医学参考书目1016cyclic nucleotide sign

1、Methods inMolecular Biology 1016Chris GehringEditorCyclic Nucleotide Signaling in PlantsMethods and ProtocolsSeries EditorJohn M. Walker School of Life SciencesUniversity of Hertfordshire Hatfield, Hertfordshire, AL10 9AB, UKFor further volumes:METHODS IN MOLECULAR BIOLOGY Cyclic Nucleotide Signalin

2、g in PlantsMethods and ProtocolsEdited byChris GehringDivision of Chemical and Life Sciences and Engineering,King Abdullah University of Science and Technology, Thuwal, Saudi ArabiaEditorChris GehringDivision of Chemical and Life Sciences and Engineering King Abdullah University of Science and Techn

3、ology Thuwal, Saudi ArabiaISSN 1064-3745ISBN 978-1-62703-440-1ISSN 1940-6029 (electronic)ISBN 978-1-62703-441-8 (eBook)DOI 10.1007/978-1-62703-441-8Springer New York Heidelberg Dordrecht LondonLibrary of Congress Control Number: 2013937953© Springer Science+Business Media New York 2013This work

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9、r can accept any legal responsibility for any errors or omissions that may be. The publisher makes no warranty, express or implied, with respect to the material contained herein.Printed on acid-paperHumana Press is a brand of SpringerSpringer is part of Springer Science+Business Media ()PrefaceUnder

10、standing how whole organisms, tissues, and cells perceive and process signals has given rise to the biological discipline of “Signal Transduction.” Signal transduction research in turn is rapidly evolving not least due to novel and improved analytical methods that have led to an increase in our unde

11、rstanding of the molecular mechanisms underlying cellularsignaling. Progress has beenboth at the level of single-component analysis and in vivoimaging that can reveal rapid changes at the cellular level as well as at the systems level where transcriptomics and phosphoproteomics, in particular, affor

12、d a window into complex biological responses including long-term adaptive responses.The last two decades have seen a growing interest in cyclic nucleotide research in plants with an emphasis on the elucidation of the roles of cGMP and, perhaps to a lesser extent,cAMP. Here weboth established and nov

13、el techniques and approaches to betterunderstand the biological role of this important signaling system. Chapter 1 summarizesmajor trends in plant signal transduction and cyclic nucleotide research with an emphasis on molecular methods. The subsequent chapters cover two major themes. The first is ce

14、n- tered around the detection and qu fication of cyclic nucleotides and the discovery and characterization of novel nucleotide cyclases as well as experimental procedures to elucidate cyclic nucleotide-dependent cellular processes (Chapters 212). The second main theme covers bioinformatic methods to

15、 identify candidate nucleotide cyclases and cyclic nucle-otide-gated channels. In addition, we alsoa computational method to infer biologicalfunctions of candidate nucleotide cyclases (Chapters 1315).Further to the above-mentioned themes, one chapter is dedicated to methods for iden-tifying and char

16、acterizing cyclic nucleotide phosphodiesterases that obviously play animportant part in cyclic nucleotide signaling and cyclic nucleotide homeostasis (Chapter 16). Additionally, two chapters on the measurement of reactive oxygen species and nitric oxide in plant tissues have been included since thes

17、e compounds are critical components of biotic and abiotic plant stress responses and are associated with cyclic nucleotide transientsas well as downstream responses (Chapters 17, 18). The final chapter (Chapter 19)a method that allows the qufication of photosynthetic responses to cyclic nucleotides.

18、sThuwal, Saudi ArabiaChris GehringvContentsPreface. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .Contributors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .v ix1Mo

19、lecular Methods for the Study of Signal Transduction in Plants . . . . . . . . .Helen R. Irving and Chris GehringRecombinant Expression and Functional Testingof Candidate Adenylate Cyclase Domains . . . . . . . . . . . . . . . . . . . . . . . . . . . .Oziniel Ruzvidzo, Bridget T. Dikobe, David T. Ka

20、wadza,Grace H. Mabadahanye, Patience Chatukuta, and Lusisizwe Kwezi12133Qufication of Cyclic Dinucleotides by Reversed-Phase LC-MS/MS . . . . . .27Heike Burhenne and Volkhard Kaever4Determination of ADP-Ribosyl Cyclase Activity, Cyclic ADP-Ribose,and Nicotinic Acid Adenine Dinucleotide Phosphate in

21、Tissue Extracts . . . . . .Richard M. Graeff and Hon Cheung LeeIn Vivo Imaging of cGMP in Plants . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .Jean-Charles Isner and Frans J.M. MaathuisCharacterization of Heterologously Expressed Transporter Genes by Patch- and Voltage-Clamp Methods

22、: Applicationto Cyclic Nucleotide-Dependent Responses. . . . . . . . . . . . . . . . . . . . . . . . . . .Fouad Lemtiri-Chlieh and Rashid AliNoninvasive Microelectrode Ion Flux Estimation Technique (MIFE) for the Study of the Regulation of Root Membrane Transportby Cyclic Nucleotides . . . . . . . .

23、 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .Natalia Maria Ordoñez, Lana Shabala, Chris Gehring, and Sergey ShabalaCalcium Imaging of the Cyclic Nucleotide Response. . . . . . . . . . . . . . . . . . . .Martin R. McAinsh, Stephen K. Roberts, and Lyudmila V. Dubovskaya39

24、55766779581079Identification and Qutation of Signal Molecule-Dependent ProteinPhosphorylation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .Arnoud Groen, Ludivine Thomas, Kathryn Lilley, and Claudius Marondedze12110Comparative Gel-Based Phosphoproteomic

25、s in Responseto Signaling Molecules . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .Claudius Marondedze, Kathryn Lilley, and Ludivine Thomas13911An AffiPull-Down Approach to Identify the Plant CyclicNucleotide Interactome . . . . . . . . . . . . . . . . . . . . . .

26、 . . . . . . . . . . . . . . . . . . .Lara Donaldson and Stuart Meier155viiviiiContents12Structural and Functional Characterization of Receptor Kinaseswith Nucleotide Cyclase Activity . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .Victor Muleya, Janet I. Wheeler, and Helen R. I

27、rvingComputational Identification of Candidate Nucleotide Cyclasesin Higher Plants . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .Aloysius Wong and Chris GehringIdentification of Cyclic Nucleotide Gated ChannelsUsing Regular Expressions . . . . . . . . .

28、 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .K. Zelman, Adam Dawe, and Gerald A. BerkowitzInferring Biological Functions of Guanylyl Cyclaseswith Computational Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .May Alqurashi and Stuart MeierIdentification

29、 and Characterization of Cyclic NucleotidePhosphodiesterases . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .Erin B. Purcell and Rita TamayoDetection of Reactive Oxygen Species Downstreamof Cyclic Nucleotide Signals in Plants . . . . . . . . . . . . . . . . .

30、 . . . . . . . . . . . . . .Robin K. Walker and Gerald A. BerkowitzMeasurement of Nitric Oxide in Plant Tissue Using Difluorofluoresceinand Oxyhemoglobin . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .Ndiko LudidiInfrared Gas Analysis Technique for the Study o

31、f the Regulationof Photosynthetic Responses . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .Alex Valentine, Oziniel Ruzvidzo, Aleysia Kleinert, Yun Kang, and Vagner Bennedito17513195142071522516235172451825319261Index . . . . . . . . . . . . . . . . . . . . . . . . . . . .

32、 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .271ContributorsRASHID ALI Center for Vascular Biology, University of Connecticut Health Center, Farton, CT, USAMAY ALQURASHI Division of Chemical and Life Sciences and Engineering,King Abdullah University of Science and Technology

33、, Thuwal, Saudi ArabiaVAGNER BENNEDITO Genetics and Developmental Biology Program, Division of Plant and Soil Sciences, West Virginia University, Morgantown, WV, USAGERALD A. BERKOWITZ Agricultural Biotechnology Laboratory, Department of PlantScience, University of Connecticut, Storrs, CT, USAHEIKE

34、BURHENNE Research Core Unit for Mass Spectrometry - Metabolomics, Institute of Pharmacology, Hannover Medical School, Hannover, GermanyPATIENCE CHATUKUTA Department of Biological Sciences, School of Environmental andHealth Sciences, North-West University, Mmabatho, South AfricaADAM DAWE Division of

35、Computer, Electrical and Mathematical Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi ArabiaBRIDGET T. DIKOBE Department of Biological Sciences, School of Environmental andHealth Sciences, North-West University, Mmabatho, South AfricaLARA DONALDSON Divisio

36、n of Chemical and Life Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi ArabiaLYUDMILA V. DUBOVSKAYA Institute of Biophysics and Cell Engineering, National Academyof Sciences of Belarus, Minsk, BelarusCHRIS GEHRING Division of Chemical and Life Sciences and

37、 Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi ArabiaRICHARD M. GRAEFF Department of Physiology, The University of,ARNOUD GROEN Department of Biochemistry, Cambridge Centre for Proteomics, Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UKHELEN

38、R. IRVING Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, AustraliaJEAN-CHARLES ISNER Guard Cell Group, University of Bristol, Bristol, UKVOLKHARD KAEVER Research Core Unit for Mass Spectrometry - Metabolomics, Institute of Pharmacology, Hannover Medical School, Hanno

39、ver, GermanyYUN KANG Plant Biology Division, Samuel Roberts Noble Foundation, Ardmore,OK, USADAVID T. KAWADZA Department of Biological Sciences, School of Environmental and Health Sciences, North-West University, Mmabatho, South AfricaALEYSIA KLEINERT Botany and Zoology Department, Faculty of Scienc

40、e, University ofStellenbosch, Matieland, South AfricaixxContributorsLUSISIZWE KWEZI Department of Biological Sciences, School of Environmental and Health Sciences, North-West University, Mmabatho, South AfricaHON CHEUNG LEE Department of Physiology, The University of,FOUAD LEMTIRI-CHLIEH Division of

41、 Chemical and Life Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi ArabiaKATHRYN LILLEY Department of Biochemistry, Cambridge Centre for Proteomics,Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UKNDIKO LUDIDI Department of Biotechno

42、logy, University of the Western Cape, Belville, South AfricaFRANS J.M. MAATHUIS Biology Department, University of York, York, UKGRACE H. MABADAHANYE Department of Biological Sciences, School of Environmental and Health Sciences, North-West University, Mmabatho, South AfricaMARTIN R. MCAINSH Lancaste

43、r Environment Centre, Lancaster University,Lancaster, UKCLAUDIUS MARONDEDZE Division of Chemical and Life Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi ArabiaSTUART MEIER Division of Chemical and Life Sciences and Engineering, King AbdullahUniversity of

44、Science and Technology, Thuwal, Saudi ArabiaVICTOR MULEYA Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, AustraliaNATALIA MARIA ORDOÑEZ Division of Chemical and Life Sciences and Engineering,King Abdullah University of Science and Technology, Thuwal, Saudi Arabi

45、aERIN B. PURCELL Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USASTEPHEN K. ROBERTS Biomedical and Life Sciences Division, Lancaster University,Lancaster, UKOZINIEL RUZVIDZO Department of Biological Sciences, School of Environmental and Hea

46、lth Sciences, North-West University, Mmabatho, South AfricaLANA SHABALA School of Agricultural Science, University of Tasmania, Hobart,TAS, AustraliaSERGEY SHABALA School of Agricultural Science, University of Tasmania, Hobart, TAS, AustraliaRITA TAMAYO Department of Microbiology and Immunology, Uni

47、versity of North Carolina,Chapel Hill, NC, USALUDIVINE THOMAS Division of Chemical and Life Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi ArabiaALEX VALENTINE Botany and Zoology Department, Faculty of Science, University ofStellenbosch, Matieland, South

48、AfricaROBIN K. WALKER Department of Physiology and Biophysics, College of Medicine, Howard University, Washington, DC, USAJANET I. WHEELER Monash Institute of Pharmaceutical Sciences, Monash University,Parkville, VIC, AustraliaALOYSIUS WONG Division of Chemical and Life Sciences and Engineering, Kin

49、g Abdullah University of Science and Technology, Thuwal, Saudi ArabiaK. ZELMAN Agricultural Biotechnology Laboratory, Department of Plant Science,University of Connecticut, Storrs, CT, USAChapter 1Molecular Methods for the Study of Signal Transduction in PlantsHelen R. Irving and Chris GehringAbstra

50、ctNovel and improved analytical methods have led to a rapid increase in our understanding of the molecular mechanism underlying plant signal transduction. Progress has beenboth at the level of single-component analysis and in vivo imaging as well as at the systems level where transcriptomics and par

51、ticularly phosphopro- teomics afford a window into complex biological responses. Here we review the role of the cyclic nucleotides cAMP and cGMP in plant signal transduction as well as the discovery and biochemical and biological charac- terization of an increasing number of complex multi-domain nuc

52、leotide cyclases that catalyze the synthesis of cAMP and cGMP from ATP and GTP, respectively.Key words Plant signal transduction, Receptors, Second messengers, In vivo imaging, Systems analysis, cAMP, cGMP, Nucleotide cyclases1Signal Transduction: From Single-Component Imaging to Systems ApproachesT

53、he perception of environmental and intracellular stimuli or signals is an essential feature of living systems. When such signals are received, they need to be processed and transmitted in a tempo- rally and spatially controlled manner so that the cells can respond appropriately in the short term, fo

54、r instance with change of ion channel activities, and/or adapt with an altered transcriptional and translational program. An ever-increasing body of research centers around the question of signal processing and transduction in bio- logical systems. The methods used in these studies have greatly adva

55、nced in the last few decades both at the level of the study of structural and functional features of single components or interac- tions between individual molecules as well as at the systems level. NMR and X-ray crystallography studies as well as molecular imag-ing have and will yield increasinglye

56、d information about themolecular mechanism of signaling processes while bioinformaticapproaches and system-level studies, particularly phosphopro- teomic, will continue to enable the study of signaling processes atChris Gehring (ed.), Cyclic Nucleotide Signaling in Plants: Methods and Protocols, Met

57、hods in Molecular Biology, vol. 1016, DOI 10.1007/978-1-62703-441-8_1, © Springer Science+Business Media New York 201312Helen R. Irving and Chris GehringFig. 1 Overview of nucleotide cyclase (NC)- and cyclic nucleotide (CN)-dependent pathwaysthe whole cell, tissue, or organ level. Given that signaling is a dynamic process, in vivo imaging has an important role in signal transduction research, and real-time resolution of second messen- gers such as calcium (Ca2+) and cyclic nucleotides continues to pro- vide new insights into complex signaling events.Her