The enzymes, volume 40

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Academic Press is an imprint of Elsevier 50 Hampshire Street, 5th Floor, Cambridge, MA 02139, United States 525 B Street, Suite 1800, San Diego, CA 92101-4495, United States The Boulevard, Langford Lane, Kidlington, Oxford OX5 1GB, United Kingdom 125 London Wall, London, EC2Y 5AS, United Kingdom First edition 2016 Copyright © 2016 Elsevier Inc All rights reserved No part of this publication may be reproduced or transmitted in any form or by any means, electronic or mechanical, including photocopying, recording, or any information storage and retrieval system, without permission in writing from the publisher Details on how to seek permission, further information about the Publisher’s permissions policies and our arrangements with organizations such as the Copyright Clearance Center and the Copyright Licensing Agency, can be found at our website: www.elsevier.com/permissions This book and the individual contributions contained in it are protected under copyright by the Publisher (other than as may be noted herein) Notices Knowledge and best 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: 978-0-12-804752-1 ISSN: 1874-6047 For information on all Academic Press publications visit our website at https://www.elsevier.com/ Publisher: Zoe Kruze Acquisition Editor: Kristen Shankland Editorial Project Manager: Hannah Colford Production Project Manager: Surya Narayanan Jayachandran Cover Designer: Miles Hitchen Typeset by SPi Global, India CONTRIBUTORS D Chandran Regional Center for Biotechnology, NCR Biotech Science Cluster, Faridabad, India C.-Y Chen Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei, Taiwan A Fu The Key Laboratory of Western Resources Biology and Biological Technology; Shaanxi Province Key Laboratory of Biotechnology, College of Life Sciences, Northwest University, Xian, China K He Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China F Kragler Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany X Liu Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China L.K Mishra University of Delhi South Campus, New Delhi, India G.K Pandey University of Delhi South Campus, New Delhi, India S Rao University of Delhi South Campus, New Delhi, India S.K Sanyal University of Delhi South Campus, New Delhi, India E Saplaoura Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany M Sharma University of Delhi South Campus, New Delhi, India D Wang The Key Laboratory of Western Resources Biology and Biological Technology; Shaanxi Province Key Laboratory of Biotechnology, College of Life Sciences, Northwest University, Xian, China M.C Wildermuth University of California, Berkeley, CA, United States vii viii Contributors K Wu Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei, Taiwan Y Wu Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China S Yang Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China C.-W Yu Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei, Taiwan PREFACE This volume of “Developmental Signaling in Plants” is essentially the continuation of Volume 35 in a collective effort to examine the current state of our knowledge and research on the Signaling Pathways in Plants Volume 35 focuses on the discussion of hormonal signaling in plants, whereas Volume 40 explores functions of selective molecules and enzymes exerting functions in different tissues or cellular compartments, including mobile RNAs in phloem sieves, receptor kinases on the plasma membrane, histone-modifying enzymes in the nucleus, calcium sensor kinases on membrane systems, and redox enzymes on thylakoid membrane Phloem serves as a unique highway system of plants Among different types of molecules being distributed via this highway, various classes of RNAs that move along the phloem system are particularly interesting because they transport not only materials but also signaling information Eleftheria Saplaoura and Friedrich Kragler discuss the function of viral RNAs, small interfering RNAs, microRNAs, transfer RNAs, and messenger RNAs transported through phloem and possible mechanisms facilitating RNA distribution via phloem Although calcium signaling across different cellular membrane systems is ubiquitous in different evolutionary lineages, the mechanism and function mediating plant response to environmental stresses is particularly critical to the well-being of plants as sessile organisms Girdhar Pandey and colleagues describe how the sensor–responder complex calcineurin B-like protein (CBL)/CBL-interacting protein kinases and the associated phosphorylation networks mediate plant stress signals Different from animals that rely on adaptive and innate immune systems for defense, plants primarily count on innate immunity to detect and fight against pathogen invasions The plasma membrane system serves as not only barrier defending cells against invading pathogens but also information gateway that leads to the innate immunity Mary Wildermuth and colleagues provide an overview on plant–microbe interactions with focus on function of endoduplication during these interactions Kai He and Yujun Wu contributed a review concerning specifically on receptor-like kinases and their roles in pathogen-associated molecular pattern-triggered immunity Redox homeostasis is another important type of signaling mechanism in both animals and plants In plants, however, light represents a critical environmental factor that triggers redox change through photosynthesis in the chloroplast ix x Preface Aigen Fu discusses an intriguing proposition that in addition to the photosynthetic oxygen-evolving electron transport chain, chloroplasts may also possess a respiratory electron chain on the thylakoid membrane This process is not only important to chloroplast function and plant development, but also vital in protecting plants from environmental stresses Most signaling processes in plants are eventually transduced into the nucleus to achieve specific genome expression patterns as a response to the initial signals and a way to adapt to these signals Keqiang Wu and colleagues review the functions and molecular mechanisms of acetyltransferases and histone deacetylases in plant growth and development Reversible histone acetylation is one of the best-known forms of nuclear protein modification instrumental to the control of gene expression in response to internal and external signals We thank all the authors who contribute to this volume of the Enzymes We would also like to express our appreciation to Hannah Colford at Elsevier for handeling and copyediting of this volume CHENTAO LIN SHENG LUAN FUYUHIKO TAMANOI CHAPTER ONE Mobile Transcripts and Intercellular Communication in Plants E Saplaoura, F Kragler1 Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany Corresponding author: e-mail address: kragler@mpimp-golm.mpg.de Contents Introduction Identification of Mobile RNAs 2.1 Phloem Exudate Analysis 2.2 Grafting 2.3 Tissue-Specific Gene Activity vs Transcript Presence Classes of Mobile RNAs 3.1 Viral RNAs 3.2 sRNAs: Small Interfering RNAs and microRNAs 3.3 RNAs Involved in Translation: Ribosomal RNAs and Transfer RNAs 3.4 Other RNAs: tRNA Halves, Small Nucleolar RNAs, Spliceosomal RNAs, and Signal Recognition Particle RNA Mobile mRNAs Phloem Proteins–RNP Complexes and Transport 5.1 Phloem Proteomics 5.2 RNA-Binding Proteins 5.3 Chaperones: The 70 kDa HSC70 Function of mRNA Movement 6.1 RNA Diffusion vs Active Transport Along the Phloem Outlook Acknowledgments References 3 6 10 11 15 15 16 17 19 20 21 21 22 Abstract Phloem serves as a highway for mobile signals in plants Apart from sugars and hormones, proteins and RNAs are transported via the phloem and contribute to the intercellular communication coordinating growth and development Different classes of RNAs have been found mobile and in the phloem exudate such as viral RNAs, small interfering RNAs (siRNAs), microRNAs, transfer RNAs, and messenger RNAs (mRNAs) Their transport is considered to be mediated via ribonucleoprotein complexes formed between phloem RNA-binding proteins and mobile RNA molecules Recent advances in the analysis of the mobile transcriptome indicate that thousands of transcripts move The Enzymes, Volume 40 ISSN 1874-6047 http://dx.doi.org/10.1016/bs.enz.2016.07.001 # 2016 Elsevier Inc All rights reserved E Saplaoura and F Kragler along the plant axis Although potential RNA mobility motifs were identified, research is still in progress on the factors triggering siRNA and mRNA mobility In this review, we discuss the approaches used to identify putative mobile mRNAs, the transport mechanism, and the significance of mRNA trafficking INTRODUCTION In multicellular organisms to ensure proper body shape formation, coordinated growth, and adaptation to environmental changes, cells have to communicate with each other This is achieved via so-called noncellautonomous signals in the form of small molecules such as hormones, or macromolecules such as proteins and RNAs, that can be perceived in neighboring cells or in distant tissues In plants, macromolecules predominantly move from cell to cell via plasmodesmata These are intercellular pores stretching across the cell wall of neighboring cells In the vasculature the molecules enter via the companion cells, the sugar-conducting sieve tubes, forming a distribution pipeline to distant apical tissues It is thought that the phloem-mediated signaling route to distant tissues follows the symplastic source to sink flow from mature sugar-producing to young or nonphotosynthetic sugar-catabolizing plant parts It is suggested that transported macromolecules gain access to the symplastic pathway through plasmodesmata by diffusion However, for a number of viruses and endogenous RNAs and proteins, an actively regulated recognition and transport system seems to be in place For example, the phloem-allocated florigenic FLOWERING LOCUS T (FT) protein interacts with an endoplasmic reticulum (ER)-associated protein named FTIP1 in phloem companion cells This interaction mediates the transport of FT via the phloem to the shoot meristem where FT protein initiates the flower formation program [1,2] More recently, evidence gained on chimeric plants produced by stem or hypocotyl grafting methods revealed that a high number of small RNAs (sRNAs) and proteinencoding messenger RNA molecules, which represent approximately 25% of the transcriptome, are exchanged between source (mature leaves) and sink (apices, roots) tissues [3–5] Although little is known about how RNAs enter or exit the phloem in distant tissues, it is suggested that mobile transcripts interact with specific RNA-binding phloem proteins, and that at least some mobile mRNAs harbor a motif triggering their transport This review focuses on the identified mobile RNAs and their interacting proteins Finally, we address the potential function of RNA molecules found in the phloem and in distant tissues Mobile Transcripts and Intercellular Communication IDENTIFICATION OF MOBILE RNAs The three main approaches used to identify mobile macromolecules in plants are assays on (i) phloem exudate samples, (ii) heterografted/chimeric plants, and (iii) tissue-specific gene activity vs transcript presence (Fig 1) Note that sampling of phloem sap and the respective detailed protocols were recently reviewed by Dinant and Kehr [9] and are only briefly mentioned here 2.1 Phloem Exudate Analysis The vascular phloem tissue is the long-distance transport pathway for mobile RNAs RNA molecules produced in cells symplastically connected to companion cells were shown to move into sieve tubes [10] Thus, presence of a transcript in the phloem exudate reflecting the systemically transported content of the sieve tubes [11,12] is a good indicator for an actively transported macromolecule One of the most challenging steps is gaining access to the sieve elements and the extraction of the phloem sap Several methods have been developed that are depending on the studied plant species The most common being used are spontaneous exudation (bleeding) [13], EDTAfacilitated exudation [14], and insect stylectomy [15] Plants that possess the trait of spontaneous exudation after wounding allow the easy collection of phloem sap, usually in large amounts Cuts of the petiole or shallow incisions in stem or petiole have been successfully used for phloem sap analysis in various species such as cucurbits [6,16,17], lupin (Lupinus albus) [18,19], rapeseed (Brassica napus) [7,20], and castor bean (Ricinus communis) [21,22] Usually the phloem sap is rather pure if the damage is minimal and the first exudate is removed However, most plants prevent the phloem bleeding upon wounding by oxygen-induced rapid aggregation of P-proteins [23] and formation of callose plugs at the sieve plate pores [24] Another widely used method employs EDTA to facilitate exudation by impeding the sealing of the phloem [14] EDTA is a calcium chelator, and as such, it can block the Ca2+-induced response to phloem injury It is a simple, low-tech method where cut petioles are allowed to exude in EDTAcontaining collection fluid or water, after incubation with EDTA It also allows the collection of phloem sap from species that not exude spontaneously [18,19,25–28] However, the risk of contamination is higher due to the use of EDTA, which softens and potentially harms the tissue, and the long duration of sampling Moreover, the exudate is diluted and thus not suitable for quantitative studies E Saplaoura and F Kragler Methods for identification of mobile transcripts and proteins (i) Phloem-exudate RNA and protein analysis (a) Shoot-allocated (b) Source leaf (c) Root-allocated (a) (b) (c) (ii) Transcript presence in heterografted/chimeric plants Genotype A Stock/shoot graft Genotype B Chimeric grafted plant Exposure to various growth conditions (iii) Tissue-specific gene activity vs transcript presence Sampling of distinct cell types RIP and RNA seq Transcript X (1) (2) Epidermis e.g., Leaves e.g., Roots None Phloem Instable Phloem Neutral Epidermis Mobile (1) RNA polymerase II-enriched RNA (nucleus) (2) Poly(A)-RNA/ribosomal-enriched (cytosolic) High presence Low/no presence Fig Methods for identification of mobile transcripts and proteins (i) Phloem exudate sampling The phloem exudate (¼phloem sap) is thought to reflect the content of the sieve tubes which is transferred from source to sink Phloem sap then can be harvested from cut petioles, stems, or shoot/root apices by capillaries This is used on species such as pumpkin, cucumber, watermelon, castor beans, and rapeseed An alternative approach is submerging the cut surface in EDTA supplemented phosphate buffer to facilitate phloem sap collection in species that are not continuously bleeding such as Arabidopsis and tomato Harvested phloem sap can be analyzed for metabolite, RNA, and protein presence using metabolomics, deep sequencing, or proteomics platforms [6–8] (ii) Chimeric plants made by grafting or by tissue culture Mobile heterologous transcripts and proteins present in heterografted/chimeric plants can be detected in Mobile Transcripts and Intercellular Communication Insect stylectomy was introduced in 1953 [15] and concerns plant species that can be infected by aphids or other phloem-feeding insects It is a technically challenging method as it requires the careful removal of the insect by cutting off the stylet after it is inserted in the sieve elements [29] The phloem sap is then allowed to exude from the cut stylet and the collected sample is used for subsequent analyses [30–32] Although insect stylectomy is the most natural and less invasive method of collecting phloem sap, insects can interfere with sap purity via saliva secretion leading to alterations in phloem composition [33,34] 2.2 Grafting Grafting is a technique which was already used by ancient Greek and Romans in the Mediterranean region by the 5th century BCE and recorded in the middle ages [35] as a method to propagate and improve dicotyledonous crop species such as apple and orange trees, and grapevines More recently, grafting is used in scientific studies to improve root stock breeding programs in Solanaceae such as tomato (Lycopersicon esculentum), and in the widely used plant biology model species Arabidopsis thaliana to characterize and identify long-distance signals and mobile macromolecules such as the florigenic FT protein produced in source leaves and moving into shoot apices where it induces flower formation [1,2,36,37] To detect and identify mobile transcripts, there should be a genetic variation between the grafted stock (e.g., root) and the scion (e.g., shoot) plant parts The grafts can be interspecies, using graft-compatible plant species or closely related ecotypes, or intraspecies using mutants or transgenic lines Grafts between different genotypes are called heterografts Grafts of the same genotype are called autografts, which are used as controls in experiments Graft junctions are formed by healing of the cut and aligned stems or petioles and the reestablishment of a fully functional vascular connection between the attached stock and scion tissues Once this connection is successful, small distant cells or tissues Mobile mRNAs and/or proteins moving to neighboring cells or distant tissues are detected in distant cells isolated by, e.g., fluorescence-aided cell sorting (FACS) or in distant tissues such as roots or apices formed on grafted heterologous plants (iii) Tissue-specific gene expression activity vs transcript presence Distinct tissues or cells can be harvested by FACS or cutting and submitted to specific RNAcoimmunoprecipitation (RIP) protocols aiming to enrich, e.g., nascent DNA-dependent RNA polymerase II transcripts (nuclear) and translated ribosomal-associated mRNA transcripts (cytosolic) A difference in their presence in, e.g., phloem tissue vs epidermis or mesophyll indicates potential mobility of the protein-encoding transcripts Author Index Suzuki, T., 12–14, 13–14t, 66–69, 74, 91–92, 150 Svab, Z., 161 Swain, J.D., 108 Swiderski, M.R., 124–125 Symons, G.M., 108 Szczyglowski, K., 82–87, 83–86t T Tabata, S., 82–87, 83–86t Tabler, M., 7–8 Tada, Y., 66–69, 74, 91–92 Tafrov, S.T., 178 Taga, M.E., 79–81 Tagkalaki, P., 118, 128–129t Tai, Y.C., 83–86t Taiz, L., 144–145 Takagi, H., 149–150, 152, 160–161 Takahashi, G., 152–153 Takahashi, N., 74, 77 Takahashi, S., 156–157 Takahashi, T., 122 Takahashi, Y., 40, 44 Takai, R., 109–110, 128–129t Takaichi, S., 149–150, 152, 160–161 Takano, Y., 116 Takatsuka, H., 74 Takayama, S., 109–110, 128–129t Takebayashi, Y., 175–177t, 182–183 Takeda, N., 82–87, 83–86t Takeda, R., 7–8 Takio, K., 112–113, 128–129t Talbot, N.J., 113–114, 128–129t Taly, A., 151–154, 157, 161–162 Tamaki, S., 5–6 Tameling, W.I., 117–118, 128–129t Tamiru, M., 149–150, 152, 160–161 Tan, T., 12, 13–14t Tan, X., 106–107 Tanaka, A., 152–153 Tanaka, K., 114, 128–129t Tanaka, M., 175–177t, 182–183 Tang, D., 124, 128–129t Tang, R.J., 38, 47–49, 52, 55–56 Tang, W., 108, 118–119, 124 Tanriverdi, O., 189 Tao, X., 7–8 Taoka, K.-I., 5–6 223 Taranto, P., 180–181 Tarayre, S., 72, 82, 83–86t Tatsumi, R., 152–153 Taverna, S.D., 177 Tax, F.E., 114–115, 118–120, 128–129t Taylor, B.G., 147–148, 162–163 Telfer, A., 158 Tempst, P., 180–181 Tena, G., 109–110 Terauchi, R., 149–150, 152, 160–161 Terry, M.J., 149–150, 152, 160–161, 184 Tetyuk, O., 3, 15 Thieme, C.J., 2, 10–14, 11f, 13–14t, 20–21 Thines, B., 191–192 Thivierge, K., 18 Thomann, A., 75–76 Thomas, J.D., 147–148, 162–163 Thomas, M.R., 108 Thomashow, M.F., 188–189 Thomma, B.P., 106–107, 111–112, 117–118, 120–121, 128–129t Thompson, D.M., 10 Thompson, G.A., 3, 15 Thompson, R.D., 175–177t, 182 Thorn, G., 190 Tian, L., 175–177t, 179–182, 184–186 Tian, L.N., 190 Tian, X., 116, 123–124 Tielens, A.G.M., 151–152 Tilney-Bassett, R.A.E., 147 Timmermann, T., 179 Timmers, T., 82 Tintor, N., 111–112, 116 Tisne, S., 70 Tjoitang, D., 118, 128–129t To, T.K., 175–177t, 188–189 Toal, T.W., 15–16 Tolstikov, V., 4–5f Tominaga, R., 74–75 Tomizawa, K.I., 162 Tong, H., 116–117 Toonen, M.A., 118–119 Toop, M., 152 Tor, M., 106–107, 111–112, 117–121, 128–129t Torrance, L., 18 Torres Acosta, J.A., 71–72 Tourasse, N.J., 151–154, 157, 161–162 224 Tournier, B., Tracewell, C.A., 158 Tran, L.P., 57–58 Triezenberg, S.J., 188–189 Tromas, A., 82–87, 83–86t Trotta, A., 87–88 Trouillard, M., 157, 161–162 Tsaftaris, A., 179, 190 Tsagris, M., 7–8 Tsai, C.H., 110–111, 128–129t Tsang, E.W., 43t Tsay, Y.F., 49–51 Tsementzi, D., 189 Tseng, C.Y., Tsikou, D., 18 Tsuda, K., 113–114, 116, 119–120, 128–129t Tsuge, C., 152–153 Tsukaya, H., 77, 108 Tsuyama, M., 156–157 Tundo, S., 116, 128–129t Turgeon, R., 3, 15 Turlings, T.C., 116 Turnbull, C., 2, 4–5f, 5–6, 21 Tuteja, N., 46–47, 55 Tyagi, A.K., 57–58 Tzeng, Y.H., 108 U Ubalijoro, E., 18 Ueno, Y., 175–177t, 184–186 Uhrig, J.F., 18, 77 Um, J.H., 74, 92–93 Umbach, A.L., 145, 149–150, 152–153, 156 Umeda, M., 66–69, 72–77, 91–92 Undan, J.R., 149–150, 152, 160–161 Unyayar, S., 109–110 Urbain, A., 93 Usami, T., 117–118, 128–129t Utsushi, H., 149–150, 152, 160–161 V Valerius, O., 113 Valkonen, J.P.T., 18 Vallat, A., 116 van Bel, A.J.E., 3, Van Cappelle, E., 83–86t, 89–90 Van Damme, D., 83–86t, 90 Author Index Van De Slijke, E., 83–86t, 90 Van de Velde, W., 79–81 Van den Ackerveken, G.F., 117–118, 128–129t van den Berg, G.C., 117–118, 128–129t van den Burg, H.A., 117–118, 128–129t Van Den Daele, H., 70–74 van der Burgh, A.M., 122 Van der Hoorn, R.A., 106–107 Van Der Schueren, E., 71–72, 75–76 van der Wel, N.N., van Esse, H.P., 111–112, 117–118, 128–129t Van Hummelen, P., 74–75 Van Isterdael, G., 71–72, 83–86t, 90 Van Kan, J.A., 117–118, 128–129t van Kan, P.J., 162 Van Leene, J., 71–72, 83–86t, 90 van Lent, J., van Lent, J.W.M., Van Lijsebettens, M., 189–190 Van Norman, J.M., 15 van Verk, M.C., 115–116 Vanhoutte, I., 118–119 Vanlerberghe, G.C., 149–150 Vanstraelen, M., 72–74, 89, 93–94 Varkonyi-Gasic, E., 3, 4–5f, 5–6, 8–9, 11–12, 16, 20 Vaubert, D., 79–81, 89 Vaucheret, H., 8, 19–20 Veiga, R., 18 Velasquez, A.C., 113–114, 128–129t Vener, A.V., 162 Ver Loren van Themaat, E., 95–96 Verberne, M.C., 117–118, 128–129t Vercruysse, S., 74–76 Vergnes, S., 119–120 Verica, J.A., 116–117 Verkest, A., 75–76, 83–86t, 90 Verma, R., 114–115 Veronese, P., 123 Verret, F., Versees, W., 189–190 Verslues, P.E., 55 Vert, G., 118–119 Vidal, M., 95–96 Vieira, P., 83–86t, 88–90 Vielle-Calzada, J.P., 118–119 Author Index Viitanen, P.V., 148–149 Vilaine, F., 12, 13–14t Vile, D., 70 Villar, C.B., 181 Vinardell, J.M., 82, 83–86t, 89 Vincent, C., 2, 5–6, 21 Vlachonasios, K.E., 188–189 Vleminckx, K., 118–119 Vlieghe, K., 71–74, 89 Voevodskaya, N., 152–153 Vogel, J.P., 83–86t, 92–94 Vogelsang, R., 117–118, 128–129t Voinnet, O., Volkmann, D., 116–117 Von Gabain, A., 18 Voß, U., 91–92, 95 Vothnecht, U.C., 144, 159 Voytas, D.F., 147–149, 152, 159–160 Vrettos, J.S., 158 Vrmass, W.F., 146 Vuylsteke, M., 74–75 W Waadt, R., 38–39, 47–49 Wada, M., 113–114 Wada, T., 74–75 Wade, P.A., 181 Wafula, E.K., 6, 13–14t Wagemakers, L., 118, 128–129t Waites, R., 72–74 Walker, G.C., 79–81 Walker, J.C., 118–119 Walker, J.D., 74–75 Walker, R.K., 114–115 Wallace, A.J., 7–8 Waller, F., Wallington, E., 111–112 Wallmeroth, N., 118 Walser, M., 180–181 Walther, D., 2, 8–15, 11f, 13–14t, 20–21 Walz, C., 3, 15 Wan, J., 112–114, 128–129t Wang, B., 12, 13–14t, 106–107, 128–129t Wang, C.Z., 175–177t, 191–192 Wang, D., 121–122, 128–129t Wang, E., 113–114 Wang, E.H., 179 Wang, G., 106–107, 117 225 Wang, G.L., 106–107, 128–129t, 175–177t, 192 Wang, H., 93, 109–112 Wang, H.H., 111–112 Wang, H.-L., 11f, 16–17 Wang, J., 110–113, 118, 152 Wang, J.J.J., 12, 13–14t Wang, K., 74–75 Wang, R., 118–119, 124 Wang, S., 109–112, 159 Wang, X., 34–35, 93, 108, 120–122, 128–129t Wang, X.P., 49–51 Wang, Y., 7–8, 47–51, 110–111, 123, 156, 181 Wang, Y.Y., 175–177t, 190–191 Wang, Z., 12, 13–14t, 121–122, 124, 175–177t, 182–183 Wang, Z.Y., 118–119, 124 Wargent, J.J., 71 Warren, R.F., 124–125, 128–129t Wassarman, D.A., 180–181 Watanabe, A., 66–69, 91–92 Watanabe, Y., Watson, L.A., 183 Wege, C., 18 Wei, S., 56–57 Wei, X., 124 Weigel, D., 95–96 Weinl, C., 75–76 Weinl, S., 33–39, 36–37t, 41 Wen, B., 75–76 Wen, J., 118–119 Wen, T., 157 Wessling, R., 95–96 West, C.E., 77 West, G., 74–75 Westhoff, P., 144, 159 Westphal, L., 123 Westwood, J.H., 6, 13–14t Wetzel, C.M., 147–149, 152, 159–160 Wetzel, C.W., 148–149 Wheeler, T.A., 119–120, 128–129t White, W.S., 149–150, 152, 159–160 Wierzba, M., 118, 120, 128–129t Wigge, P.A., 2, 5–6, 21 Wiig, A., 125 Wilce, J.A., 150 226 Wildermuth, M.C., 66–96, 83–86t Wiley, K., 95–96 Wilkinson, R.C., 119–120 Will, T., Williamson, B., 87 Willmann, M.R., 109–110 Willmann, R., 113–114, 128–129t Windeisen, V., 18 Winter, N., 10, 11f, 21 Witters, E., 71–72 Wolf, E., 178 Wolf, S., 3, 11–12, 13–14t, 15–16 Wollman, F.A., 151–154, 157, 161–162 Wong, H.L., 5–6 Woo, Y.M., 70 Woods-Tor, A., 106–107, 117 Workman, J.L., 179 Wright, D.A., 147, 149, 152, 159 Wu, A.J., 125 Wu, D., 147–149, 152, 159–160 Wu, H., 90–91 Wu, J., 7–8 Wu, K., 12, 13–14t, 174–193, 175–177t Wu, K.Q., 175–177t, 190–192 Wu, M., 12, 13–14t Wu, P.C., Wu, S., 110, 123, 128–129t Wu, W., 120–121 Wu, W.H., 47–51 Wu, Y., 72–74, 106–128 Wyrsch, I., 109–110 X Xia, X., 55–56 Xia, Y., 12, 13–14t Xiang, T., 123–125, 128–129t Xiang, Y., 3, 15 Xiao, Y., 121 Xie, C., 43t, 56 Xie, Q., 116, 123–124 Xin, X.F., 95–96 Xing, M., 12, 13–14t Xoconostle-Ca´zares, B., 5–6, 9–10, 11f, 15–21 Xu, A., 11f, 16–17 Xu, C.R., 175–177t, 186 Xu, F., 121–122, 128–129t Xu, G., 121 Author Index Xu, H., 19–20, 19f Xu, J., 43t, 47–51, 124 Xu, J.R., 113–114, 128–129t Xu, P., 74 Xu, Q., 33–34, 41, 45–46 Xu, S., 118–119 Xu, X., 113–114, 118, 122, 128–129t Xu, Y.Y., 12, 13–14t Xu, Z.H., 175–177t, 186 Xun, Y., 7–8, 20 Y Yabu, Y., 150 Yalovsky, S., 34, 38, 49 Yamada, K., 8, 116, 119–120 Yamaguchi, S., 160–161 Yamaguchi, Y., 114–115, 128–129t Yamamoto, H., 161 Yamasaki, S., 10 Yamashita, E., 145 Yamashita-Yamada, M., 116, 119–120 Yamaya, T., 11f, 16–17 Yan, H., 124, 128–129t Yan, L., 124 Yan, Z., 118–119 Yanagisawa, S., 15 Yang, C., 124 Yang, E.J., 117 Yang, F., 116, 123–124 Yang, J., 109–114, 128–129t Yang, L., 2, 10–14, 11f, 13–14t, 20–21, 95–96 Yang, S., 121–122, 174–193 Yang, Y., 2, 12–14, 13–14t, 34, 43t, 46–47, 48t, 118, 128–129t Yano, R., 175–177t, 182–183 Yao, Q., 15–16 Ye, Q., 108 Yeh, Y.H., 110–111 Yerk-Davis, G.L., 70 Yi, H., 12, 13–14t Yi, J., 118–119 Yin, H., 118–121 Yin, W., 55–56 Yin, Y., 12, 13–14t, 108 Ying, L., 74 Yokoi, S., 5–6 Yokota, T., 149–150, 152, 160–161 Author Index Yonekura-Sakakibara, K., 11f, 16–17 Yoneyama, T., 15 Yoo, B.-C., 3, 4–5f, 8–9, 11–12, 11f, 16–17, 20 Yoo, M.J., 78–79 Yoo, S.D., 124 Yoo, Y.J., 117 Yoon, E.K., 74, 92–93 Yoon, H.J., 82–87, 83–86t Yoro, E., 82–87, 83–86t Yoshida, A., 2, 11–14, 13–14t, 20 Yoshida, K., 149–150, 152, 160–161 Yoshida, S., 120–121 Yoshimura, M., 72–74 You, J.Y., 121 Young, J.C., 17–18 Yu, C.-W., 174–193, 175–177t Yu, F., 152, 154–155, 159 Yu, L., 110–111, 123 Yu, Q., 154–155, 157–158 Yu, T.S., 15, 19–20, 19f Yu, X., 11f, 16–17, 121 Yu, Y., 15, 19f, 20–21 Yuan, L., 174 Yuan, T., 120–121 Yun, U.J., 117 Z Zabotina, O.A., 161–163 Zalmas, L.P., 72–74, 89, 93–94 Zapata, J.M., 161 Zeevaart, J.A.D., Zeiger, E., 144–145 Zeng, L., 113–114, 128–129t Zeng, W., 110 Zerbini, F.M., Zhai, W.X., 106–107, 128–129t Zhan, Y., 121 Zhang, B., 4–5f Zhang, C., 42–44, 43t Zhang, H., 12, 13–14t, 38, 55–56, 118 Zhang, J., 12, 13–14t, 106–107, 113–114, 123–125, 128–129t Zhang, J.S., 156 Zhang, K., 174 Zhang, L., 118, 128–129t, 175–177t, 190–192 Zhang, M., 109–110 227 Zhang, Q., 123 Zhang, S., 9–12, 108–112, 121 Zhang, W., 2, 8, 10–14, 11f, 13–14t, 20–21, 118, 128–129t Zhang, X., 12, 13–14t, 110–111, 113–114, 121–125, 128–129t Zhang, X.C., 112–114, 128–129t Zhang, Y., 12, 13–14t, 110–111, 113, 116, 118, 121–125, 128–129t, 180–181 Zhang, Z., 2, 11–16, 13–14t, 20, 113, 117–118, 121–122, 128–129t Zhang, Z.Z., 12, 13–14t Zhao, F., 175–177t, 186 Zhao, H., 12, 13–14t Zhao, J., 118–121 Zhao, J.H., 175–177t, 191 Zhao, L., 191 Zhao, Q., 52 Zhao, T., 93, 124, 128–129t Zhao, X., 12, 13–14t Zhao, Y., 77, 114–115 Zhao-Hui, C., 111–112 Zheng, Y., 2, 11–16, 13–14t, 20, 175–177t, 190–191 Zheng, Z., 12, 13–14t Zhong, G.-Y., 2, 12–14, 13–14t Zhong, S., 12, 13–14t Zhong, X., 7–8 Zhong, X.C., 175–177t, 191 Zhou, C., 191–192 Zhou, C.H., 175–177t, 191 Zhou, D.X., 175–177t, 183–184, 189 Zhou, H., 39, 41–42, 124 Zhou, J., 15–16, 74–75, 110 Zhou, J.L., 183 Zhou, J.M., 106–113, 116, 118, 123–125, 128–129t Zhou, X., 43t, 51–52, 56 Zhou, X.F., 189–190 Zhou, Z., 110–111, 123 Zhou, Z.J., 189–190 Zhu, C., 159 Zhu, J., 174, 188–189 Zhu, J.K., 33–49, 43t, 55, 174, 190–191 Zhu, L.H., 106–107, 128–129t Zhu, N., 124 Zhu, S., 118–119, 124 Zhu, W., 108 228 Zhu, Y., 7–8, 20 Zhu, Z., 72–74 Zhu, Z.Q., 175–177t, 191–192 Zhuang, X., 93 Zhu-Salzman, K., 123 Ziegler, A., 18 Zimmer, C., 18 Zimmerli, L., 110–111, 128–129t Author Index Zimmermann, M.H., Zipfel, C., 106–112, 117–121, 123, 128–129t Zito, F., 162 Zou, B., 121 Zou, X., 12, 13–14t Zou, Y., 123–125, 128–129t Zwirglmaier, K., 151–152 SUBJECT INDEX Note: Page numbers followed by “f ” indicate figures, and “t” indicate tables A Abiotic stresses ABO1 in, 189–190 cold acclimation process, 188–189 cold-regulated (COR) gene expression, 188–189 GCN5, 189 HAC1 mutations, 189–190 HATs, 188–190 HDACs, 188–189 histone acetylation, 188–189 mannitol treatment, 191 phytohormone ABA, 190 Pi-responsive genes, 190–191 salt treatment, 191 seed germination, 191 SGF29a mutation, 189 transgenic seedlings, 190–191 Abscisic acid (ABA) pathways, 182–183 Activation loop, 40–41 Affinity purification assay, 112–113 Alternative oxidase (AOX), 146, 149–150, 151f AOX See Alternative oxidase (AOX) Arabidopsis, mutations of, 183 ATP binding pocket, 40–41 B BAK1 cell death control in Arabidopsis, 120–121 BON1, 121–122 cysteine-rich receptor-like kinase (CRK), 121 ER–QC, 121 NahG gene, 120–121 seedling lethality, 120–121 PRR-associated RLKs Arabidopsis, antiviral resistance in, 119–120 brassinolide (BL), 118–119 brassinosteroids (BRs), 118–119 BRI1, coreceptor of, 118–119 cellulose-binding elicitor lectin (CBEL), 119–120 C408Y mutation, 120 elicitor ethylene-inducing xylanase (Eix), 119–120 flagellin recognition, 120 flg22 treatment, 119–120 SOBIR1 bir1, defense responses in, 122 cellular responses, 122 LRRs, 122 Bean common mosaic necrosis virus (BCMNV), BEL1-like transcription factor, 19f, 20 BIK1, 123–124 Biotic stresses HDA6, 191–192 HDA19, overexpression of, 191 histone acetylation, 191 jasmonate (JA), 191 OsHDT701 overexpression of, 192 silencing of, 192 OsSRT1, downregulation of, 192 SRT2, 191–192 BSK1, 124 C Calcineurin, 45–46 Calcineurin B-like protein (CBL) Ca2+ binding proteins, 39 lipid modification site of acylation, 38 myristoylation, 38 N-terminus, 38 tonoplast-targeting sequence (TTS), 38 motifs in calcineurin, 34 catalytic subunit (CNA), 34 EF-hands, 34 neuronal calcium sensor (NCS), 34 229 230 Calcineurin B-like protein (CBL) (Continued ) regulatory subunit (CNB), 34 phosphorylation, 46–47 3D structure of Ca2+ ion, 35–38 CNBs, 35 EF-hands, 35–38, 36–37t helix–loop–helix structural domain, 35 Calcium chelator See EDTA-facilitated exudation Calcium signature, 32–33 CaM-dependent kinase (CaMKs), 33, 39 Carotenoid biosynthesis, 148–149 Ca2+ sensors, 33 CBLs, 33–39 Ca2+ signal, 32–33 CBL–CIPK modules functions abiotic stress, 56 bimolecular fluorescence complementation (BiFC), 47–49 biotic stress, 56–57 Ca2+ binding to CBL, 46 calcineurin, 45–46 canonical SOS pathway, 55–56 effector-triggered immunity (ETI), 56–57 kinase-associated domain1 (KA1), 47 NAF domain, 46 pattern-triggered immunity (PTI), 56–57 phosphorylation and activation, 46–47, 48t programmed cell death, 56–57 ROS, 56–57 simultaneous alternate complex formation, 49 SOS3–SOS2 complex, 46 subcellular localization analysis, 47 target modulation by ABA-signaling pathway, 51–52 AKT1, 49–51 AKT1 interacting protein phosphatase (AIP1), 49–51 CIPK26, 52 downstream interactors, 49 E3-ligase KEG, 51–52 Subject Index K+ concentration, 49–51 nitrate uptake system, Arabidopsis, 49–51 phosphorylation dependent control, 49–51 RBHOF, 52 salt stress, 49–51 SOS2/CIPK24 protein, 55 tonoplast/vacuoles, 52 CBL-interacting protein kinases (CIPK) activation, 46–47 kinase activity, 42–44 kinase domain of, 40 molecular insight of, 41–42 motifs in, 39 regulatory domain of, 40 Ser/Thr kinases, 44 Cell identity, 15–16 Chaperones, 17–18 heat-shock proteins, 17–18 HSC70 proteins, 18 nuclear inclusion a (NIa), 18 RNA-dependentRNApolymerase (RdRP), 18 Chitin, 112–113 Chitin elicitor receptor kinase (CERK1) affinity purification assay, 112–113 biochemical assay, 113–114 chitin-binding affinity of, 113–114 ectodomain shedding of, 113 kinase activation, 112–113 lysine motifs (LysMs), 112–113 mycorrhizal interaction, 113–114 peptidoglycans (PGNs), 113–114 polyubiquitination, 113–114 Chitin tetramer, 118 Chlorophyll biosynthesis, 184 Chloroplast photosynthetic electron transfer chain, 144–145 Chloroplasts, 145 biogenesis, 160 import assays, 149 respiratory activity, 146 Chlororespiration, 146, 161–162 Chlorotic siliques, 148 Chromatin, 174 Chromatin-remodeling capacity, 180–181 Coat proteins (CPs), 6–7 231 Subject Index Coimmunoprecipitation (Co-IP), 123 Cold acclimation process, 188–189 Cold-regulated (COR) gene expression, 188–189 Coreceptor, 125–126 Cowpea mosaic virus (CPMV), Cucumber mosaic virus (CMV), Cyclophilin (Cyp), 15–16 Cysteine protease inhibitor (CPI), 17 D Damage-associated molecular patterns (DAMPs), 106–107 PEPRs, 114–116, 127f Diiron-carboxylate (DOX) protein, 152–153 Dimerization domain (D-Domain), 154 Double fertilization, 182 E EDTA-facilitated exudation, 3, 12 Effector-triggered immunity (ETI), 106–107 CBL–CIPK module, 56–57 PBS1, 124–125 EF-TU receptor (EFR), 111–112, 127f EIN3 protein, 124 Elongation factor Tu (EF-Tu), 111–112 Endocycle machinery CDKB/CYC activity, 71–72 cell expansion, 71–72 endoreduplication, 71–72 onset APC/C E3-ubiquitin ligase, 72 CCS52 genes, 72–74 CDKB/CYC activity, 72 CDK/CYC, kinase activity of, 74–75 cytokinin signaling, 74 E2Fb transcription factor, 72–74 endoreduplication, 74 leaf cell ploidy, 74 phytohormones, 74 repressor complexes, 74 SIAMESE (SIM), 74–75 siamese-related proteins (SMRs), 74–75 teosinte-branched (TCP), 72–74 ubiquitin-interacting motifs, 72–74 progression and termination CDKA activity, 75–76 DNA damage repair checkpoints, 77 DNA topoisomerase, 77 G1/S transition, 75–76 KRPs, 75–76 loss-of-function analyses, 75–76 S-phase progression, 75–76 trichome development, 77 endoreduplication mutualistic biotrophs, 78 plant biotrophs, 78 plant–parasitic interactions powdery mildew-induced host endoreduplication, 90–94 root nematode-induced host endoreduplication, 88–90 plant–symbiotic interactions legume–rhizobia, 79–87 plant–endomycorrhiza, 87–88 Enzymic activity, PTOX AOX1a, 155 disulfide bond-mediated enzyme activation mechanism, 155–156 in vitro assay, 155 quinone molecules, 154–155 reactive oxygen species (ROS), 155 UQH2, 155 ETI See Effector-triggered immunity (ETI) Etiolated seedlings, 184 F Flagellin-sensitive (FLS2) bacterial flagellin, 108–109 brefeldin A (BFA)-sensitive route, 110 CLAVATA3, 109–110 ectodomain residues, 108–109 ethylene signaling, 110–111 extracellular domain (ECD) structures, 108–109 flg22, 108–110 L-type lectin receptor kinase-VI.2 (LecRK-VI.2), 110–111 Pst DC3000, 110 reticulon-like proteins, 110 toll-like receptors (TLRs), 108–109 Flowering locus C (FLC), 186–187 Flowering locus T (FT), 2, 5–6, 186–187 232 Flowering time, regulation of flowering locus C (FLC), 186–187 flowering locus T (FT), 186–187 HDA5, 186–187, 188f HDA6, 186–187, 188f G GAI See Gibberelic acid insensitive (GAI) Gibberelic acid insensitive (GAI), 19–20, 19f Glycine max, 152 Glycine-rich protein (GRP), 117 Grafting technique, 5–6 Grafts, 5–6 H HDA6, 175–177t, 186 leaf development, 184–186 root development, 186 Heat shock protein (Hsp), 17, 111–112 Heterografting experiment, Higher plants, identification of PTOX AOXs, 149 chloroplast import assays, 149 GHOST genomic DNA, 149–150 IM cDNA, 149 IM gene, 149 IM protein, 149 Histone acetylation acetyltransferases, 177–179 deacetylases, 179–181 future perspectives, 192–193 hyperacetylation, 174 hypoacetylation, 174 N-terminal lysine residues, 174 in plant development dormancy, 182–183 flowering time, regulation of, 186–187 germination, 182–183 leaf development, 184–186 photomorphogenesis, 183–184 root development, 186 seed development, 182–183 in plant response to environmental stresses abiotic stresses, 188–191 biotic stresses, 191–192 Histone acetyltransferases (HATs), 174, 174f, 177–179 A-type, 177–178 Subject Index B-type, 177–178 functions of, 174, 175–177t general control nonrepressible-related N-terminal acetyltransferase (GNAT) proteins, 178 in silico, 177–178 lysine residue, 177 MYST, 178 p300 and CBP proteins, 178 SAGA complexes, 179 subunit identification, 179 TATA-binding protein (TBP), 179 Histone deacetylases (HDACs), 174, 174f, 179–181 Arabidopsis, 179–180, 180f chromatin-remodeling capacity, 180–181 functions of, 174, 175–177t HD2, 179–180 lysine-specific histone demethylase 1A (LSD1), 181 nucleosome remodeling deacetylases (NuRD), 181 reduced potassium dependence (RPD3), 179–181, 180f silent information regulator (SIR2), 179–181 I Immutans Arabidopsis, 147, 148f carotenoid biosynthesis, 148–149 chlorotic siliques, 148 green sectors, 147–148 phytoene desaturase (PDS), 148–149 white sectors, 147 IM protein, 149 Insect stylectomy, 3, In vitro phosphorylation activity, 42–44, 43t, 45f Isoprenoid biosynthesis pathway, 158 J Jasmonic acid (JA) treatment, 116 Junction domain, 41–42 K Kinase activity CIPK ATP binding pocket, 44 233 Subject Index dead kinase, 44 fusion protein, 42–44 in vitro phosphorylation activity, 42–44, 43t, 45f mutated variant, 42–44 myelin basic protein (MBP), 42–44 native protein, 42–44 Kinase domain, 40 KNOX genes, 184–186 L Laser microdissection coupled to pressure catapulting (LMPC), 12 Leaf cell ploidy, 74 Leaf development, 184–186 Leaf primordia, 184–186 Lettuce mosaic virus (LMV), Leucine-rich repeats (LRRs), 106–107 Light irradiation, 183 Light-regulated gene expression, 183 Light signals, 183 Linear electron transfer (LET), 162 Lipid modification site, CBL acylation, 38 myristoylation, 38 N-terminus, 38 tonoplast-targeting sequence (TTS), 38 Liquid chromatography–tandem mass spectrometry (LC–MS/MS), 124 Lupin nodules, 82 M Mannitol treatment, 191 Map-based cloning method, 149 Meristem activity, 184–186 Microbe-associated molecular patterns (MAMPs), 56–57 Mobile mRNAs Arabidopsis, 12–14 expressed sequence tag (EST), 12 genetically distinct species, grafting of, 11–12 graft junctions, 15 microinjection assays, 15 phloem exudates, 11–12 phloem sap, 11–12 root to shoot tissues, 12–14 shoot to root tissue, 12–14 single-nucleotide polymorphisms (SNPs), 12 spatial distribution of, 15 vasculature and phloem, endogenous transcripts in, 11–12, 13–14t Mobile RNAs classes of RNAs involved in translation, 9–10 signal recognition particle RNA, 10 small nucleolar RNAs, 10 spliceosomal RNAs, 10 sRNAs, 8–9 tRNA halves, 10 viral RNAs, 6–8 identification of grafting, 5–6 phloem exudate analysis, 3–5 tissue-specific gene activity vs transcript presence, Mobile transcripts and intercellular communication mobile mRNAs, 11–15, 13–14t mobile RNAs classes of, 6–10 identification of, 3–6 mRNA movement, function of, 19–21 noncellautonomous signals, phloem proteins–RNP complexes and transport chaperones, 17–18 phloem proteomics, 15–16 RNA-binding proteins, 16–17 mRNA movement, function of BEL1-like transcription factor, 19f, 20 gibberelic acid insensitive (GAI), 19–20, 19f miRNAs, 19–20 PSTVd RNA, 20 RNA diffusion vs active transport along the phloem, 20–21 motifs, 20–21 trafficking, 20–21 siRNAs, 19–20 N Nitrogen-fixing symbiosis, 79–81 Nodule organogenesis, 82–87 234 Nonphotochemical oxidation, 146 Nucleotide-binding site (NBS), 106–107 O Oxygen-evolving enhancer protein (OEE2), 117 Oxygen scavenger, 150 P PAMP-triggered immunity (PTI), 106–107 Pathogen-associated molecular patterns (PAMPs), 106–107 PBS1, 124–125 Pepino mosaic virus (PepMV), 18 PEPRs AtPep1, 114–115 DAMPs, 114–115 guanylyl cyclase (GC) activity, 114–115 jasmonic acid (JA) treatment, 116 oligogalacturonides (OGs), 116 photoaffinity labeling, 114–115 PROPEPs, 115–116 Phloem exudate analysis, 3–5, 4–5f EDTA facilitated exudation, insect stylectomy, 3, phloem sap, RNA molecules, sieve tubes, spontaneous exudation, Phloem proteins–RNP complexes and transport chaperones, 17–18 phloem proteomics, 15–16 RNA-binding proteins, 16–17 Phloem proteomics, 15–16 Phloem sap analysis, Phosphorylation CIPKs, 39 MYB3R4, 91–92 Ser228, 44 Ser residue, 41–42 Photomorphogenesis Arabidopsis, mutations of, 183 chlorophyll biosynthesis, 184 etiolated seedlings, 184 HDA15, 184, 185f histone acetylation, 183–184 light irradiation, 183 Subject Index light-regulated gene expression, 183 phytochrome A (PHYA), 183–184, 185f phytochrome interacting factor (PIF3), 184, 185f skotomorphogenesis, 183 Photoprotection, 158 Photosynthesis, 146 light reaction of, 145 Photosynthetic electron transfer chain (PETC) components of, 145 Phylogenetics amino acid identity, 150 AOX and PTOX, 150, 151f chlamydomonas mutants, 152 cyanobacteria, 151–152 cyanophages, 151–152 eukaryotic photosynthetic algae, 152 glycine max, 152 oxygen scavenger, 150 physcomitrell, 152 Physcomitrell, 152 Physiological functions carotenoid biosynthesis Arabidopsis im, 159–160 electron transport activity, 159 isoprenoid biosynthesis pathway, 158 lycopene, 158 PDS activity, 159 PETC, 159 photoprotection, 158 photosynthesis, 158 phytoene synthesis, 158 thylakoid membranes, lipid phase of, 158 photodamage, safety valve acclimation process, 156–157 Arabidopsis, 157–158 cold adaptation, 156 electron transport, 157 light stress, 156–157 lodgepole pine, 156–157 plastoquinone pool (PQ) oxidation, 157 PTOX, 156 ROS activity, 157–158 tobacco transgenic plants, 156–158 Subject Index Physiological functions, PTOX in chloroplast and leaf development chloroplast biogenesis, 160 light-shift experiment, 160 strigolactone metabolism, 160–161 chlororespiration ATP formation, 161 in Chlamydomonas, 161 cyclic electron transfer (CET), 162 ETC of, 161 in land plants, 161–162 linear electron transfer (LET), 162 PETC, 161–162 respiratory electron transfer chain, 161 state transition, 162 Phytochrome A (PHYA), 183–184, 185f Phytochrome interacting factor (PIF3), 184, 185f Phytoene desaturase (PDS), 148–149 Phytoene synthesis, 158 Plant–biotroph interactions B-type cyclins, 66–69 CDKA/CYCA complexes, 66–69, 67–68f chromatin, 71 cyclin dependent kinases (CDKs), 66–69 endocycle machinery onset, 72–75 progression and termination, 75–77 endopolyploidy, 69 endoreduplication plant–parasitic interactions, 88–94 plant–symbiotic interactions, 79–88 karyoplasmic ratio theory, 70 mitotic cell cycle, 66–69, 67–68f MYB3R1, 66–69 progression, 66–69 Plant immunity PRR-associated RLKs, 118–123 RLCKs, 123–125, 128–129t RLKs, 108–117, 128–129t RLPs, 117–118, 128–129t Plant mitochondria, 145–146 Plant–parasitic interactions powdery mildew-induced host endoreduplication asexual reproduction, 90–91 cell cycle reporters, 91 235 defense signaling pathways, 93–94 endoreduplication, 94 haustorium formation, 94 mesophyll cell, 91, 94 MYB3R4, 91–92 pectin, 93 plant ubiquitin X (PUX), 92 ploidy analysis, 92 PMR6, 93 quantitative real-time PCR, 93–94 surface hyphae, 90–91 3D-reconstructed confocal microscopy, 91 trichome birefringence-like (TBL) protein, 92–93 root nematode-induced host endoreduplication CCS52 OEX, 89 cytokinesis inhibition, 90 DEL1, 89 expression analysis, 89 feeding sites, 88–89 galls, 88–89 KRP, 90 loss-of-function, 90 syncytia, 88–90 Plant stress responses calcineurin B-like protein (CBL) Ca2+ binding proteins, 39 lipid modification site of, 38–39 motifs in, 34 3D structure of, 35–38 CBL–CIPK modules functions, 45–49, 55–57 target modulation by, 49–55 CBL-interacting protein kinases (CIPK) kinase activity, 42–44 kinase domain of, 40 molecular insight of, 41–42 motifs in, 39 regulatory domain of, 40 Ser/Thr kinases, 44 future perspective, 57–58 Plant–symbiotic interactions legume–rhizobia boron (B)-deficient nodules, 82 CCS52A expression, 82, 83–86t DNA replication genes, 82 236 Plant–symbiotic interactions (Continued ) DNA topoisomerase, 82–87 endoreduplication, 79–81 epidermal–cortical interface, 82–87 indeterminate nodules, 79–81, 80–81f Lupin nodules, 82 nitrogen-fixing symbiosis, 79–81 nodule organogenesis, 82–87 sixfold reduction, 82 symbiosis, 82–87 plant–endomycorrhiza arbuscules, 87 chromatin decondensation, 88 endopolyploidy, 88 endoreduplication, 87 nuclear hypertrophy, 88 nuclei movement, 87 Plant ubiquitin X (PUX), 92 Plant variegation mutants, 147 mechanisms, 147 Plasmodesmata HSC70s interaction, 18 HSP40s, 18 macromolecules, siRNA signals, viroids, 7–8 Plastids, 144–145 Plastid terminal oxidase (PTOX) discovery of higher plants, identification, 149–150 immutans, 147–149 variegation mutants, 147 enzymic activity of, 154–156 in vitro assay of, 154 photosynthetic electron transfer chain (PETC) chloroplast, 144–145 chlororespiration, 146 plant mitochondria, 145–146 phylogenetics of, 150–152 physiological functions carotenoid biosynthesis, 158–160 in chloroplast, 160–161 chlororespiration, 161–162 in leaf development, 160–161 photodamage, safety valve to, 156–158 structure of, 152–154, 153f Plastocyanin (PC), 145 Subject Index Plastoquinone pool (PQ), 145–146, 157, 161–162, 163f Posttranscriptional gene silencing (PTGS), Potato spindle tuber viroid (PSTVd), 7–8 Protein–phosphatase interaction (PPI), 39 PRR-associated RLKs, 118–123, 127f R RbohD, 123 Reactive oxygen species (ROS), 55, 106–107, 155 Receptor-like cytoplasmic kinases (RLCKs) BIK1, 123–124 BSK1, 124 PBS1, 124–125 RIPK, 125 Receptor-like kinases (RLKs) BAK1 and cell death control SOBIR1, 122–123 and plant immunity CERK1, 112–114 EFR, 111–112 FLS2, 108–111 PEPRs, 114–116 WAK1, 116–117 plasma membrane-localized pattern recognition receptors (PRRs) BAK1, 118–120 receptor-like cytoplasmic kinases (RLCKs) BIK1, 123–124 BSK1, 124 PBS1, 124–125 RIPK, 125 receptor-like proteins (RLPs), 117–118 Receptor-like proteins (RLPs) Cf-9-interacting protein, 117–118 chitin tetramer, 118 ectodomains, 117 ER–QC, 117–118 PAMP, 118 plant immunity, 117–118 snc2-1D, 118 Respiratory electron transport chain (RETC), 145 RNA-binding proteins (RBPs) cell-to-cell transport, 16–17 C maxima PSRP1 (CmPSRP1), 16 237 Subject Index CmRBP50, 17 cysteine protease inhibitor (CPI), 17 heterografting experiments, 16–17 phloem small rnabinding protein (PSRP1), 16 RNR R2-type proteins, 152–153 Root development, 186 Root epidermis, 186 Root stock breeding programs, 5–6 Root to shoot tissues, 12–14 ROS See Reactive oxygen species (ROS) RPM1-induced protein kinase (RIPK), 125 S Salt stress, 47–51 Seed development, 182 Seed dormancy, 182–183 Seed germination, 182–183 Semiautosome organelle, 144–145 Ser/Thr kinases, 44 Sessile organisms, 106–107 Shoot to root tissue, 12–14 Sieve tubes, Signal recognition particle RNA (SRP RNA), 10 Silent information regulator (SIR2), 179–181 Skotomorphogenesis, 183 Small nucleolar RNAs (snoRNAs), 10 Small RNAs (sRNAs), classes, double-stranded RNAs (dsRNAs), microRNAs (miRNAs), 8–9 mobile signal, posttranscriptional gene silencing (PTGS), small interfering RNAs (siRNAs), Spliceosomal RNAs, 10 Spontaneous exudation, State transition, 162 Strigolactone metabolism, 160–161 Symbiogenesis, 144–145 T Thylakoid membranes, 146 Tissue-specific gene activity vs transcript presence, 4–5f, Tobacco mosaic virus (TMV), Transcriptome sequencing (RNA seq), 12 Transgenic seedlings, 190–191 Translation ribosomal RNAs (rRNAs), 9–10 transfer RNA(tRNA), 9–10 Trichostatin A (TSA), 182–183 tRNA halves, 10 tRNA-like structures (TLSs), 10, 11f TSA treatment, 186 2C protein phosphatase (PP2C), 40 U Ubiquinone (UQ), 145 V Vasculature, Viral ribonucleoprotein (vRNP) complex, Viral RNAs cell-to-cell transport, 6–7 coat proteins (CPs), 6–7 mechanisms, phloem-mediated transport, 6–7 plasmodesmata, 6–7 viral-encoded movement protein(s) (MPs), 6–7 viral ribonucleoprotein (vRNP) complex, viroids, 7–8 W Wall-associated kinase (WAK1), 116–117 ... ribonucleoprotein (vRNP) complex In the first case, the assembly of the virion is essential for the transport and the CP is the main component of the capsid protecting the viral genome A tubular structure... found among them [20], suggesting that the mobile form of the miRNA signal is either the processed mature form or that processing of miRNA precursors can take place in the phloem tissue In the phloem... cell via plasmodesmata These are intercellular pores stretching across the cell wall of neighboring cells In the vasculature the molecules enter via the companion cells, the sugar-conducting sieve
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