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practice in this field are constantly changing As new research and experience broaden our understanding, changes in research methods, professional practices, or medical treatment may become necessary Practitioners and researchers must always rely on their own experience and knowledge in evaluating and using any information, methods, compounds, or experiments described herein In using such information or methods they should be mindful of their own safety and the safety of others, including parties for whom they have a professional responsibility To the fullest extent of the law, neither the Publisher nor the authors, contributors, or editors, assume any liability for any injury and/or damage to persons or property as a matter of products liability, negligence or otherwise, or from any use or operation of any methods, products, instructions, or ideas contained in the material herein ISBN: 978-0-12-801922-1 ISSN: 1874-6047 For information on all Academic Press publications visit our website at store.elsevier.com Printed and bound in USA CONTRIBUTORS Hiroo Fukuda Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan Yuki Hirakawa WPI-Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Nagoya, Japan Takato Imaizumi Department of Biology, University of Washington, Seattle, Washington, USA Toshinori Kinoshita Institute of Transformative Bio-Molecules (WPI-ITbM) Nagoya, Japan Yuki Kondo Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan Jiayang Li State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China Chentao Lin Department of Molecular, Cell & Developmental Biology, University of California, Los Angeles, California, USA Yasunori Machida Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya, Japan Makoto Matsuoka Bioscience and Biotechnology Center, Nagoya University, Chikusa Nagoya, Japan Paula Nguyen Department of Molecular, Cell & Developmental Biology, University of California, Los Angeles, California, USA Michiko Sasabe Department of Biology, Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Japan Ken-ichiro Shimazaki Department of Biology, Faculty of Science, Kyushu University, Fukuoka, Japan Kazuo Shinozaki RIKEN Center for Sustainable Resource Science, Tsukuba, Japan ix x Contributors Fuminori Takahashi RIKEN Center for Sustainable Resource Science, Tsukuba, Japan Ken-ichiro Taoka Laboratory of Plant Molecular Genetics, Graduate School of Biological Sciences, Nara Institute of Science and Technology, Nara, Japan Hiroyuki Tsuji Laboratory of Plant Molecular Genetics, Graduate School of Biological Sciences, Nara Institute of Science and Technology, Nara, Japan Miyako Ueguchi-Tanaka Bioscience and Biotechnology Center, Nagoya University, Chikusa Nagoya, Japan Taishi Umezawa Faculty of Agriculture, Tokyo University of Agriculture and Technology, Tokyo, Japan Qin Wang The Basic Forestry and Biotechnology Center, Fujian Agriculture and Forestry University, Fuzhou, China, and Department of Molecular, Cell & Developmental Biology, University of California, Los Angeles, California, USA Xu Wang The Basic Forestry and Biotechnology Center, Fujian Agriculture and Forestry University, Fuzhou, China, and Department of Molecular, Cell & Developmental Biology, University of California, Los Angeles, California, USA Yin Wang Institute for Advanced Research, Nagoya University, and Institute of Transformative BioMolecules (WPI-ITbM) Nagoya, Japan Yonghong Wang State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China Guosheng Xiong State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China Hideki Yoshida Bioscience and Biotechnology Center, Nagoya University, Chikusa Nagoya, Japan Brian D Zoltowski Department of Chemistry, Southern Methodist University, Dallas, Texas, USA PREFACE Plant growth is regulated by physiologically active substances called plant hormones and is further influenced by various environmental stimuli, including light Studies of such active substances can be traced back to observations and writings of Charles Darwin and his son Francis more than 100 years ago They observed that light induces bending of the plant hypocotyl and stimulates the stomatal opening, and hypothesized the involvement of effective substances in these phenomena Research on the molecular mechanisms behind such phenomena had to wait until molecular genetic studies with model plants such as Arabidopsis thaliana were developed Although plants endogenously produce plant hormones, exogenously supplied plant hormones can also trigger responsive reactions similar to those of endogenously induced ones Based on these characteristics, mutants of model plants that exhibit abnormalities in response to specific plant hormones and environmental stimuli have been isolated, and causative genes and corresponding proteins have been identified Furthermore, molecular studies using protein–protein interactions, plant–pathogen interactions, and actions of growth inhibitors have also contributed to the identification of key molecules, such as receptors and downstream controllers that transmit signals generated by these stimuli These molecular studies have accelerated biochemical understanding of the intracellular signaling pathways responsible for plant responses to stimuli This book includes reviews on current understanding of signaling pathways that control physiologically critical processes in plants Most of the key molecules in these pathways were discovered within the past decade In 2005, Matsuoka’s group reported on the F-box-containing receptor of gibellin (GA), which was selected as a “Breakthrough of the Year 2005” by Science In the history of abscisic acid (ABA) research, although several receptor candidates had been considered, one molecule was eventually proposed in 2009 to control activities of a specific protein phosphatase and kinase downstream of the receptor Strigolactone (SL), identified in 2008 as the 8th plant hormone, is the new functional substance that induces germination of a parasitic plant and controls the branching pattern Although at least two factors and a receptor candidate, including the F-box, have been identified within the SL signaling pathway, some points still remain to be elucidated xi xii Preface Discoveries of peptides that act as signaling molecules in plants and their corresponding receptors contributed important knowledge to the field of developmental biology Genome analyses have predicted that thousands of functional peptides exist in plants Although florigen, which induces flowering, had long been hypothesized, its molecular features were eventually revealed around 2000 in Arabidopsis and rice Cytokinesis in plants is distinctive from that occurring in other eukaryotes Molecular studies with plant cells demonstrated that the unidentified transcriptional signal specifically generated at the G2-M transition of the cell cycle activates the mitotic kinesin-mediated MAP kinase cascade that is essential for the execution of complex and integrated cytokinetic events Concerning the typical environmental stimulus light, research on a blue light photoreceptor and its downstream signaling pathway has recently shown remarkable progress The plant cryptochrome (CRY) involved in controlling photomorphogenesis and the circadian clock was first identified in plants in 1993 as a blue light receptor that controls COP1-mediated protein degradation Around 2000, two new blue light receptors, phototropin controlling the stomatal opening and ZTL (ZEITLUPE) responsible for the circadian clock, were also discovered in plants and together commonly encode the LOV domain In addition, the former also codes the protein kinase domain, whereas the latter codes the F-box domain, which suggests that they may function in light signaling pathways Recent advancements in these investigations are introduced in this book Interestingly, four out of nine signaling pathways (for GA, SL, CRY, and ZTL) described in this book include protein degradation systems involving an F-box protein family Additionally, signaling pathways stimulated by auxin and jasmonic acid, although not touched on here, also include the F-box proteins Thus, the ubiquitin–proteasome system of protein degradation is widely conserved as a central mechanism for the perception of various signals in plants Although protein kinase and phosphatase are responsible for many plant signaling pathways, by connecting with characteristic interacting factors, they are integrated uniquely into plant systems This book introduces typical pathways mediated by such stimuli as ABA, peptide ligands, cell cycle signaling, and phototropin Many factors remain unknown in the signaling pathways introduced here Identification of these as-yet unknown molecules should be critical for our understanding of the overall frameworks of the pathways Further research advancements in this field will likely contribute to opening up new research areas in basic plant biology as well as molecular breeding to Preface xiii generate useful plants We hope that readers in many research areas will find topics of interest in this book We thank the authors for their excellent contributions and Helene Kabes and Mary Ann Zimmerman of Elsevier for their guidance and editing of the chapters YASUNORI MACHINDA CHENTAO LIN FUYUHIKO TAMANOI June 2014 CHAPTER ONE Regulatory Networks Acted Upon by the GID1–DELLA System After Perceiving Gibberellin Hideki Yoshida, Miyako Ueguchi-Tanaka, Makoto Matsuoka1 Bioscience and Biotechnology Center, Nagoya University, Chikusa Nagoya, Japan Corresponding author: e-mail address: makoto@nuagr1.agr.nagoya-u.ac.jp Contents Gibberellin Perception System in Higher Plants Suppression of DNA-Binding Activity of TFs by DELLA (Trapping Function of DELLA) 2.1 Phytochrome-Interacting Factor Family of Proteins Involved in Hypocotyl Elongation and Chlorophyll Biosynthesis 2.2 Alcatraz and Spatula Involved in Valve Margin Development and Cotyledon Expansion, Respectively 2.3 Squamosa Promoter Binding-Like Proteins Involved in Floral Transition 2.4 Ethylene-Insensitive and EIN3-Like Involved in the GA–Ethylene Crosstalk for Apical Hook Development 2.5 Brassinazole-Resistant Involved in the GA–Brassinosteroid Crosstalk for Hypocotyl Elongation 2.6 Jasmonate ZIM Domain and MYC2 Proteins Involved in the GA–Jasmonate Acid Crosstalk Under Certain Conditions Transcriptional Regulation of Downstream Genes Via the Interaction of DELLA with Their Promoters (Direct Targeting Function of DELLA) 3.1 Backgrounds 3.2 ABA-Insensitive and ABI5 Involved in GA–Abscisic Acid Crosstalk 3.3 Indeterminate Domain Proteins Involved in the Feedback Regulation of GA Signaling 3.4 Botrytis-Susceptible Interactor and Its Related Proteins Involved in the Transrepression Activity of DELLA Other Functions of DELLA Besides Transcriptional Regulation 4.1 Prefoldin and PFD5 Involved in Cortical Microtubule Arrangement 4.2 D14 Involved in GA–Strigolactone Crosstalk Future Perspectives References The Enzymes, Volume 35 ISSN 1874-6047 http://dx.doi.org/10.1016/B978-0-12-801922-1.00001-4 # 2014 Elsevier Inc All rights reserved 5 8 10 11 11 13 13 15 16 16 17 18 19 Hideki Yoshida et al Abstract Recent studies have revealed that DELLA proteins (DELLAs) interact with various kinds of transcription factors (TFs) and other kinds of proteins to regulate GA signaling Here, we enumerate some of these DELLA interactors to show the multiple functions of DELLAs in the GA signaling pathway Through interaction with TFs, DELLAs regulate the expression of many genes in an inhibitory or enhancing manner under various biological events including the crosstalk between GA and other phytohormones, and the development of organs and tissues DELLA-interacting TFs can be categorized into two types in terms of the effect of DELLA on their transacting activity The first group includes those that are inhibited by DELLAs in terms of their DNA-binding activity, which includes the phytochrome interacting factor family of proteins involved in hypocotyl elongation, chlorophyll biosynthesis, fruit patterning, and cotyledon expansion; squamosa promoter binding-like proteins involved in floral transition; ethylene insensitive and EIN3-like proteins involved in GA–ethylene crosstalk; brassinazole-resistant involved in GA– brassinosteroid crosstalk; and jasmonate ZIM domain and MYC2 proteins involved in GA–jasmonate crosstalk The second group includes those TFs that affected in terms of their transcriptional activity but not DNA-binding activity upon interaction with DELLA, which includes the ABA-insensitive and ABI5 involved in GA–abscisic acid crosstalk, indeterminate domain involved in feedback regulation of GA signaling, and Botrytis-susceptible interactor proteins involved in DELLAs transrepression activity We also mentioned that interaction of DELLAs with proteins besides TFs regulates the crosstalk between GA and strigolactone, and tubulin folding The interaction of all of these various TFs and proteins with DELLAs strongly demonstrates that DELLA functions as a hub protein linking GA signaling to a myriad of biological events GIBBERELLIN PERCEPTION SYSTEM IN HIGHER PLANTS Gibberellin (GA) is one of the plant hormones that regulate a wide range of processes involved in plant growth, organ development, and environmental responses These include seed germination, stem elongation, leaf expansion, transition to flowering, and the development of flowers, fruits, and seeds [1] About 75 years ago, GA was first identified in the pathogenic fungus, Gibberella fujikuroi, as the causal chemical for the rice “bakanae” (foolish seedling) disease in which infected plants show excessive leaf elongation Since its first discovery, more than 130 GAs have been identified in plants, fungi, and bacteria, although only a few of them possess biological activity [2] During the past decade, most of the components important for GA perception or signaling have been identified through genetic studies on rice and DELLA-Mediated Gibberellin Signaling Pathways Arabidopsis mutants Among these components, DELLA proteins (DELLAs) have been considered as key intracellular repressors of the GA response of downstream genes [3–7] DELLAs comprise a subfamily within a family of plant-specific putative transcriptional regulators called GRAS, the name of which was coined after its first three members: GA insensitive (GAI), repressor of ga1-3 (RGA), and scarecrow (SCR) All proteins of the GRAS family contain a GRAS domain consisting of five distinct motifs: leucinerich region I, VHIID, leucine-rich region II, PFYRE, and SAW [8] On the other hand, DELLAs are distinguishable from other GRAS proteins by way of additional DELLA and TVHYNP motifs at their N-terminus The DELLA subfamily is highly conserved among angiosperms, gymnosperms, and ferns, but not in Physcomitrella patens, a model organism for mosses (bryophytes) [9,10] Arabidopsis thaliana, a model plant for dicots, has five kinds of DELLAs, namely, GAI, RGA, RGA-like (RGL1), RGL2, and RGL3 [3,4,11,12], whereas, rice, a model plant for monocots, only has one DELLA, namely, slender rice1 (SLR1) [6] In GA signaling, DELLAs become rapidly degraded in the presence of GA, resulting in various GA responses Another important component for GA perception is the GA receptor, GA-insensitive dwarf1 (GID1) In rice, it is encoded by only a single gene and its loss of function results in the gid1 mutant [13] In Arabidopsis, however, three GID1 orthologs (GID1a, GID1b, and GID1c) exist, all of which exhibit some overlapping and yet distinct functions in regulating different developmental processes [14–16] Biochemical analyses revealed that GID1 proteins bind specifically and strongly to bioactive GAs but not to inactive ones [13,17] GID1 is related to the α/β-hydrolase fold superfamily due to their similarity in terms of primary structure [18,19] However, although α/βhydrolases possess three conserved amino acids (serine, aspartic acid, and histidine) or catalytic triad important for their enzymatic activity, GID1 has other amino acids in place of histidine, making it devoid of hydrolase activity [13] In GA signaling, GID1 is known to interact with DELLA after initially binding with GA Although GID1s are localized in both the cytoplasm and the nucleus [13,16], their interaction with DELLAs is only confined to the nucleus where DELLA is present Such interaction is important for the rapid degradation of DELLA [13] Recently, it has been revealed that the receptor for another phytohormone, strigolactone, is also a member of the α/βhydrolase family, as exemplified by the D14 of rice and Arabidopsis, and the DAD2 of petunia [20–23] Unlike GA receptor GID1, the strigolactone receptors retain the conserved catalytic triad, and thus function as an enzyme Hideki Yoshida et al to hydrolyze the enol–ether linkage of active SLs, the catabolism of which is essential for strigolactone perception in plants [21–23] Interaction between the GA-binding GID1 receptor and DELLA induces a subsequent interaction between DELLA and an F-box protein (GID2 in rice; sleepy1 (SLY1) and sneezy (SNZ) in Arabidopsis), the third important component for GA perception [24–26] F-box proteins exist widely throughout the eukaryote kingdom, ranging from yeast to humans, and they function as substrate-recruiting subunits of the Skp1-cullin1-F-box-protein (SCF) ubiquitin ligase The SCFGID2/SLY1/SNZ promotes the polyubiquitination of DELLA in the GID1–GA–DELLA complex and induces its degradation via the 26S proteasome complex, thus, triggering the downstream GA response (Fig 1.1) Although the above molecular mechanism involving GID1, DELLA, and F-box proteins satisfy the basic principle for GA perception, we are still far from unveiling the complete picture of how DELLAs repress the broad range of GA responses Recently, however, the identification of some of the DELLA-interacting factors (discussed here) helped reveal the diverse functions of DELLAs for GA signaling In this review, we provide an overview of the role of DELLA in the GA signaling pathway, particularly in terms of its dual transcriptional regulatory function (trapping function and direct targeting function; discussed earlier) on downstream genes, and also its crosstalk with other signaling pathways through its interaction with various kinds of transcription factors (TFs) and proteins Figure 1.1 GA perception mechanism mediated by GID1 and DELLA Author Index Takahara, M., 201, 209 Takahashi, F., 29–31, 35, 40, 44–47, 48, 49, 53 Takahashi, H., 34, 50, 91, 106, 107 Takahashi, K., 197–201, 203, 204, 207–210 Takahashi, S., 30, 48 Takahashi, Y., 34, 50, 116, 134, 136, 138, 144, 149, 150, 152–154, 158, 159, 162, 201, 204, 209 Takaki, T., 146, 161 Takanabe, R., 217, 220, 221, 235 Takano, M., 134, 143 Takasaki, T., 99, 110 Takase, T., 220, 221, 226, 236 Takashi, Y., 20 Takayama, S., 99, 100, 110, 111 Takeba, G., 129, 142 Takeda, K., 41, 54 Takeda, M., 19, 25 Takeda, T., 68, 82 Takeda-Kamiya, N., 17, 25 Takehara, S., 19, 25 Takemiya, A., 194, 197, 201, 204, 205, 207, 209 Takeuchi, H., 98, 109, 110 Takeuchi, M., 97, 109 Takiguchi, Y., 15, 24 Takimoto, A., 129, 142 Tama, N., 216, 235 Tamai, A., 97, 109 Tamai, T K., 168, 183 Tamaki, S., 116–121, 123, 124, 126, 128, 134, 138–140, 142, 143 Tamaki, T., 87, 90, 104 Tamerler, C., 97, 109 Tamura, N., 13, 23 Tan, M., 39, 53 Tan, M H E., 32, 50 Tan, X., 10, 22, 71, 83 Tanahashi, T., 3, 19 Tanaka, A., 13, 23 Tanaka, H., 34, 51, 149, 152, 153, 155, 157, 162 Tanaka, N., 134, 144 Tanaka, W., 91, 106, 114, 138 Tanaka, Y., 97, 109 Tandstad, N M., 95, 96, 108 Tang, C., 136, 144 269 Tang, W., 134–136, 144 Tanigawa, Y., 133, 143 Tanihigashi, H., 220, 221, 226, 236 Tanisaka, T., 134, 144 Tanokura, M., 3, 4, 17, 20, 28–32, 47, 47 Tanoue, T., 36, 52 Tantikanjana, T., 99, 110 Tao, Y., 40, 53 Tao, Z., 18, 25, 119, 120, 129, 140 Taoka, K., 114, 117–121, 123, 124, 128, 137, 139, 140 Tarone, A M., 136, 144 Tasaka, M., 97, 109 Tax, F E., 93, 94, 107, 108 Taylor, A., 233, 239 Taylor, B., 215, 221, 234 Tejos, R., 95, 108 Tena, G., 36, 52 Terada, M., 149, 152, 153, 155, 157, 162 Terashima, I., 193, 196, 197, 205, 206 Terazima, M., 225, 226, 229, 232, 237 Terry, M J., 5, 21 Teshima, K M., 136, 144 Theres, K., 120, 140 Thiele, K., 146, 161 Thiessen, W E., 28, 47 Thimmapuram, J., 45, 56 Thomann, M., 114, 135, 137 Thomas, B., 116, 125, 138, 233, 239 Thomas, M., 30, 48 Thomas, S G., 3, 4, 8, 11, 18, 19, 20, 23 Thomashow, M F., 10, 18, 22 Thompson, K L., 202, 210 Thong, Z., 114, 124, 131, 138 Thorner, J., 36, 52 Thouroude, T., 119, 140 Thum, K E., 170, 185 Tian, F., 114, 136, 137, 144 Timmermans, M C., 125, 141 Timofejeva, L., 102, 112 Tintor, N., 87, 104 Titarenko, E., 5, 21 Tiwari, S B., 133, 143 To, B J., 133, 143, 220, 228, 232, 236 Tobin, E M., 214, 218, 219, 234, 235 Toda, T., 158, 164 Todaka, D., 33, 50 Todesco, M., 114, 135, 136, 137, 144 270 Todo, T., 168, 183, 220, 223, 225, 230, 236, 238 Toh, S., 13, 23, 24 Tohge, T., 12, 23 Tokioka, Y., 217, 220, 221, 235, 236 Tokutomi, S., 220, 223, 225, 226, 228–232, 236–238 Toledo-Ortiz, G., 5, 20 Tomioka, A., 148, 161 Tomita, Y., 117, 138 Tomiyama, M., 198, 208 Ton, J., 47, 56 Tong, X H., 10, 18, 22 Toriba, T., 91, 106, 107 Torii, K U., 96–98, 109 Torti, S., 125, 141 Toth, R., 175, 188 Totsuka, N., 3, 4, 17, 20 Toualbia, Y., 119, 140 Tougou, M., 13, 23 Tournier, C., 36, 52 Toyoda, T., 47, 56 Traas, J., 199, 208 Tran, H G., 131, 142, 219, 220, 222, 223, 225, 226, 228, 236 Tran, P T., 158, 164 Traw, M B., 114, 135, 136, 137, 144 Tremblay, R., 14, 24 Trotochaud, A E., 88, 105, 106 Troy, A., 16, 24 Tseng, T S., 225, 237 Tsubouchi, H., 94, 108 Tsuchida-Mayama, T., 170, 186 Tsuchiya, Y., 13, 23, 70, 82 Tsuchiya, Y N., 91, 106 Tsuda, K., 87, 104 Tsuji, H., 114, 116–121, 123, 124, 128, 137–140 Tsukamoto, C., 99, 110 Tsutsui, H., 98, 109, 110 Tsutsumi, N., 91, 106 Tsutsumi, T., 194, 205 Tsuzuki, T., 198, 208 Tu, D C., 168, 183 Tu, H., 158, 164 Tu, Y H., 158, 164 Turck, F., 133, 143 Turnbull, C., 117, 138 Author Index Turner, S., 90, 106 Tuskan, G A., 126, 141 Tuteja, N., 40, 53 Twell, D., 148, 161 Tzeng, Y H., 88, 105 U Uchida, N., 97, 109 Ueda, T., 3, 4, 17, 20 Ueda, Y., 99, 110 Ueguchi-Tanaka, M., 2–4, 8, 12–15, 18, 19, 19, 20, 23–25, 71, 72, 83 Uehara, R., 148, 161 Ueno, K., 195, 206 Ugalde, R A., 225, 237 Uhlenhaut, N H., 124, 141 Ulm, R., 167, 170, 182 Umehara, M., 17, 25, 58, 61, 68, 76, 77, 80, 83 Umehara, Y., 134, 143 Umen, J., 201, 210 Umezawa, T., 28–35, 40, 44–47, 47–51, 56 Underwood, W., 199, 208 Ungerer, M., 114, 135, 137 Uno, Y., 33, 50 Uozumi, N., 35, 51 Upadyayula, N., 114, 136, 137 Usami, T., 170, 185 Utsugi, S., 117, 139 V Vaccaro, B., 223, 225, 237 Vahisalu, T., 34, 50 Vaidya, A T., 225, 237 Vaistij, F E., 7, 8, 21 Vale, R D., 148, 161 Valerio, G., 34, 50 Vallee, B., 117, 139 Vallon, O., 201, 210 Valon, C., 197, 207 Valverde, F., 131, 133, 142, 143, 174, 187 Van Damme, D., 146, 148, 158, 159, 161, 164 Van de Peer, Y., 95, 108 Van de Velde, W., 91, 107 van der Horst, G T., 175, 176, 188 Van Der Straeten, D., 9, 22 van Dongen, W., 87, 104 Van Gelder, R N., 168, 183 Author Index van Grondelle, R., 223, 225, 226, 236, 237 van Kleeff, P J., 119, 140 Van Montagu, M., 148, 162 Van Poucke, K., 158, 164 van Stokkum, I H., 223, 237 van Stokkum, I H M., 223, 237 van Stokkum, N H M., 223, 226, 237 van Verk, M., 93, 107 van Wilderen, L J., 223, 236 Vandekerckhove, J., 202, 210 Vandermeeren, C., 195, 206 Vandervelde, L., 126, 141 Vanhoutte, I., 87, 104 Vanneste, S., 95, 108 Vanoosthuyse, V., 100, 111 Vansiri, A., 217, 235 Vantard, M., 158, 164 Varkonyi-Gasic, E., 117, 119, 120, 129, 139, 140 Vavasseur, A., 31, 32, 49, 193, 194, 205, 206 Vera, C E., 102, 112 Verbrugghe, K J., 146, 158, 161, 164 Vercher, Y., 5, 21 Verhey, S D., 30, 49 Verma, D P., 146, 161 Vermeulen, M., 45, 55 Vernı`, F., 158, 164 Vernoud, V., 102, 112 Verslues, P E., 31, 49 Vicente, O., 154, 163 Vie, A K., 86, 103 Vilhjalmsson, B J., 136, 144 Vincent, C., 117, 125, 138, 139, 141 Vince-Prue, D., 116, 125, 138 Visconti, S., 202, 210 Vlad, F., 32, 49 V€ olker, A., 148, 162 Volkmann, D., 199, 209 von Caemmerer, S., 193, 205 von Wiren, N., 91, 106 Voogd, C., 119, 120, 129, 140 Vriezen, W H., 9, 22 Vugrek, O., 148, 161 W Wada, M., 193, 205, 214, 219–221, 229, 231, 234, 236, 238 Wagner, D., 124, 141 271 Wagner, V., 148, 158, 159, 161, 164 Wagner, W., 148, 162 Wahl, G M., 158, 164 Waizenegger, I., 146, 161 Wakabayashi, K., 200, 209 Walbot, V., 102, 112 Waldie, T., 67, 68, 70, 71, 82 Walker, J C., 88, 96, 98, 105, 108, 109 Walker-Simmons, M K., 30, 49 Wang, A., 136, 144, 198, 207 Wang, C., 9, 22, 136, 144 Wang, C J R., 102, 112 Wang, F., 3, 5, 21 Wang, G., 45, 55 Wang, G F., 102, 112 Wang, H., 96, 98, 108, 109, 178, 188, 197, 207 Wang, J., 39, 53, 130, 142 Wang, J W., 8, 21, 124, 141 Wang, L., 36, 52, 133–136, 143, 144, 218, 219, 222, 228, 235, 236, 238 Wang, L J., 11, 18, 23 Wang, M., 36, 52, 196, 206 Wang, N -N., 41, 54 Wang, P., 30, 31, 41, 44–47, 48, 54 Wang, R., 9, 22 Wang, R -S., 41, 54 Wang, S., 8, 21 Wang, T., 119, 140 Wang, W., 3, 19 Wang, X -F., 38, 53 Wang, X -J., 35, 38, 51, 53 Wang, X -Q., 30, 49 Wang, Y., 3–5, 19–21, 45, 47, 56, 67, 68, 71, 82, 83, 119, 120, 129, 140, 158, 164, 193, 196–198, 205–208 Wang, Y -F., 34, 35, 50, 51 Wang, Y M., 158, 164 Wang, Z X., 134, 144 Wang, Z Y., 9, 22, 87, 92, 104, 107 Wanner, G., 146, 161 Ward, J M., 197, 207 Ware, D., 114, 125, 136, 137, 141, 144 Warthmann, N., 129, 142 Wasteneys, G O., 148, 161 Watanabe, A., 13, 23, 24, 155, 163, 198, 208 Watanabe, M., 99, 100, 110, 111 272 Waters, M T., 17, 25, 58–60, 63–65, 74, 80–82 Watson, M B., 30, 49 Weber, M J., 35, 52 Weber, S., 223, 225, 237 Weckwerth, W., 44, 45, 55, 56, 203, 210 Wei, C., 36, 52 Wei, K J., 148, 161 Wei, X., 136, 144 Weidtkamp-Peters, S., 90, 106 Weigel, D., 114–121, 124, 128, 129, 135, 136, 137–141, 144 Weiller, G F., 87, 104 Weingartner, M., 157, 163 Weinig, C., 114, 135, 137 Weisshaar, B., 5, 20 Welch, D., 18, 25 Weller, J L., 170, 179, 185 Wellmer, F., 124, 141 Wells, N J., 158, 164 Wen, C K., 3, 19 Weng, Q., 136, 144 Weng, X., 134–136, 144 Wenkel, S., 133, 143 Werber, M., 5, 20 West, G M., 32, 50 Weston, E., 170, 185 Wheatley, K., 133, 143 Whippo, C W., 170, 186 White, J G., 158, 164 Whitford, R., 90, 91, 95, 106–108 Whitmarsh, A J., 36, 52 Whittington, A T., 148, 161 Wibowo, J., 91, 106 Wicker-Planquart, C., 158, 164 Wickett, N., 126, 141 Widmann, C., 35, 52 Widom, J., 228, 230, 238 Wienkoop, S., 44, 55 Wierzba, M., 94, 108 Wigge, P A., 119, 124, 128, 129, 140–142 Wiig, A., 199, 208 Wild, M., 5, 10, 18, 21, 22 Wilker, E W., 121, 140 Willems, G., 136, 144 Williams, M., 197, 207 Williams, R W., 88, 105 Willige, B C., 3, 20 Author Index Willmann, R., 36, 53 Willmer, C M., 192, 205 Wilson, C., 154, 163 Wilson, J M., 88, 105 Wilson, R N., 8, 21 Wink, R H., 90, 106 Winter, V J., 117, 118, 121, 128, 139 Wisman, E., 9, 21 Withers, J., 10, 22 Witman, G B., 201, 210 Witters, E., 10, 22 Wolf, S., 117, 138 Wolschin, F., 44, 55 Wong, A Y., 14, 24 Wong, C E., 125, 141 Wong, H L., 116, 117, 138 Woo, H R., 62, 81 Wood, T A., 7, 21 Worthington, E N., 168, 183 Wremerth-Weich, E., 126, 128, 141 Wright, A J., 146, 160 Wright, L., 221, 236 Wu, C., 134, 144 Wu, G., 8, 21, 124, 141, 172, 187 Wu, G J., 91, 107 Wu, H M., 101, 111 Wu, J., 42, 55, 114, 137–138 Wu, L., 170, 186 Wu, M F., 124, 141 Wu, N., 120, 140 Wu, Y., 45, 47, 56, 133, 143 Wu, Z S., 3, 4, 20 Wuest, S E., 124, 141 Wyser-Rmili, C., 91, 106 X Xi, W., 117, 119, 120, 129, 139, 140 Xia, K., 10, 18, 22 Xiang, H., 3, 19 Xiao, L T., 10, 18, 22 Xiao, Y -G., 197, 206 Xie, C., 3, 4, 20 Xie, D., 10, 22 Xie, L F., 102, 112 Xie, X., 58, 80 Xiea, L F., 101, 112 Xin, Q., 38, 53 Xing, Y., 38, 53, 134–136, 144 Author Index Xoconostle-Cazares, B., 117, 139 Xu, C., 134–136, 144 Xu, H E., 3, 4, 20 Xu, M., 136, 144 Xu, P., 170, 180, 181, 186, 189 Xu, R., 36, 52 Xu, S., 39, 53 Xu, T H., 3, 4, 20 Xu, X., 175, 188 Xu, Y., 3, 4, 20 Xuan, Y H., 134, 144 Xue, L., 30, 31, 44–47, 48 Xue, Q., 36, 52 Xue, S., 34, 35, 50 Xue, W., 134–136, 144 Xue, X Y., 11, 18, 23 Xue, Y L., 3, 4, 17, 20 Y Yabe, S., 98, 110 Yaeno, T., 196, 206 Yaffe, M B., 121, 140 Yahata, S., 97, 109 Yamada, K., 87, 104 Yamada, M., 87, 105 Yamada, Y., 220, 221, 226, 236 Yamaguchi, A., 117, 119, 123, 124, 128, 138, 139, 141 Yamaguchi, I., 3, 12, 19, 20, 23 Yamaguchi, J., 3, 19 Yamaguchi, M., 118–121, 123, 124, 128, 139 Yamaguchi, S., 2, 13, 15, 17, 18, 19, 23–25, 91, 106 Yamaguchi, Y., 93, 100, 107, 111 Yamaguchi-Shinozaki, K., 31–33, 49, 50, 88, 105 Yamamoto, A., 231, 238 Yamamoto, K., 134, 143 Yamamoto, M., 158, 164 Yamamoto, S., 30, 31, 48, 119, 123, 128, 139 Yamamoto, Y., 72, 83 Yamane, H., 114, 137–138 Yamanouchi, U., 114, 134, 137–138, 143, 144 Yamashino, T., 218, 235 Yamashita, A., 158, 164 Yamauchi, S., 194, 205 273 Yamazaki, R., 125, 141 Yamazaki, Y., 149, 152, 153, 155, 157, 162 Yan, H., 60, 81 Yan, J., 61, 71, 81, 136, 144 Yan, L., 35, 51 Yan, Y., 10, 18, 22 Yanagisawa, S., 117, 138 Yanase, T., 118–121, 123, 124, 128, 139 Yang, C Y., 152, 153, 163 Yang, D L., 10, 18, 22 Yang, H., 88, 104 Yang, H Q., 133, 143, 169, 170, 184, 186 Yang, L., 124, 141 Yang, N., 136, 144 Yang, Q., 136, 144 Yang, S L., 101, 102, 112 Yang, S Y., 17, 25 Yang, W C., 100–102, 111, 112 Yang, X., 40, 54, 136, 144 Yang, X -C., 40, 41, 54 Yang, Y., 9, 22, 32, 35, 49, 51, 196, 198, 206, 207, 222, 228, 236, 238 Yang, Z., 10, 18, 22 Yanina, L I., 126, 142 Yano, M., 114, 116, 134, 135, 137–138, 143, 144 Yanofsky, M F., 124, 140 Yanovsky, M., 214, 219, 220, 234 Yanovsky, M J., 170, 172, 175, 185, 187, 217, 219, 235 Yant, L J., 124, 141 Yan,Y., 78, 84 Yao, J., 10, 18, 22 Yasuda, J., 36, 52 Yasuda, M., 47, 56 Yasuhara, H., 146, 147, 152, 159, 161, 165 Yasuhara, M., 217, 220, 221, 235, 236 Yasumura, Y., 5, 19 Yasuno, N., 125, 141 Yates, H., 114, 136, 137 Yazawa, M., 220, 234, 236 Ye, D., 101, 102, 112 Ye, J., 136, 144 Ye, T., 45, 47, 56 Yeoh, S., 148, 162 Yi, W., 3, 4, 20 Yoda, M., 125, 141 Yokoi, S., 116, 117, 134–136, 138, 143, 144 274 Yokoo, T., 97, 109 Yoneyama, K., 17, 25, 58, 80 Yoneyama, T., 117, 138 Yoo, S C., 130, 142 Yoo, S J., 117, 138 Yoo, S Y., 117, 118, 121, 128, 139 Yoshida, A., 75, 83, 91, 106, 107 Yoshida, H., 14, 15, 18, 24, 125, 141 Yoshida, R., 30, 31, 33, 35, 45, 46, 48–50 Yoshida, S., 17, 25, 77, 84, 92, 107 Yoshida, T., 13, 23, 31, 33, 49, 50 Yoshida, Y., 47, 56 Yoshimura, A., 134, 144 Yoshioka, T., 13, 23 Yoshizumi, T., 15, 24 You, C., 134, 144 Yu, H., 10, 18, 22, 25, 114, 117, 119, 120, 124, 129, 131, 133, 138–140, 143 Yu, J., 114, 136, 137 Yu, L., 5, 21 Yu, L P., 88, 106 Yu, M -J., 45, 55 Yu, N., 67, 82 Yu, S., 8, 21, 134–136, 144 Yu, S M., 17, 25 Yu, T S., 130, 142 Yu, X., 169, 170, 172, 184, 186 Yu, X -C., 35, 51 Yuan, M., 158, 164 Yuan, Q., 168, 183 Yuan, T., 88, 104 Yuan, Z., 14, 24 Yuceer, C., 126, 141 Yue, K., 86, 103 Yui, R., 98, 109, 110 Yun, J., 133, 143 Z Zagotta, M T., 174, 187 Zale, J M., 4, 20 Zalewska, A., 12, 23 Zeevaart, J A., 17, 25, 116, 138 Zeiger, E., 194, 197, 205 Zelwer, C., 117, 139 Zeng, J., 170, 185 Zeng, L J., 10, 18, 22 Zentella, R., 3, 8, 9, 11, 15, 18, 19, 22–24 Author Index Zentgraf, U., 180, 188 Zhang, A., 39, 53 Zhang, B., 10, 22 Zhang, C., 3, 4, 20 Zhang, D., 36, 52 Zhang, H., 39, 53 Zhang, J., 38, 39, 41, 53, 54 Zhang, M., 41, 54 Zhang, N., 148, 161 Zhang, Q., 134–136, 144, 179, 188 Zhang, Q F., 136, 144 Zhang, S., 36, 52, 96, 98, 108, 109, 150, 162 Zhang, T Q., 8, 21 Zhang, X., 9, 22, 125, 136, 141, 144, 197, 207 Zhang, X Q., 102, 112 Zhang, Y., 39, 53 Zhang, Y C., 8, 21, 133, 143, 180, 189 Zhang, Z., 36, 52, 114, 136, 137, 144, 146, 161 Zhang, Z L., 3, 8, 11, 15, 18, 19, 23, 24 Zhao, D Z., 102, 112 Zhao, J., 62, 64, 70, 81 Zhao, L H., 3, 4, 20, 63, 64, 66, 72, 74, 81 Zhao, Q., 136, 144 Zhao, R., 35, 38, 51, 53 Zhao, Y., 32, 49, 134–136, 144, 198, 207 Zhao, Z., 41, 54 Zheng, N., 10, 22, 72, 73, 83 Zheng, Z., 68, 82 Zhiponova, M., 87, 104 Zhong, D., 3, 4, 20 Zhong, T., 136, 144 Zhou, F., 60, 64–66, 70, 72–75, 81 Zhou, H., 134–136, 144 Zhou, H W., 9, 22 Zhou, J., 5, 21 Zhou, R., 125, 141 Zhou, T., 136, 144 Zhou, X., 45, 55 Zhou, X E., 3, 4, 20, 32, 50 Zhou, Y., 41, 54 Zhu, C., 40, 53, 136, 144 Zhu, H., 168, 183 Zhu, J Y., 9, 22 Zhu, J.-K., 29–32, 47, 48, 49 Author Index Zhu, S.-Y., 35, 38, 51, 53 Zhu, T., 133, 143 Zhu, Y., 39, 53 Zhu, Z., 9, 22 Zhulin, I B., 215, 221, 234 Zikihara, K., 220, 223, 225, 226, 228, 229, 232, 236–238 Zimmermann, I., 152, 153, 163 Zipfel, C., 87, 104 275 Zoltowski, B D., 222, 223, 225–228, 230, 236–238 Zong, X., 41, 54 Zou, D., 41, 54 Zou, J., 58, 59, 80 Zourelidou, M., 3, 20 Zugaj, D L., 12, 23 Zuo, Z., 174, 178, 187 Zupanska, A K., 119, 140 SUBJECT INDEX Note: Page numbers followed by “f ” indicate figures and “t ” indicate tables A Abscisic acid (ABA) MAPK, 29 physiological functions, 28, 28f signaling, 28 signal perception and transduction, 28–29, 29f SnRK2, 29 Alcatraz (ALC) and DELLAs, and spatula (SPT), Arabidopsis CO-independent functions, GI, 133 CO protein, 131–133 genetics, 213–214 GI–FKF1 complex, 131 gigantea (GI)–constans (CO)–FT module, 131 HAP complex and CCAAT-box DNA, 133 HOS1 protein, 131–133 LOV1 domain, 228–229 MAPK (see Mitogen-activated protein kinase (MAPK)) photoperiodic flowering pathway, 219–220 phytochrome B-dependent degradation, CO, 133 and rice, 58–59 SnRK2 protein (see SnRK2 protein) xylem of tomato, 60 ZTL/LKP2, yeast, 220–221 Auxin Binding Protein1 (ABP1), 199–200 Auxin polar transport CTLH proteins, 69–70 gene expression, 69–70 PIN1 endocytosis, 69–70 shoot branching, 70–71 B Blue-light-induced stomatal opening Arabidopsis guard-cell protoplasts, 195 autophosphorylation, 193–194 dual beam protocol, 194 electrochemical gradient, 194 H+-ATPase-mediated stomatal movement, 193–194, 193f K+in channel mutants, 196–197 peptide mapping and phosphoamino acid analysis, 195 photosynthetic CO2 uptake, 195–196 phototropins (phot1, phot2), 193–194 protein kinase inhibitors, 194–195 signal transduction pathway, 193–194 Blue-light photoreceptor LOV domain, 221 phototropins, 214–215 Blue Light Signaling1 (BLUS1), 193–194 Blue light-stimulated photomorphogenesis Arabidopsis CRY1 cDNA, 171–172 cotyledon expansion, 171–172 hypocotyl elongation, 170–171, 171f transgenic seedlings, 171–172 Botrytis-susceptible interactor (BOI) proteins, 15–16 and quadruple mutants, 15–16 Brassinosteroid (BR) GA, 9–10 signaling and transcriptional activity, 9–10 C Ca2+-dependent protein kinase (CDPK) calmodulin (CaM), 34–35 CPK3 and CPK6, 35 and SnRK2, 35 Carlactone Arabidopsis and rice, 58–59, 60 MAX1 function, 58–59 CCE See Cryptochrome C-terminal extensions (CCE) CDKs See Cyclin-dependent kinases (CDKs) 277 278 Circadian clock F-box and Kelch repeat domains, 217 HSP90, 217 hypocotyl phenotypes, 215–216 intracellular localization, ZTL, 216–217, 216f LKP2 and FKF1, 218–219 LOV domain, 216–217 molecular genetic approaches, 214 PRR5 proteins, 218 TOC1, 217–218 ZTL, 214–215 Clavata3 (CLV3) and CLE45, 102–103 perception, 87–88 SAM, 87–88 Clavata3/embryo surrounding region (CLE) CLE10, 91 CLE40, 90 CLE45, 90–91 CLV3, 87–89 description, 87 in species, 91 TDIF, 90 Clp protease family protein d14 and d3 phenotypes, 65 D14 and KAI2, 66–67 D53 transcripts, 65–66 in rice, 66 SMAX1, 66 CLV3 See Clavata3 (CLV3) Cryptochrome C-terminal extensions (CCE), 168–169 Cryptochrome-mediated light responses, plants blue light-stimulated photomorphogenesis, 170–172 and circadian clock, 174–176 light-controlled stomatal opening and development, 176–178 photoperiodic control, flowering time, 172–174 C-terminally encoded peptides (CEP), 96 Cyclin-dependent kinases (CDKs) M-phase-specific NACK1 transcription, 155–157, 156f repression, early M phase, 157–158 Subject Index D DELLA proteins DELLA-interacting proteins GA-biosynthetic genes, 11–12 rice, 12–13 in GA signaling abscisic acid (ABA), 13 DBD, 12–13 function, 11 SLR1, 12–13 E Epidermal patterning factor (EPF1) Arabidopsis, 96–97 CHALLAH (CHAL), 97 EPF2, 97 ligand-receptor interaction assays, 97 stomagen, 97 YODA-MAPK phosphorylation, 98 Ethylene insensitive (EIN3) Arabidopsis seedlings, 8–9 and DELLAs, 8–9 F FAC See Florigen activation complex (FAC) F-box protein Arabidopsis max2 mutant, 60–62 components, 60, 61f and Kelch repeat domains, 213–214 and LOV, 231–232 MAX2, 62–63 phylogenetic analysis, 60–62 SCF complex functions, 217 shoot branching, 62–63 Flavin C4a position, 222–223 electron transfer event, 223–225 environments, 227 hydrogen–bonding patterns, 227 semiquinone and Cys radical, 223–225 Flavinbinding, Kelch repeat, F-box (FKF1) in amino acid sequence levels, 218–219 and LKP2, 218–219 photoperiodic flowering regulation, 219–221 ZTL, 218–219 279 Subject Index Florigen apical meristem to floral transition, 114 FAC (see Florigen activation complex (FAC)) floral transition, 114 flowering time, 114 FT promoter activity and mRNA accumulation, 116–117 functions, 114, 115f heading date 3a (Hd3a) gene, 116 mutant tobacco cultivar and soybean plants, 116 natural variation, 135–136 OsFTL12 (rice protein), 116–117 shoot apical meristem, 114 Florigen activation complex (FAC) AP1 in Arabidopsis, 124 biochemical interaction experiments, 120 C-terminal residues, OsFD1, 121 formation, 121 microRNA156-regulated SPL genes, 124 mouse CREB bZIP–C-box DNA complex, 121 14-3-3 protein, florigen receptor (see 14-3-3 Protein, florigen receptor) SAP motif, 120 structure, 121, 122f transcriptome analysis, 125 Flowering locus T (FT) gene flowering promotion identification, 117 FTIPs (see FT-interacting proteins (FTIPs)) Hd3a and 14-3-3 receptors, 118–119 intercellular transport (see Intercellular transport, FT) molecular function (see Molecular function, FT) PEBP family, 117 photoperiodic regulation, 130–135 pleiotropic functions (see Pleiotropic functions, FT) segment B region, 118 structure, 117, 118f α/β-Fold hydrolase DAD2, 63–64 GR24, 64 KAI2, 64–65 rice mutant d14, 63 FT See Flowering locus T (FT) gene FT-interacting proteins (FTIPs) C2 domain, 120 OsFD1 coexpression, 119 14-3-3 proteins, 119 TCPs, 120 transcription factors, 120 two-hybrid (Y2H) screening, 119 G GA-insensitive dwarf1 (GID1) and DELLA, D14 functions, 17 Gibberellin (GA) components, 2–3 DELLA, 3–4 description, F-box-protein, GID1, 3–4 perception mechanism, 4, 4f Guard cells H+ release, 194 hyperpolarization, 194–195 Nicotiana tabacum MPK4, 42 phosphorylation signals, 41 plant stomatal movement, 42 signaling factors, 193–194 transcriptome analysis, 41–42 V faba, 195 H Hypocotyl elongation, H+-ATPase, 199–201 I Inflorescence deficient in abscission (IDA) preproprotein, 95 signaling, 96 Interaction network BZR1 and DELLAs, 9–10 DELLA, 11–16 D14 with SLR1, 17 GRAS, 18–19 jasmonate ZIM domain, 10 PIFs and DELLAs, protein–protein, 15–16 signaling pathways, 280 Intercellular transport, FT AtFT mutants, 130 floral induction, 129 florigen signal, phloem, 129 FTIP1 identification, 129–130 VSR residues, 130 J Jasmonate ZIM domain (JAZ) DELLAs, 10 function, 10 Jasmonic acid, 92 L Ligand See Peptides Light-controlled stomatal opening and development, 176–178 Light-Oxygen-Voltage-sensing (LOV) domains amino acid, 221–222 bacterial, 225 crystal structures, 223–225, 224f and PAS, 222–223 photoreceptors, 226–227 signaling mechanisms, 230–231, 231f structure and photochemistry, 222f, 223 UV-light-activated pathway, 226–227 ZTL/FKF1/LKP2 family, 223 LOV Kelch protein (LKP2) in Arabidopsis, 220–221 and FKF1, 218–219, 223–225 ZTL, 220–221 LUREs A thaliana pollen tubes, 98 cysteine-rich polypeptide (CRP), 98 downstream pathway, 99 M MAP kinase See Mitogen-activated protein kinase (MAPK) MAP kinase kinase kinases (MAPKKKs), 150 MAP kinase kinases (MAPKKs), 150 Mitogen-activated protein kinase (MAPK) ABA treatment, 36–38 abiotic and biotic stimuli responses, 39–40 components, 36 cytokinetic defects, 159 Subject Index cytokinetic events, 149 eukaryotes, 150 functions, 40 guard cells, 41–42 maize, 39 miRNA biogenesis factors, 40 MPK6 pathway, 38–39, 38f NPK1, 153–154 OsMPK1, 39 phosphoproteomic analysis, 40–41 plant cytokinesis, 150 plants and animals, 36, 37t protein kinases, 35–36, 150 protein phosphatase 2C (PP2C), 36–38 putative phosphorylation sites, 158–159 ROS signaling, 38 Molecular function, FT differential regulation, plant growth and FT paralogs, 127f, 129 TCPs, 128–129 transcriptional regulation, 128 unbiased PCR mutagenesis analysis, 128–129 N NACK-PQR pathway anaphase spindle elongation factor (Ase1p), 158 MAP kinase kinase kinases (MAPKKKs), 150 MAP kinase kinases (MAPKKs), 150 MAP65-3 mutations, 159 MT dynamics, 158 NPK1 MAPKKK and NACK1 Kinesin, 150–153 NtMAP65-1a, 158–159 protein regulator of cytokinesis (PRC1), 158 tobacco BY-2 cells, 158 NPK1 MAPKKK and NACK1 kinesin ANP2 and ANP3, 150–152 functional yeast genetic system, 152 HINKEL/AtNACK1, 152–153, 153f phragmoplast during cytokinesis, 150–152, 151f Nucleus- and phragmoplast-localized protein kinase (NPK1) Arabidopsis plants, 154 Subject Index kinase-defective mutant, 154 logarithmic growth phase, tobacco cells, 150–152 yeast genetic system, 153–154 P Peptides CEPs, 96 classification, 86 EPF1, 96–98 function, 86–87 hydroxyproline-rich SlSys, 92 IDA, 95–96 LUREs, 98–99 plant cell walls, 86 plant elicitor peptide, 93 PSK, 93–94 PSY1, 94 RALF, 100–101 RGF, 94–95 SCR, 99–100 TPD1, 101–102 xylogen, 101 Phospho-mimic mutations, 158 Phosphoproteomics protein kinase activity, 44 protein phosphorylation network, 45–46 screening protein kinase, 43–44, 43f SnRK2 mutants (see SnRK2 protein) strong cation-exchange (SCX), 43–44 Phosphorylation ABA-induced inhibition, 197–198 H+ release, 193–194 peptide mapping and phosphoamino acid analyses, 195 Photocycle biological functions, 225 kinetics and signaling, 232–233 LOV domain, 223–227 ZTL, 226–227 Photoperiodic flowering Arabidopsis, 131–133 environmental factors, 172 floral initiation, 172–174, 173f molecular genetics analysis, 130–131 quantitative trait locus (QTL), 172–174 rice, 134–135 281 temperature-dependent floral initiation, 172–174 temperature-dependent signaling transduction, 172–174 Photoperiodic flowering regulation in Arabidopsis, 219–220 CDF2 protein, 221 constans (CO) protein, 219–220 FKF1, 219 FKF1 protein, 220–221 ZTL and FKF1, 221 ZTL and LKP2 mRNA expression patterns, 219 Photoperiodism See Photoperiodic flowering regulation Photoreceptors agriculture productivity, 181–182 CRY2, 172–174 Drosophila (dCRY), 168 light entrainment, circadian clock, 174–175 Phragmoplasts centrifugal development, cell plates, 146–148, 147f characteristic cytokinetic machinery, 146 cytokinesis, 150–152 cytokinetic events, 146–148 MAPK, 149 MT array, 146–148 NACK protein, 152 Phytochrome-interacting factor (PIF) bHLH superfamily, DNA-binding activity, TFs, 5, 6f Phytosulfokine (PSK) biosynthesis, 94 description, 93–94 receptor, 94 Plant cryptochromes agronomical traits, 181 Arabidopsis thaliana, 168 Archaea genomes, 168 auxin sensitivities, 178 CCE, 168–169 crop productivity, 181–182 cryptochrome-interacting bHLH1, 179–180 cyclobutane pyrimidine dimers, 168 Drosophila (dCRY), 168 enhanced anthocyanin accumulation, 179 282 Plant cryptochromes (Continued ) evolutionary descendants, DNA photolyases, 168 GmCRY1a, 179–180 light-independent transcription repressors, 168 light-responsive photoreceptors, 168 monocot plants, 180 physiological functions, 178–181 plant growth and development, 169–170 sequence and photobiochemical properties, 168 signaling pathways, 181–182 signal transduction mechanisms, 169–170 soybean cryptochrome, 179–180 spore germination, 178 tomato development, 179 wheat dbESTs, 180–181 Plant cytokinesis augmin-g-tubulin complex, 148 biochemical screening, 148 callose, 146 CDKs, 154–158 cytoskeletal structures and components, 146–148 MAPs and KLPs, 148 molecular processes, 148 NACK1 and NACK2, 149 NACK-PQR pathway, 149, 149f and phragmoplast expansion, 146–148, 147f Plant hormones auxin, cytokinin, 78 SLs, 78–79 transcriptome analysis, 78–79 Plant peptide containing sulfated tyrosine (PSY1), 94 Plants See Peptides Plasma membrane H+-ATPase ABA-induced stomatal closure, 197–198 ABA-sensitive and -insensitive systems, 200–201 blue-light-induced activation, 194–195 blue-light-induced stomatal opening, 192–194 flowering locus T, 198 hypocotyl elongation, 199–201 nonvascular plant bryophytes, 201–202 Subject Index photosynthesis inhibitors DCMU and DBMIB, 203 physiological signals, 202–203 regulatory system, 203–204 RPM1-interacting protein (RIN4), 198–199 secondary transporters and channels, 192 and stomatal movements, 192–199 structure, 201–202 Pleiotropic functions, FT cultivated sugar beet (Beta vulgaris), 126 differential regulation, plant growth and FT paralogs, 127, 127f flower and bulb formation, onion (Allium cepa), 126–127 plant survival and fitness, 125 poplar trees, 126 segment B region, 127 tuber formation, potato (Solanum tuberosum), 126 Prefoldin (PFD3) DELLAs, 16–17, 17f and PFD5, 16–17 Protein degradation protein–protein interactions, 227–228 ZTL, 217–218 14-3-3 Protein, florigen receptor FAC formation models, 122f, 123–124 Hd3a–GF14b–OsFD1 complex, 123 subcellular localization, 123–124 Protein kinase ABA, 30 MAPK, 35–36 phosphoproteomics, 43f signal transduction pathway, 29–30 SnRK2, 29–30 staurosporine-resistant, 32 Protein phosphorylation network, 45–46 protein–protein interactions degradation and formation, 227–228 FKF1, 220–221 LOV domain, 216–217 ZTL gene, 214–215 ZTL/LKP2, 220–221 R Rapid alkalinization factor (RALF) Arabidopsis, 101 Subject Index biosynthetic process, 100 cytoplasmic event, 101 treatment, 100 Receptors classification, 87–88, 88f CLE, 87 CLV3 signaling, 87–88 and peptide ligands, 86 PSK, 94 SlSys peptide, 92 TDIF, 90 RGF See Root meristem growth factor (RGF) Rice Arabidopsi, 60 mutant d14, 63 photoperiodic flowering blue light signaling, 135 COP1, CO/Hd1 regulation, 134 early heading date1 (Ehd1), 134, 135 GI–CO–FT regulatory module, 134 grain number, plant height and heading date (Ghd7), 134, 135 OsMADS50–Ehd1–RFT1 pathway, 134–135 TPR protein, 75 Root meristem growth factor (RGF) Arabidopsis tpst-1 mutants, 94–95 GLV/CLEL peptides, 95 S SCR See S-locus cysteine-rich (SCR) protein Shoot branching auxin polar transport, 69–71 SL function, 68 TPL/TPR corepressors, 75 transcription response, 68–69 ubiquitin proteasome systems, 71–75 Signaling BES1, 67–68 CLE40, 90 Clp protease family protein, 65–67 CLV3 peptide, 87–88 components, 87–88 cytokinin, 91 D14 and MAX2, 67 description, 60 283 F-box protein, 60–63 α/β-fold hydrolase, 63–65 hormone, 86–87 molecules, plants, 86 PSY1R, 94 RALF, 100–101 shoot branching, 68–71 TPD1, 101–102 Signal transduction pathway protein kinase, 32 role, 31 S-locus cysteine-rich (SCR) protein ARM-repeat containing protein, 99–100 A thaliana, 100 protein 11, 99 and S-locus glycoprotein (SLG), 99 SnRK2 protein ABA signaling, 30 in Arabidopsis and rice genomes, 30–31 bZIP-type transcription factors, 32–34 CDPK interacts, 34–35 CDPK/MAPK pathways, 32, 33f C-terminal region, 32 phosphorylation, 31–32 physiological functions, 31 PYR/PYL/RCAR proteins, 32 SLAC1, 34 SNF1 and AMPK, 30 transcription factor, 34 Spatula (SPT) and DELLA, 7–8 function, 7–8 Squamosa promoter binding-like (SPLs) genes description, 124 GA-biosynthetic gene, microRNA156, Stomagen, 97 Stomatal movements and H+-ATPase “guard cells”, 192 light and abscisic acid (ABA), 192 osmotica releasing, 192 Strigolactones (SLs) biosynthesis and signaling, 58 carlactone, 58–59 description, 17, 58 function and biosynthesis, 58–59, 59f 284 Strigolactones (SLs) (Continued ) and nodulation signaling pathway (NSP1), 76–77 Pi-deficient conditions, 77–78 plant hormones, 78–79 root formation, 76–77 signaling pathway, 60–75 transport, 60 Systemin (SlSys) jasmonic acid, 92 protease inhibitor proteins, 91–92 receptor, 92 T Tapetum determinant1 (TPD1) amino-acid protein, 101–102 and maize multiple archesporial cells (MAC1), 102 mutant phenotype, 102 Terpene synthase 21 (TPS21), 11 Transcriptome analysis, 11–12, 78–79 Transport Inhibitor Response 1/Auxin Signaling F-Box (TIR1/AFB), 199–200 Trapping and targeting function, DELLA ALC and SPT, 7–8 brassinosteroid (BR), 9–10 EIN3, 8–9 jasmonate ZIM domain (JAZ), 10–11 Subject Index PIF, SPLs, U Ubiquitin proteasome systems D14/DAD2, 72–73 DELLA proteins, 71–72 D53 gene, 73 F-box protein, 71 GID1, 71–72 GR24 treatment, 74–75 KAI2, 74 MAX2, 73 X Xylogen, 101 Z Zeitlupe (ZTL) chemical and structural signaling, 232–233 circadian clock regulation, 214–219 C-terminal helical elements, 229–230 E–F loop, 232 N-terminal, 227–228 photoreceptors, 213–214 plant, fungal and bacterial species, 228 sequence analysis, 228, 229f ... ago They observed that light induces bending of the plant hypocotyl and stimulates the stomatal opening, and hypothesized the involvement of effective substances in these phenomena Research on the. .. indicating the contrasting physiological functions of PIFs and DELLAs They revealed that the interaction of DELLA with the bHLH domain of PIF4 diminishes the ability of the latter to bind to the promoters... controlling the stomatal opening and ZTL (ZEITLUPE) responsible for the circadian clock, were also discovered in plants and together commonly encode the LOV domain In addition, the former also codes the