasun Ray, and Kelly D. Craven PART II METHODOLOGY CHAPTERS 5 Mining and Quantifying In Vivo Molecular Interactions in Abiotic Stress Acclimation...................................... 87 Thorsten Seidel and Derya Kirasi 6 Generation of a Stress-Inducible Luminescent Arabidopsis and Its Use in Genetic Screening for Stress-Responsive Gene Deregulation Mutants ..... 109 Si-in Yu and Byeong-ha Lee 7 Detection of Differential DNA Methylation Under Stress Conditions Using Bisulfite Sequence Analysis .................................. 121 Ibtisam Al Harrasi, Rashid Al-Yahyai, and Mahmoud W. Yaish 8 ChIP-Seq Analysis for Identifying Genome-Wide Histone Modifications Associated with Stress-Responsive Genes in Plants...................... 139 Guosheng Li, Guru Jagadeeswaran, Andrew Mort, and Ramanjulu Sunkar 9 Isolation of Polysomal RNA for Analyzing Stress- Responsive Genes Regulated at the Translational Level in Plants .................... 151 Yong-Fang Li, Ramamurthy Mahalingam, and Ramanjulu Sunkar 10 Global Proteomic Profiling and Identification of Stress- Responsive Proteins Using Two-Dimensional Gel Electrophoresis ......................... 163 Pragya Barua, Dipak Gayen, Nilesh Vikram Lande, Subhra Chakraborty, and Niranjan Chakraborty 11 Phosphoproteomics Analysis for Probing Plant Stress Tolerance ........... 181 Christof Rampitsch vii viii Contents 12 Probing Posttranslational Redox Modifications ........................ 195 Patrick Treffon, Michael Liebthal, Wilena Telman, and Karl-Josef Dietz 13 Zymographic Method for Distinguishing Different Classes of Superoxide Dismutases in Plants ................................. 221 Ashwini R. Jamdhade, Ramanjulu Sunkar, and Vandana K. Hivrale 14 Determination of Enzymes Associated with Sulfite Toxicity in Plants: Kinetic Assays for SO, APR, SiR, and In-Gel SiR Activity 229 Galina Brychkova, Assylay Kurmanbayeva, Aizat Bekturova, Inna Khozin, Dominic Standing, Dmitry Yarmolinsky, and Moshe Sagi 15 Determination of Total Sulfur, Sulfate, Sulfite, Thiosulfate, and Sulfolipids in Plants ......................................... 253 Assylay Kurmanbayeva, Galina Brychkova, Aizat Bekturova, Inna Khozin, Dominic Standing, Dmitry Yarmolinsky, and Moshe Sagi 16 Determining Glutathione Levels in Plants ............................ 273 Smita Sahoo, Jay Prakash Awasthi, Ramanjulu Sunkar, and Sanjib Kumar Panda 17 Porous Graphitic Carbon Liquid Chromatography–Mass Spectrometry Analysis of Drought Stress-Responsive Raffinose Family Oligosaccharides in Plant Tissues 279 Tiago F. Jorge, Maria H. Florêncio, and Carla António 18 Profiling Abscisic Acid-Induced Changes in Fatty Acid Composition in Mosses .................................................... 295 Suhas Shinde, Shivakumar Devaiah, and Aruna Kilaru 19 Detection of Free Polyamines in Plants Subjected to Abiotic Stresses by High-Performance Liquid Chromatography (HPLC) ................. 305 Xiaoqing Gong and Ji-Hong Liu 20 Determination of Polyamines by Dansylation, Benzoylation, and Capillary Electrophoresis ..................................... 313 Gounipalli Veeranagamallaiah and Chinta Sudhakar 21 Rapid Quantification of Abscisic Acid by GC-MS/MS for Studies of Abiotic Stress Response........................................ 325 Paul E. Verslues 22 Silencing of Stress-Regulated miRNAs in Plants by Short Tandem Target Mimic (STTM) Approach .................................. 337 Sachin Teotia and Guiliang Tang 23 Rhizosphere Sampling Protocols for Microbiome (16S/18S/ITS rRNA) Library Preparation and Enrichment for the Isolation of Drought Tolerance-Promoting Microbes.................................... 349 Venkatachalam Lakshmanan, Prasun Ray, and Kelly D. Craven Index........................................................... 363 Contributors IBTISAM AL HARRASI • Department of Biology, College of Science, Sultan Qaboos University, Muscat, Oman RASHID AL-YAHYAI • Department of Crop Science, College of Agriculture and Marine Sciences, Sultan Qaboos University, Muscat, Oman CARLA ANTÓNIO • Plant Metabolomics Laboratory, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB-UNL), Oeiras, Portugal JAY PRAKASH AWASTHI • Department of Life Science and Bioinformatics, Plant Molecular Biotechnology Laboratory, Assam University, Silchar, Assam, India PRAGYA BARUA • National
Load more

Recommended publications
  • GLUTATHIONE TRANSFERASE N STRUCTURE and GENE REGULATION
    GLUTATHIONE TRANSFERASE n STRUCTURE AND GENE REGULATION By Chu-Lin Xia This report is in part-fulfillment of the requirements for the degree of doctor of philosophy in the University of London University College, University of London January 1992 ProQuest Number: 10609162 All rights reserved INFORMATION TO ALL USERS The quality of this reproduction is dependent upon the quality of the copy submitted. In the unlikely event that the author did not send a com plete manuscript and there are missing pages, these will be noted. Also, if material had to be removed, a note will indicate the deletion. uest ProQuest 10609162 Published by ProQuest LLC(2017). Copyright of the Dissertation is held by the Author. All rights reserved. This work is protected against unauthorized copying under Title 17, United States C ode Microform Edition © ProQuest LLC. ProQuest LLC. 789 East Eisenhower Parkway P.O. Box 1346 Ann Arbor, Ml 48106- 1346 ABSTRACT In the early stage of this research, amino acid residues that are essential for the activity of human pi class glutathione transferase (GST n) were identified using chemical modification with group-specific reagents. Protection from inactivation by substrates, substrate analogues and inhibitors was used as the criterion for active site specificity. The results suggested the apparent involvement of one cysteine (Cys), one lysine (Lys), one arginine (Arg), one histidine (His) or tyrosine (Tyr) or both, one aspartate (Asp) or glutamate (Glu) and tryptophan (Trp) residues in the glutathione binding site (G-site) of GSTtc. It was concluded that without the knowledge of the three-dimensional structure of GST 7i, further work in this area would not be profitable and therefore, attention was turned to the regulation of GST n gene expression.
    [Show full text]
  • United States Patent (19) 11 Patent Number: 5,869,438 Svendsen Et Al
    USOO5869438A United States Patent (19) 11 Patent Number: 5,869,438 Svendsen et al. (45) Date of Patent: Feb. 9, 1999 54) LIPASE WARIANTS 52 U.S. Cl. ......................... 510/226; 435/198; 435/69.1; 435/252.3; 435/320.1; 435/196; 536/23.2; 75 Inventors: Allan Svendsen, Birkerød; Shamkant 536/23.7; 530/350; 510/392; 510/305 Anant Patkar, Lyngby; Erik Gormsen, 58 Field of Search ..................................... 435/198, 196, Virum; Jens Sigurd Okkels; Marianne 435/187-188, 69.1, 252.3, 320.1, 71.1; Thellersen, both of Frederiksberg, all of 424/94.1; 536/22.2, 23.7; 510/305, 226, Denmark 392 73 Assignee: Novo Nordisk A/S, Bagsvaerd, 56) References Cited Denmark FOREIGN PATENT DOCUMENTS 21 Appl. No.: 479,275 O305 216 A1 3/1989 European Pat. Off.. O 407 225A1 1/1991 European Pat. Off.. 22 Filed: Jun. 7, 1995 WO95/09909 4/1995 WIPO. Related U.S. Application Data Primary Examiner Robert A. Wax ASSistant Examiner Tekchand Saidha 63 Continuation-in-part of PCT/DK94/00162, Apr. 22, 1994, which is a continuation-in-part of PCT/DK95/00079, Feb. Attorney, Agent, or Firm-Steve T. Belson; Elias J. 27, 1995, which is a continuation-in-part of Ser. No. 434, Lambiris 904, May 1, 1995, abandoned, which is a continuation of Ser. No. 977,429, which is a continuation of PCT/DK91/ 57 ABSTRACT 00271, Sep. 13, 1991, abandoned. The present invention relates to lipase variants which exhibit 30 Foreign Application Priority Data improved properties, detergent compositions comprising Said lipase variants, DNA constructs coding for Said lipase Sep.
    [Show full text]
  • The Role of the Rho Gtpases in Neuronal Development
    Downloaded from genesdev.cshlp.org on September 24, 2021 - Published by Cold Spring Harbor Laboratory Press REVIEW The role of the Rho GTPases in neuronal development Eve-Ellen Govek,1,2, Sarah E. Newey,1 and Linda Van Aelst1,2,3 1Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, 11724, USA; 2Molecular and Cellular Biology Program, State University of New York at Stony Brook, Stony Brook, New York, 11794, USA Our brain serves as a center for cognitive function and and an inactive GDP-bound state. Their activity is de- neurons within the brain relay and store information termined by the ratio of GTP to GDP in the cell and can about our surroundings and experiences. Modulation of be influenced by a number of different regulatory mol- this complex neuronal circuitry allows us to process that ecules. Guanine nucleotide exchange factors (GEFs) ac- information and respond appropriately. Proper develop- tivate GTPases by enhancing the exchange of bound ment of neurons is therefore vital to the mental health of GDP for GTP (Schmidt and Hall 2002); GTPase activat- an individual, and perturbations in their signaling or ing proteins (GAPs) act as negative regulators of GTPases morphology are likely to result in cognitive impairment. by enhancing the intrinsic rate of GTP hydrolysis of a The development of a neuron requires a series of steps GTPase (Bernards 2003; Bernards and Settleman 2004); that begins with migration from its birth place and ini- and guanine nucleotide dissociation inhibitors (GDIs) tiation of process outgrowth, and ultimately leads to dif- prevent exchange of GDP for GTP and also inhibit the ferentiation and the formation of connections that allow intrinsic GTPase activity of GTP-bound GTPases (Zalc- it to communicate with appropriate targets.
    [Show full text]
  • ROLE of BRAIN SOLUBLE EPOXIDE HYDROLASE in CARDIOVASCULAR FUNCTION by KATHLEEN WALWORTH SELLERS a DISSERTATION PRESENTED TO
    ROLE OF BRAIN SOLUBLE EPOXIDE HYDROLASE IN CARDIOVASCULAR FUNCTION By KATHLEEN WALWORTH SELLERS A DISSERTATION PRESENTED TO THE GRADUATE SCHOOL OF THE UNIVERSITY OF FLORIDA IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY UNIVERSITY OF FLORIDA 2004 Copyright 2004 by Kathleen Walworth Sellers This work is dedicated to my family, who has taught me to embrace life with love, perseverance, and grace. ACKNOWLEDGMENTS I could not have completed this work without the assistance from many colleagues and friends. First and foremost, I would like to thank my mentor, Dr. Mohan Raizada, who has consistently supported and encouraged me these last several years. It was by chance that I worked in his research group before starting my graduate program, and I could not have found a better group with which to work. Dr. Raizada’s excitement and fervor for new ideas have helped shape my appreciation for scientific research and the pursuit of knowledge. I also want to acknowledge all of the members of the Raizada research group, past and present. I am fortunate to work in such a friendly and intellectually-stimulating environment. Specifically, I want to thank Drs. Beverly Falcon and Matthew Huentelman, the two graduate students in our research group who both helped me tremendously. In addition, I would like to thank Drs. Carlos Diez, Cheng-wen Sun, Jorge Vazquez, Shereeni Veerasingham and Hong Yang for all of their intellectual guidance. I greatly acknowledge the members of my committee, Drs. Michael Katovich, Gerard Shaw, Colin Sumners and Charles Wood. Each has provided me with unique experience and expertise to further my research and career.
    [Show full text]
  • Rho Gtpases of the Rhobtb Subfamily and Tumorigenesis1
    Acta Pharmacol Sin 2008 Mar; 29 (3): 285–295 Invited review Rho GTPases of the RhoBTB subfamily and tumorigenesis1 Jessica BERTHOLD2, Kristína SCHENKOVÁ2, Francisco RIVERO2,3,4 2Centers for Biochemistry and Molecular Medicine, University of Cologne, Cologne, Germany; 3The Hull York Medical School, University of Hull, Hull HU6 7RX, UK Key words Abstract Rho guanosine triphosphatase; RhoBTB; RhoBTB proteins constitute a subfamily of atypical members within the Rho fa- DBC2; cullin; neoplasm mily of small guanosine triphosphatases (GTPases). Their most salient feature 1This work was supported by grants from the is their domain architecture: a GTPase domain (in most cases, non-functional) Center for Molecular Medicine Cologne, the is followed by a proline-rich region, a tandem of 2 broad-complex, tramtrack, Deutsche Forschungsgemeinschaft, and the bric à brac (BTB) domains, and a conserved C-terminal region. In humans, Köln Fortune Program of the Medical Faculty, University of Cologne. the RhoBTB subfamily consists of 3 isoforms: RhoBTB1, RhoBTB2, and RhoBTB3. Orthologs are present in several other eukaryotes, such as Drosophi- 4 Correspondence to Dr Francisco RIVERO. la and Dictyostelium, but have been lost in plants and fungi. Interest in RhoBTB Phn 49-221-478-6987. Fax 49-221-478-6979. arose when RHOBTB2 was identified as the gene homozygously deleted in E-mail [email protected] breast cancer samples and was proposed as a candidate tumor suppressor gene, a property that has been extended to RHOBTB1. The functions of RhoBTB pro- Received 2007-11-17 Accepted 2007-12-16 teins have not been defined yet, but may be related to the roles of BTB domains in the recruitment of cullin3, a component of a family of ubiquitin ligases.
    [Show full text]
  • The P110 Isoform of Phosphoinositide 3-Kinase Signals Downstream of G
    The p110␤ isoform of phosphoinositide 3-kinase signals downstream of G protein-coupled receptors and is functionally redundant with p110␥ Julie Guillermet-Guibert*, Katja Bjorklof*, Ashreena Salpekar*, Cristiano Gonella*, Faruk Ramadani†, Antonio Bilancio*, Stephen Meek‡, Andrew J. H. Smith‡, Klaus Okkenhaug†, and Bart Vanhaesebroeck*§ *Center for Cell Signaling, Institute of Cancer, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, United Kingdom; †Laboratory of Lymphocyte Signaling and Development, Babraham Institute, Cambridge CB2 3AT, United Kingdom; and ‡Gene Targeting Laboratory, The Institute for Stem Cell Research, University of Edinburgh, West Mains Road, Edinburgh EH9 3JQ, United Kingdom Edited by Peter K. Vogt, The Scripps Research Institute, La Jolla, CA, and approved April 7, 2008 (received for review August 16, 2007) The p110 isoforms of phosphoinositide 3-kinase (PI3K) are acutely embryonic lethality of the p110␤ KO mice and the fact that regulated by extracellular stimuli. The class IA PI3K catalytic sub- proliferating cells could not be derived from these embryos (2). units (p110␣, p110␤, and p110␦) occur in complex with a Src Recent progress has been made by the generation of small- homology 2 (SH2) domain-containing p85 regulatory subunit, molecule inhibitors with selectivity for p110␤, allowing scientists which has been shown to link p110␣ and p110␦ to Tyr kinase to define a role for p110␤ in platelet function and thrombus signaling pathways. The p84/p101 regulatory subunits of the formation (3). Some evidence has also been presented for the p110␥ class IB PI3K lack SH2 domains and instead couple p110␥ to coupling of p110␤ to GPCRs, either by in vitro studies that G protein-coupled receptors (GPCRs).
    [Show full text]
  • Biochemical and Functional Characterization of Rhosap: a Rhogap of the Postsynaptic Density
    Institut für Anatomie and Zellbiologie Direktor: Professor Dr. med. Tobias M. Böckers Biochemical and functional characterization of RhoSAP: A RhoGAP of the postsynaptic density Dissertation zur Erlangung des Doktorgrades Dr. biol. hum. der Medizinischen Fakultät der Universität Ulm Eingereicht von: Janine Dahl aus Ludwigslust 2008 Dekan: Prof. Dr. med. Klaus-Michael Debatin Erster Gutachter: Prof. Dr. med. Tobias M. Böckers Zweiter Gutachter: Prof. Dr. rer. nat. Dietmar Fischer Tag der Promotion: Abstract Biochemical and functional characterization of RhoSAP: A Rho GAP of the postsynaptic density By Janine Dahl Ulm University Glutamatergic synapses in the central nervous system are characterized by an electron dense network of proteins underneath the postsynaptic membrane including cell adhesion molecules, cytoskeletal proteins, scaffolding and adaptor proteins, membrane bound receptors and channels, G-proteins and a wide range of different signalling modulators and effectors. This so called postsynaptic density (PSD) resembles a highly complex signaling machinery. We performed a yeast two-hybrid (YTH) screen with the PDZ domain of the PSD scaffolding molecule ProSAP2/Shank3 as bait and identified a novel interacting protein. This molecule was named after its Rho GAP domain: RhoSAP (Rho GTPase Synapse Associated Protein), which was shown to be active for Cdc42 and Rac1 by a GAP activity assay. Besides its Rho GAP domain, RhoSAP contains an N-terminal BAR domain that might facilitate membrane curvature in endocytic processes. At the C-terminus RhoSAP codes for several proline rich motifs that could possibly act as SH3 binding regions. Therefore, a second YTH screen was carried out with RhoSAP’s proline rich C- terminus as bait to discover putative interacting proteins.
    [Show full text]
  • Expression Profile of Rhogtpases and Rhogefs During RANKL-Stimulated Osteoclastogenesis: Identification of Essential Genes in Osteoclasts
    Expression profile of RhoGTPases and RhoGEFs during RANKL-stimulated osteoclastogenesis: identification of essential genes in osteoclasts. Hélène Brazier, Sébastien Stephens, Stéphane Ory, Philippe Fort, Nigel Morrison, Anne Blangy To cite this version: Hélène Brazier, Sébastien Stephens, Stéphane Ory, Philippe Fort, Nigel Morrison, et al.. Expression profile of RhoGTPases and RhoGEFs during RANKL-stimulated osteoclastogenesis: identification of essential genes in osteoclasts.. Journal of Bone and Mineral Research, American Society for Bone and Mineral Research, 2006, 21 (9), pp.1387-98. 10.1359/jbmr.060613. hal-00189080 HAL Id: hal-00189080 https://hal.archives-ouvertes.fr/hal-00189080 Submitted on 20 Nov 2007 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Revised Manuscript Expression profile of RhoGTPases and RhoGEFs during RANKL-stimulated osteoclastogenesis: identification of essential genes in osteoclasts. Hélène Brazier1,3, Sébastien Stephens1,2,3, Stéphane Ory1, Philippe Fort1, Nigel Morrison2 and Anne Blangy1,4. 1: Centre de Recherches en Biochimie Macromoléculaire, CNRS FRE 2593, Montpellier, FRANCE. 2: School of Medical Science, Griffith University, Queensland, Australia. 3: HB and SS contributed equally to this work. 4: Corresponding author. Anne Blangy. Centre de Recherches en Biochimie Macromoléculaire, CNRS FRE 2593.
    [Show full text]
  • The RHO Family Gtpases: Mechanisms of Regulation and Signaling
    cells Review The RHO Family GTPases: Mechanisms of Regulation and Signaling Niloufar Mosaddeghzadeh and Mohammad Reza Ahmadian * Institute of Biochemistry and Molecular Biology II, Medical Faculty of the Heinrich Heine University, Universitätsstrasse 1, Building 22.03.05, 40225 Düsseldorf, Germany; [email protected] * Correspondence: [email protected] Abstract: Much progress has been made toward deciphering RHO GTPase functions, and many studies have convincingly demonstrated that altered signal transduction through RHO GTPases is a recurring theme in the progression of human malignancies. It seems that 20 canonical RHO GTPases are likely regulated by three GDIs, 85 GEFs, and 66 GAPs, and eventually interact with >70 downstream effectors. A recurring theme is the challenge in understanding the molecular determinants of the specificity of these four classes of interacting proteins that, irrespective of their functions, bind to common sites on the surface of RHO GTPases. Identified and structurally verified hotspots as functional determinants specific to RHO GTPase regulation by GDIs, GEFs, and GAPs as well as signaling through effectors are presented, and challenges and future perspectives are discussed. Keywords: CDC42; effectors; RAC1; RHOA; RHOGAP; RHOGDI; RHOGEF; RHO signaling 1. Introduction Citation: Mosaddeghzadeh, N.; The RHO (RAS homolog) family is an integral part of the RAS superfamily of guanine Ahmadian, M.R. The RHO Family nucleotide-binding proteins. RHO family proteins are crucial for several reasons: (i) ap- GTPases: Mechanisms of Regulation proximately 1% of the human genome encodes proteins that either regulate or are regulated and Signaling. Cells 2021, 10, 1831. by direct interaction with RHO proteins; (ii) they control almost all fundamental cellular https://doi.org/10.3390/cells10071831 processes in eukaryotes including morphogenesis, polarity, movement, cell division, gene expression, and cytoskeleton reorganization [1]; and (iii) they are associated with a series Academic Editor: Bor Luen Tang of human diseases (Figure1)[2].
    [Show full text]
  • Identification and Characterisation of Novel Substrates and Binding Partners of the Asparaginyl Hydroxylase, FIH
    Identification and Characterisation of Novel Substrates and Binding Partners of the Asparaginyl Hydroxylase, FIH Rachel Jane Hampton-Smith B. Sc. (Hons) A thesis submitted in fulfilment of the requirements of the degree of Doctor of Philosophy (Science). September 2015 Discipline of Biochemistry School of Biological Sciences i ii Contents Contents ................................................................................................................................................. iii Figures quick reference ..................................................................................................................... viii Tables quick reference .......................................................................................................................... x Abstract .................................................................................................................................................. xi Declaration .......................................................................................................................................... xiii Acknowledgements ............................................................................................................................. xv Author contributions ......................................................................................................................... xvii 1 Introduction ................................................................................................................................ 1 1.1 Oxygen
    [Show full text]
  • Budding of Ebola Virus Particles Requires The
    The Journal of Infectious Diseases SUPPLEMENT ARTICLE Budding of Ebola Virus Particles Requires the Rab11-Dependent Endocytic Recycling Pathway Asuka Nanbo and Yusuke Ohba Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Sapporo, Japan The Ebola virus-encoded major matrix protein VP40 traffics to the plasma membrane, which leads to the formation of filamentous viral particles and subsequent viral egress. However, the cellular machineries underlying this process are not fully understood. In the present study, we have assessed the role of host endocytic recycling in Ebola virus particle formation. We found that a small GTPase Rab11, which regulates recycling of molecules among the trans-Golgi network, recycling endosomes, and the plasma membrane, was incorporated in Ebola virus-like particles. Although Rab11 predominantly localized in the perinuclear region, it distributed diffusely in the cytoplasm and partly localized in the periphery of the cells transiently expressing VP40. In contrast, Rab11 exhibited a perinuclear distribution when 2 VP40 derivatives that lack ability to traffic to the plasma membrane were expressed. Finally, expression of a dom- inant-negative form of Rab11 or knockdown of Rab11 inhibited both VP40-induced clusters at the plasma membrane and release of viral-like particles. Taken together, our findings demonstrate that Ebola virus exploits host endocytic recycling machinery to facilitate the trafficking of VP40 to the cell surface and the subsequent release of viral-like particles for its
    [Show full text]
  • Carbon Partitioning in Nitrogen-Fixing Root Nodules
    CARBON PARTITIONING IN NITROGEN-FIXING ROOT NODULES Dissertation zur Erlangung des Doktorgrades der Mathematisch-Naturwissenschaftlichen Fakultäten der Georg-August-Universität zu Göttingen vorgelegt von Maria Schubert, geb. Ramenskaia aus St. Petersburg, Russland Göttingen 2002 D 7 Referent: Prof. Dr. Hans-Walter Heldt Korreferentin: Prof. Dr. Christiane Gatz Tag der mündlichen Prüfung: 30.10.2002 Content 1. Introduction.............................................................................................................1 1.1. Degradation of sucrose in sink organs................................................................ 1 1.1.1. The role of sucrose in the plant cell................................................................. 1 1.1.1.1. Sucrose synthase .................................................................................... 2 1.1.1.2. Invertases ................................................................................................ 2 1.2. Transport of sugars ............................................................................................... 4 1.2.1. Phloem loading................................................................................................ 4 1.2.2. Phloem unloading and post-phloem transport................................................. 5 1.2.2.1. Symplastic sugar transport ...................................................................... 5 1.2.2.2. Apoplastic phloem unloading and post-phloem transport........................ 6 1.2.2.3. Sugar transporters in
    [Show full text]