Cyclic Nucleotide Signaling in Plants: Methods and Protocols

272 Pages·2013·4.101 MB·English

by  Helen R. Irving, Chris Gehring (auth.), Chris Gehring (eds.)

Methods in
Molecular Biology 1016
Chris Gehring Editor
Cyclic Nucleotide
Signaling in Plants
Methods and Protocols
M M B ™
ETHODS IN OLECULAR IOLOGY
Series Editor
John M. Walker
School of Life Sciences
University of Hertfordshire
Hat fi eld, Hertfordshire, AL10 9AB, UK
For further volumes:
http://www.springer.com/series/7651

Cyclic Nucleotide Signaling

in Plants
Methods and Protocols
Edited by
Chris Gehring
Division of Chemical and Life Sciences and Engineering,
King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
Editor
Chris Gehring
Division of Chemical and Life Sciences and Engineering
King Abdullah University of Science and Technology
Thuwal, Saudi Arabia
ISSN 1064-3745 ISSN 1940-6029 (electronic)
ISBN 978-1-62703-440-1 ISBN 978-1-62703-441-8 (eBook)
DOI 10.1007/978-1-62703-441-8
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Preface
Understanding 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 understanding of the molecular mechanisms underlying cellular
signaling. Progress has been made both at the level of single-component analysis and in vivo
imaging that can reveal rapid changes at the cellular level as well as at the systems level
where transcriptomics and phosphoproteomics, in particular, afford 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 we detail both established and novel techniques and approaches to better
understand the biological role of this important signaling system. Chapter 1 summarizes
major trends in plant signal transduction and cyclic nucleotide research with an emphasis
on molecular methods. The subsequent chapters cover two major themes. The fi rst is cen-
tered around the detection and quantifi cation 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 2 – 12 ). The second main theme
covers bioinformatic methods to identify candidate nucleotide cyclases and cyclic nucle-
otide-gated channels. In addition, we also detail a computational method to infer biological
functions of candidate nucleotide cyclases (Chapters 1 3 – 15 ).
Further to the above-mentioned themes, one chapter is dedicated to methods for iden-
tifying and characterizing cyclic nucleotide phosphodiesterases that obviously play an
important 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 these compounds are critical components of
biotic and abiotic plant stress responses and are associated with cyclic nucleotide transients
as well as downstream responses (Chapters 1 7 , 18 ). The fi nal chapter (Chapter 1 9 ) details
a method that allows the quantifi cation of photosynthetic responses to cyclic nucleotides.
Thuwal, Saudi Arabia Chris Gehring
v

Contents
Preface. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . v
Contributors. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ix
1 Molecular Methods for the Study of Signal Transduction in Plants . . . . . . . . . 1
Helen R. Irving and Chris Gehring
2 Recombinant Expression and Functional Testing
of Candidate Adenylate Cyclase Domains . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
Oziniel Ruzvidzo, Bridget T. Dikobe, David T. Kawadza,
Grace H. Mabadahanye, Patience Chatukuta, and Lusisizwe Kwezi
3 Quantification of Cyclic Dinucleotides by Reversed-Phase LC-MS/MS. . . . . . 27
Heike Burhenne and Volkhard Kaever
4 Determination of ADP-Ribosyl Cyclase Activity, Cyclic ADP-Ribose,
and Nicotinic Acid Adenine Dinucleotide Phosphate in Tissue Extracts. . . . . . 39
Richard M. Graeff and Hon Cheung Lee
5 In Vivo Imaging of cGMP in Plants . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57
Jean-Charles Isner and Frans J.M. Maathuis
6 Characterization of Heterologously Expressed Transporter Genes
by Patch- and Voltage-Clamp Methods: Application
to Cyclic Nucleotide-Dependent Responses. . . . . . . . . . . . . . . . . . . . . . . . . . . 67
Fouad Lemtiri-Chlieh and Rashid Ali
7 Noninvasive Microelectrode Ion Flux Estimation Technique (MIFE)
for the Study of the Regulation of Root Membrane Transport
by Cyclic Nucleotides . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 95
Natalia Maria Ordoñez, Lana Shabala, Chris Gehring, and Sergey Shabala
8 Calcium Imaging of the Cyclic Nucleotide Response. . . . . . . . . . . . . . . . . . . . 107
Martin R. McAinsh, Stephen K. Roberts, and Lyudmila V. Dubovskaya
9 Identification and Quantitation of Signal Molecule-Dependent Protein
Phosphorylation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 121
Arnoud Groen, Ludivine Thomas, Kathryn Lilley,
and Claudius Marondedze
10 Comparative Gel-Based Phosphoproteomics in Response
to Signaling Molecules . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 139
Claudius Marondedze, Kathryn Lilley, and Ludivine Thomas
11 An Affinity Pull-Down Approach to Identify the Plant Cyclic
Nucleotide Interactome . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 155
Lara Donaldson and Stuart Meier
vii
viii Contents
12 Structural and Functional Characterization of Receptor Kinases
with Nucleotide Cyclase Activity. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 175
Victor Muleya, Janet I. Wheeler, and Helen R. Irving
13 Computational Identification of Candidate Nucleotide Cyclases
in Higher Plants . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 195
Aloysius Wong and Chris Gehring
14 Identification of Cyclic Nucleotide Gated Channels
Using Regular Expressions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 207
Alice K. Zelman, Adam Dawe, and Gerald A. Berkowitz
15 Inferring Biological Functions of Guanylyl Cyclases
with Computational Methods. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 225
May Alqurashi and Stuart Meier
16 Identification and Characterization of Cyclic Nucleotide
Phosphodiesterases . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 235
Erin B. Purcell and Rita Tamayo
17 Detection of Reactive Oxygen Species Downstream
of Cyclic Nucleotide Signals in Plants . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 245
Robin K. Walker and Gerald A. Berkowitz
18 Measurement of Nitric Oxide in Plant Tissue Using Difluorofluorescein
and Oxyhemoglobin. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 253
Ndiko Ludidi
19 Infrared Gas Analysis Technique for the Study of the Regulation
of Photosynthetic Responses. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 261
Alex Valentine, Oziniel Ruzvidzo, Aleysia Kleinert,
Yun Kang, and Vagner Bennedito
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 271
Contributors
RASHID ALI (cid:129) Center for Vascular Biology, University of Connecticut Health Center,
Farmington, CT, USA
MAY ALQURASHI (cid:129) Division of Chemical and Life Sciences and Engineering,
King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
VAGNER BENNEDITO (cid:129) Genetics and Developmental Biology Program, Division of Plant
and Soil Sciences, West Virginia University, Morgantown, WV , USA
GERALD A. B ERKOWITZ (cid:129) Agricultural Biotechnology Laboratory, Department of Plant
Science, University of Connecticut, Storrs , CT , USA
HEIKE BURHENNE (cid:129) Research Core Unit for Mass Spectrometry - Metabolomics,
Institute of Pharmacology, Hannover Medical School, Hannover, Germany
PATIENCE CHATUKUTA (cid:129) Department of Biological Sciences, School of Environmental and
Health Sciences, North-West University , Mmabatho, South Africa
ADAM DAWE (cid:129) Division of Computer, Electrical and Mathematical Sciences
and Engineering, King Abdullah University of Science and Technology,
Thuwal, Saudi Arabia
BRIDGET T. DIKOBE (cid:129) Department of Biological Sciences, School of Environmental and
Health Sciences, North-West University , Mmabatho, South Africa
LARA DONALDSON (cid:129) Division of Chemical and Life Sciences and Engineering,
King Abdullah University of Science and Technology, Thuwal , Saudi Arabia
LYUDMILA V. DUBOVSKAYA (cid:129) Institute of Biophysics and Cell Engineering, National Academy
of Sciences of Belarus, M insk , Belarus
CHRIS GEHRING (cid:129) Division of Chemical and Life Sciences and Engineering,
King Abdullah University of Science and Technology, Thuwal , Saudi Arabia
RICHARD M. G RAEFF (cid:129) Department of Physiology, The University of Hong Kong,
Hong Kong, China
ARNOUD GROEN (cid:129) Department of Biochemistry, Cambridge Centre for Proteomics,
Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
HELEN R. IRVING (cid:129) Monash Institute of Pharmaceutical Sciences, Monash University,
Parkville, VIC , Australia
JEAN-CHARLES ISNER (cid:129) Guard Cell Group , University of Bristol, Bristol , UK
VOLKHARD KAEVER (cid:129) Research Core Unit for Mass Spectrometry - Metabolomics,
Institute of Pharmacology, Hannover Medical School, Hannover, Germany
YUN KANG (cid:129) Plant Biology Division, Samuel Roberts Noble Foundation, Ardmore ,
OK , USA
DAVID T. KAWADZA (cid:129) Department of Biological Sciences, School of Environmental
and Health Sciences, North-West University, Mmabatho, South Africa
ALEYSIA KLEINERT (cid:129) Botany and Zoology Department, Faculty of Science, University of
Stellenbosch, Matieland, South Africa
ix