Plant Phosphoproteomics: Methods and Protocols

234 Pages·2015·6.561 MB·English

by  Waltraud X. Schulze (eds.)

Methods in
Molecular Biology 1306
Waltraud X. Schulze Editor
Plant
Phospho-
proteomics
Methods and Protocols
M M B
ETHODS IN OLECULAR IOLOGY
Series Editor
John M. Walker
School of Life and Medical Sciences
University of Hertfordshire
Hatfield, Hertfordshire , AL10 9AB, UK
For further volumes:
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Plant Phosphoproteomics
Methods and Protocols
Edited by
Waltraud X. Schulze
Department of Plant Systems Biology, Universität Hohenheim, Stuttgart, Germany
Editor
Waltraud X . Schulze
Department of Plant Systems Biology
Universität Hohenheim
Stuttgart, Germany
ISSN 1064-3745 ISSN 1940-6029 (electronic)
Methods in Molecular Biology
ISBN 978-1-4939-2647-3 ISBN 978-1-4939-2648-0 (eBook)
DOI 10.1007/978-1-4939-2648-0
Library of Congress Control Number: 2015937355
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Prefa ce
Phosphorylation is one of the most important posttranslational modifi cations involved in
many regulatory processes within living cells. Over the recent decades, proteomic meth-
ods were refi ned to study the signifi cance and dynamics of protein phosphorylation in vari-
ous biological contexts. However, working with plant tissue imposes particular challenges
to the biologist which are attributed to the rigid cell wall making protein extraction more
diffi cult, the skewed protein abundance with Rubisco as a highly abundant protein, and a
large central vacuole leading to low protein yield and increased degradative enzyme activ-
ity. The issue of M ethods in Molecular Biology on “Plant Phosphoproteomics” addresses
recent developments in phosphoproteomic techniques with a particular focus on the plant
system and is particularly designed as a protocol reference book compiled by leading
experts in the fi eld.
Stuttgart, Germany W altraud X . S chulze
v

Contents
Preface. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . v
Contributors. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . i x
1 The Plant Kinome. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
Monika Zulawski and Waltraud X . S chulze
2 Phosphatases in Plants. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
Alois S chweighofer and Irute Meskiene
3 P hosphoproteomics in Cereals. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4 7
Pingfang Yang
4 S creening of Kinase Substrates Using Kinase Knockout Mutants . . . . . . . . . . . 5 9
Taishi Umezawa
5 P hosphopeptide Profiling of Receptor Kinase Mutants . . . . . . . . . . . . . . . . . . 7 1
Xu N a Wu and W altraud X . S chulze
6 C ombining Metabolic 15N Labeling with Improved Tandem
MOAC for Enhanced Probing of the Phosphoproteome. . . . . . . . . . . . . . . . . 81
Martin Thomas , Nicola Huck, Wolfgang Hoehenwarter , U we C onrath ,
and Gerold J. M . B eckers
7 K inase Activity and Specificity Assay Using Synthetic Peptides. . . . . . . . . . . . . 9 7
Xu N a W u and Waltraud X . Schulze
8 Absolute Quantitation of Protein Posttranslational Modification Isoform . . . . 1 05
Zhu Yang and Ning L i
9 P hosphorylation Stoichiometry Determination in Plant
Photosynthetic Membranes. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 121
Björn I ngelsson , Rikard F ristedt , and Maria V. Turkina
10 Phosphopeptide Immuno-Affinity Enrichment to Enhance
Detection of Tyrosine Phosphorylation in Plants. . . . . . . . . . . . . . . . . . . . . . . 135
Sharon C . Mithoe and Frank L. H . M enke
11 T he Peptide Microarray ChloroPhos1.0: A Screening Tool
for the Identification of Arabidopsis thaliana Chloroplast
Protein Kinase Substrates . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 47
Anna S chönberg and Sacha B aginsky
12 P lant Protein Kinase Substrates Identification Using Protein Microarrays . . . . 1 59
Shisong M a and Savithramma P. D inesh-Kumar
13 T argeted Analysis of Protein Phosphorylation by 2D Electrophoresis. . . . . . . . 1 67
Kristin Mayer , S ally A lbrecht , and Andreas Schaller
14 Computational Phosphorylation Network Reconstruction: Methods
and Resources. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 177
Guangyou Duan and Dirk Walther
vii
viii Contents
15 Computational Identification of Protein Kinases and Kinase-Specific
Substrates in Plants. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 195
Han Cheng , Y ongbo Wang , Zexian L iu , and Y u X ue
16 Databases for Plant Phosphoproteomics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 07
Waltraud X. S chulze , Q iuming Y ao , and Dong Xu
17 P hosphorylation Site Prediction in Plants . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 17
Qiuming Yao , Waltraud X . S chulze , and Dong X u
Index. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 229
Contributors
SALLY ALBRECHT • Institute of Plant Physiology and Biotechnology, U niversity of Hohenheim ,
Stuttgart, G ermany
SACHA BAGINSKY • Department of Plant Biochemistry, Institute of Biochemistry and
Biotechnology , M artin-Luther-U niversity Halle-Wittenberg , Halle (Saale), Germany
GEROLD J. M . B ECKERS • Plant Biochemistry and Molecular Biology Group,
Department of Plant Physiology , RWTH Aachen University , A achen, Germany
HAN CHENG • Department of Biomedical Engineering, College of Life Science and
Technology, H uazhong University of Science and Technology , W uhan, H ubei, China
UWE C ONRATH • Plant Biochemistry and Molecular Biology Group, Department of Plant
Physiology, R WTH Aachen University , A achen, G ermany
SAVITHRAMMA P. D INESH-KUMAR • Department of Plant Biology and the Genome Center,
College of Biological Sciences, U niversity of California Davis , D avis , C A , U SA
GUANGYOU DUAN • Max Planck Institute for Molecular Plant Physiology , Potsdam-G olm ,
Germany
RIKARD FRISTEDT • Biophysics of Photosynthesis Physics and Astronomy Faculty of Sciences,
VU University Amsterdam, Amsterdam, The Netherlands
WOLFGANG H OEHENWARTER • Leibniz Institute of Plant Biochemistry , H alle (Saale),
Germany
BJÖRN INGELSSON • Division of Cell Biology, Department of Clinical and Experimental
Medicine, Linköping University , Linköping, S weden
NING LI • Division of Life Science, T he Hong Kong University of Science and Technology ,
Hong Kong, S AR, China
ZEXIAN LIU • Department of Biomedical Engineering, College of Life Science and
Technology, H uazhong University of Science and Technology , W uhan, Hubei, C hina
SHISONG M A • Department of Plant Biology and the Genome Center, College of Biological
Sciences, U niversity of California Davis , Davis, CA , U SA
KRISTIN MAYER • Institute of Plant Physiology and Biotechnology, U niversity of Hohenheim ,
Stuttgart, Germany
FRANK L. H . MENKE • Proteomics, The Sainsbury Laboratory , N orwich, U K
IRUTE MESKIENE • Institute of Biotechnology , University of Vilnius , V ilnius , L ithuania ;
Max F. Perutz Laboratories, University and Medical University of Vienna , V ienna,
Austria
SHARON C. MITHOE • John Innes Centre , Norwich, UK
NICOLA HUCK • Plant Biochemistry and Molecular Biology Group, Department of Plant
Physiology, RWTH Aachen University, Aachen, Germany
ANDREAS SCHALLER • Institute of Plant Physiology and Biotechnology, U niversity of
Hohenheim , S tuttgart, G ermany
ANNA S CHÖNBERG • Department of Plant Biochemistry, Institute of Biochemistry and
Biotechnology , M artin-Luther-U niversity Halle-Wittenberg , Halle (Saale), Germany
WALTRAUD X. S CHULZE • Department of Plant Systems Biology , U niversität Hohenheim ,
Stuttgart, G ermany
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