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Lopez JA, Sun Y, Blair PB, Mukhtar MS. TCP three-way handshake: linking developmental processes with plant immunity. TRENDS IN PLANT SCIENCE 2015; 20:238-45. [PMID: 25655280 DOI: 10.1016/j.tplants.2015.01.005] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Revised: 12/22/2014] [Accepted: 01/12/2015] [Indexed: 05/08/2023]
Abstract
The TCP gene family encodes plant-specific transcription factors involved in growth and development. Equally important are the interactions between TCP factors and other pathways extending far beyond development, as they have been found to regulate a variety of hormonal pathways and signaling cascades. Recent advances reveal that TCP factors are targets of pathogenic effectors and are likely to play a vital role in plant immunity. Our focus is on reviewing the involvement of TCP in known pathways and shedding light on other linkages in the nexus of plant immunity centered around TCP factors with an emphasis on the convergence of effectors, interconnected hormonal networks, utility of the circadian clock, and the potential mechanisms by which pathogen defense may occur.
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Affiliation(s)
- Jessica A Lopez
- Department of Biology, University of Alabama at Birmingham, AL 35294, USA
| | - Yali Sun
- Department of Biology, University of Alabama at Birmingham, AL 35294, USA
| | - Peter B Blair
- Department of Biology, University of Alabama at Birmingham, AL 35294, USA
| | - M Shahid Mukhtar
- Department of Biology, University of Alabama at Birmingham, AL 35294, USA; Nutrition Obesity Research Center, University of Alabama at Birmingham, AL 35294, USA.
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202
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Clavel M, Pélissier T, Descombin J, Jean V, Picart C, Charbonel C, Saez-Vásquez J, Bousquet-Antonelli C, Deragon JM. Parallel action of AtDRB2 and RdDM in the control of transposable element expression. BMC PLANT BIOLOGY 2015; 15:70. [PMID: 25849103 PMCID: PMC4351826 DOI: 10.1186/s12870-015-0455-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 02/13/2015] [Indexed: 05/03/2023]
Abstract
BACKGROUND In plants and animals, a large number of double-stranded RNA binding proteins (DRBs) have been shown to act as non-catalytic cofactors of DICERs and to participate in the biogenesis of small RNAs involved in RNA silencing. We have previously shown that the loss of Arabidopsis thaliana's DRB2 protein results in a significant increase in the population of RNA polymerase IV (p4) dependent siRNAs, which are involved in the RNA-directed DNA methylation (RdDM) process. RESULTS Surprisingly, despite this observation, we show in this work that DRB2 is part of a high molecular weight complex that does not involve RdDM actors but several chromatin regulator proteins, such as MSI4, PRMT4B and HDA19. We show that DRB2 can bind transposable element (TE) transcripts in vivo but that drb2 mutants do not have a significant variation in TE DNA methylation. CONCLUSION We propose that DRB2 is part of a repressive epigenetic regulator complex involved in a negative feedback loop, adjusting epigenetic state to transcription level at TE loci, in parallel of the RdDM pathway. Loss of DRB2 would mainly result in an increased production of TE transcripts, readily converted in p4-siRNAs by the RdDM machinery.
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Affiliation(s)
- Marion Clavel
- />Université de Perpignan Via Domitia, LGDP UMR CNRS-UPVD 5096, 58 Av. Paul Alduy, 66860 Perpignan Cedex, France
- />CNRS UMR5096 LGDP, Perpignan Cedex, France
- />Present address: IBMP, UPR 2357, 12, rue du général Zimmer, 67084 Strasbourg cedex, France
| | - Thierry Pélissier
- />Université de Perpignan Via Domitia, LGDP UMR CNRS-UPVD 5096, 58 Av. Paul Alduy, 66860 Perpignan Cedex, France
- />CNRS UMR5096 LGDP, Perpignan Cedex, France
- />Present address: UMR6293 CNRS - INSERM U1103 – GreD, Clermont Université, 24 avenue des Landais, B.P. 80026, 63171 Aubière Cedex, France
| | - Julie Descombin
- />Université de Perpignan Via Domitia, LGDP UMR CNRS-UPVD 5096, 58 Av. Paul Alduy, 66860 Perpignan Cedex, France
- />CNRS UMR5096 LGDP, Perpignan Cedex, France
| | - Viviane Jean
- />Université de Perpignan Via Domitia, LGDP UMR CNRS-UPVD 5096, 58 Av. Paul Alduy, 66860 Perpignan Cedex, France
- />CNRS UMR5096 LGDP, Perpignan Cedex, France
| | - Claire Picart
- />Université de Perpignan Via Domitia, LGDP UMR CNRS-UPVD 5096, 58 Av. Paul Alduy, 66860 Perpignan Cedex, France
- />CNRS UMR5096 LGDP, Perpignan Cedex, France
| | - Cyril Charbonel
- />Université de Perpignan Via Domitia, LGDP UMR CNRS-UPVD 5096, 58 Av. Paul Alduy, 66860 Perpignan Cedex, France
- />CNRS UMR5096 LGDP, Perpignan Cedex, France
| | - Julio Saez-Vásquez
- />Université de Perpignan Via Domitia, LGDP UMR CNRS-UPVD 5096, 58 Av. Paul Alduy, 66860 Perpignan Cedex, France
- />CNRS UMR5096 LGDP, Perpignan Cedex, France
| | - Cécile Bousquet-Antonelli
- />Université de Perpignan Via Domitia, LGDP UMR CNRS-UPVD 5096, 58 Av. Paul Alduy, 66860 Perpignan Cedex, France
- />CNRS UMR5096 LGDP, Perpignan Cedex, France
| | - Jean-Marc Deragon
- />Université de Perpignan Via Domitia, LGDP UMR CNRS-UPVD 5096, 58 Av. Paul Alduy, 66860 Perpignan Cedex, France
- />CNRS UMR5096 LGDP, Perpignan Cedex, France
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203
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Zhu Z, Lee B. Friends or foes: new insights in jasmonate and ethylene co-actions. PLANT & CELL PHYSIOLOGY 2015; 56:414-20. [PMID: 25435545 DOI: 10.1093/pcp/pcu171] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
One strategy for sessile plants to adapt to their surrounding environment involves the modulation of their various internal phytohormone signaling and distributions when the plants sense environmental change. There are currently dozens of identified phytohormones in plant cells and they act in concert to regulate plant growth, development, metabolism and defense. It has been determined that phytohormones often act together to achieve certain physiological functions. Thus, the study of hormone-hormone interactions is becoming a competitive research field for deciphering the underlying regulatory mechanisms. Among phytohormones, jasmonate and ethylene present a fascinating case of synergism and antagonism. They are commonly recognized as defense hormones that act synergistically. Plants impaired in jasmonate and/or ethylene signaling are susceptible to infections by necrotrophic fungi, suggesting that these two hormones are both required for defense. Moreover, jasmonate and ethylene also act antagonistically, such as in the regulation of apical hook development and wounding responses. Here, we highlight the recent breakthroughs in the understanding of jasmonate-ethylene co-actions and point out the potential power of studying protein-protein interactions for systematically exploring signal cross-talk.
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Affiliation(s)
- Ziqiang Zhu
- College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Benjamin Lee
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095, USA
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204
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Ma S, Bohnert HJ, Dinesh-Kumar SP. AtGGM2014, an Arabidopsis gene co-expression network for functional studies. SCIENCE CHINA-LIFE SCIENCES 2015; 58:276-86. [PMID: 25682393 DOI: 10.1007/s11427-015-4803-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 12/25/2014] [Indexed: 12/19/2022]
Abstract
Gene co-expression networks provide an important tool for systems biology studies. Using microarray data from the ArrayExpress database, we constructed an Arabidopsis gene co-expression network, termed AtGGM2014, based on the graphical Gaussian model, which contains 102,644 co-expression gene pairs among 18,068 genes. The network was grouped into 622 gene co-expression modules. These modules function in diverse house-keeping, cell cycle, development, hormone response, metabolism, and stress response pathways. We developed a tool to facilitate easy visualization of the expression patterns of these modules either in a tissue context or their regulation under different treatment conditions. The results indicate that at least six modules with tissue-specific expression pattern failed to record modular regulation under various stress conditions. This discrepancy could be best explained by the fact that experiments to study plant stress responses focused mainly on leaves and less on roots, and thus failed to recover specific regulation pattern in other tissues. Overall, the modular structures revealed by our network provide extensive information to generate testable hypotheses about diverse plant signaling pathways. AtGGM2014 offers a constructive tool for plant systems biology studies.
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Affiliation(s)
- ShiSong Ma
- Department of Plant Biology and the Genome Center, College of Biological Sciences, University of California, Davis, CA, 95616, USA,
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205
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ten Hove CA, Lu KJ, Weijers D. Building a plant: cell fate specification in the early Arabidopsis embryo. Development 2015; 142:420-30. [DOI: 10.1242/dev.111500] [Citation(s) in RCA: 150] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Embryogenesis is the beginning of plant development, yet the cell fate decisions and patterning steps that occur during this time are reiterated during development to build the post-embryonic architecture. In Arabidopsis, embryogenesis follows a simple and predictable pattern, making it an ideal model with which to understand how cellular and tissue developmental processes are controlled. Here, we review the early stages of Arabidopsis embryogenesis, focusing on the globular stage, during which time stem cells are first specified and all major tissues obtain their identities. We discuss four different aspects of development: the formation of outer versus inner layers; the specification of vascular and ground tissues; the determination of shoot and root domains; and the establishment of the first stem cells.
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Affiliation(s)
- Colette A. ten Hove
- Wageningen University, Laboratory of Biochemistry, Dreijenlaan 3, 6703 HA Wageningen, The Netherlands
| | - Kuan-Ju Lu
- Wageningen University, Laboratory of Biochemistry, Dreijenlaan 3, 6703 HA Wageningen, The Netherlands
| | - Dolf Weijers
- Wageningen University, Laboratory of Biochemistry, Dreijenlaan 3, 6703 HA Wageningen, The Netherlands
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206
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Rosa S, Ntoukakis V, Ohmido N, Pendle A, Abranches R, Shaw P. Cell differentiation and development in Arabidopsis are associated with changes in histone dynamics at the single-cell level. THE PLANT CELL 2014; 26:4821-33. [PMID: 25549670 PMCID: PMC4311217 DOI: 10.1105/tpc.114.133793] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The mechanism whereby the same genome can give rise to different cell types with different gene expression profiles is a fundamental problem in biology. Chromatin organization and dynamics have been shown to vary with altered gene expression in different cultured animal cell types, but there is little evidence yet from whole organisms linking chromatin dynamics with development. Here, we used both fluorescence recovery after photobleaching and two-photon photoactivation to show that in stem cells from Arabidopsis thaliana roots the mobility of the core histone H2B, as judged by exchange dynamics, is lower than in the surrounding cells of the meristem. However, as cells progress from meristematic to fully differentiated, core histones again become less mobile and more strongly bound to chromatin. We show that these transitions are largely mediated by changes in histone acetylation. We further show that altering histone acetylation levels, either in a mutant or by drug treatment, alters both the histone mobility and markers of development and differentiation. We propose that plant stem cells have relatively inactive chromatin, but they keep the potential to divide and differentiate into more dynamic states, and that these states are at least in part determined by histone acetylation levels.
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Affiliation(s)
- Stefanie Rosa
- Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom Plant Cell Biology Laboratory, Instituto de Tecnologia Quimica e Biologica, Universidade Nova de Lisboa, Oeiras 2781-901, Portugal
| | - Vardis Ntoukakis
- Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Nobuko Ohmido
- Graduate School of Human Development and Environment, Kobe University, Kobe 657-8501, Japan
| | - Ali Pendle
- Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Rita Abranches
- Plant Cell Biology Laboratory, Instituto de Tecnologia Quimica e Biologica, Universidade Nova de Lisboa, Oeiras 2781-901, Portugal
| | - Peter Shaw
- Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom
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207
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Wang Z, Cao H, Chen F, Liu Y. The roles of histone acetylation in seed performance and plant development. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2014; 84:125-133. [PMID: 25270163 DOI: 10.1016/j.plaphy.2014.09.010] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2014] [Accepted: 09/23/2014] [Indexed: 05/08/2023]
Abstract
Histone acetylation regulates gene transcription by chromatin modifications and plays a crucial role in the plant development and response to environment cues. The homeostasis of histone acetylation is controlled by histone acetyltransferases (HATs) and histone deacetylases (HDACs) in different plant tissues and development stages. The vigorous knowledge of the function and co-factors about HATs (e.g. GCN5) and HDACs (e.g. HDA19, HDA6) has been obtained from model plant Arabidopsis. However, understanding individual role of other HATs and HDACs require more work, especially in the major food crops such as rice, maize and wheat. Many co-regulators have been recently identified to function as a component of HAT or HDAC complex in some specific developmental processes. The described findings show a distinctive and interesting epigenetic regulation network composed of HATs, HDACs and co-regulators playing crucial roles in the seed performance, flowering time, plant morphogenesis, plant response to stresses etc. In this review, we summarized the recent progresses and suggested the perspective of histone acetylation research, which might provide us a new window to understand the epigenetic code of plant development and to improve the crop production and quality.
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Affiliation(s)
- Zhi Wang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
| | - Hong Cao
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Fengying Chen
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Yongxiu Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
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208
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Matías-Hernández L, Aguilar-Jaramillo AE, Marín-González E, Suárez-López P, Pelaz S. RAV genes: regulation of floral induction and beyond. ANNALS OF BOTANY 2014; 114:1459-70. [PMID: 24812253 PMCID: PMC4204781 DOI: 10.1093/aob/mcu069] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2013] [Accepted: 03/12/2014] [Indexed: 05/18/2023]
Abstract
BACKGROUND Transcription factors of the RAV (RELATED TO ABI3 AND VP1) family are plant-specific and possess two DNA-binding domains. In Arabidopsis thaliana, the family comprises six members, including TEMPRANILLO 1 (TEM1) and TEM2. Arabidopsis RAV1 and TEM1 have been shown to bind bipartite DNA sequences, with the consensus motif C(A/C/G)ACA(N)2-8(C/A/T)ACCTG. Through direct binding to DNA, RAV proteins act as transcriptional repressors, probably in complexes with other co-repressors. SCOPE AND CONCLUSIONS In this review, a summary is given of current knowledge of the regulation and function of RAV genes in diverse plant species, paying particular attention to their roles in the control of flowering in arabidopsis. TEM1 and TEM2 delay flowering by repressing the production of two florigenic molecules, FLOWERING LOCUS T (FT) and gibberellins. In this way, TEM1 and TEM2 prevent precocious flowering and postpone floral induction until the plant has accumulated enough reserves or has reached a growth stage that ensures survival of the progeny. Recent results indicate that TEM1 and TEM2 are regulated by genes acting in several flowering pathways, suggesting that TEMs may integrate information from diverse pathways. However, flowering is not the only process controlled by RAV proteins. Family members are involved in other aspects of plant development, such as bud outgrowth in trees and leaf senescence, and possibly in general growth regulation. In addition, they respond to pathogen infections and abiotic stresses, including cold, dehydration, high salinity and osmotic stress.
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Affiliation(s)
- Luis Matías-Hernández
- Centre for Research in Agricultural Genomics, CSIC-IRTA-UAB-UB, Campus UAB, 08193 Bellaterra, Spain
| | | | - Esther Marín-González
- Centre for Research in Agricultural Genomics, CSIC-IRTA-UAB-UB, Campus UAB, 08193 Bellaterra, Spain
| | - Paula Suárez-López
- Centre for Research in Agricultural Genomics, CSIC-IRTA-UAB-UB, Campus UAB, 08193 Bellaterra, Spain
| | - Soraya Pelaz
- Centre for Research in Agricultural Genomics, CSIC-IRTA-UAB-UB, Campus UAB, 08193 Bellaterra, Spain ICREA (Institució Catalana de Recerca i Estudis Avançats), Barcelona, Spain
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209
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Costanzo E, Trehin C, Vandenbussche M. The role of WOX genes in flower development. ANNALS OF BOTANY 2014; 114:1545-53. [PMID: 24973416 PMCID: PMC4204783 DOI: 10.1093/aob/mcu123] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Accepted: 04/29/2014] [Indexed: 05/21/2023]
Abstract
BACKGROUND WOX (Wuschel-like homeobOX) genes form a family of plant-specific HOMEODOMAIN transcription factors, the members of which play important developmental roles in a diverse range of processes. WOX genes were first identified as determining cell fate during embryo development, as well as playing important roles in maintaining stem cell niches in the plant. In recent years, new roles have been identified in plant architecture and organ development, particularly at the flower level. SCOPE In this review, the role of WOX genes in flower development and flower architecture is highlighted, as evidenced from data obtained in the last few years. The roles played by WOX genes in different species and different flower organs are compared, and differential functional recruitment of WOX genes during flower evolution is considered. CONCLUSIONS This review compares available data concerning the role of WOX genes in flower and organ architecture among different species of angiosperms, including representatives of monocots and eudicots (rosids and asterids). These comparative data highlight the usefulness of the WOX gene family for evo-devo studies of floral development.
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Affiliation(s)
- Enrico Costanzo
- Laboratory of Reproduction and Development of Plants, UMR5667 (ENS de Lyon, CNRS, INRA, UCBL), Ecole Normale Supérieure de Lyon, Lyon, France Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, Italy
| | - Christophe Trehin
- Laboratory of Reproduction and Development of Plants, UMR5667 (ENS de Lyon, CNRS, INRA, UCBL), Ecole Normale Supérieure de Lyon, Lyon, France
| | - Michiel Vandenbussche
- Laboratory of Reproduction and Development of Plants, UMR5667 (ENS de Lyon, CNRS, INRA, UCBL), Ecole Normale Supérieure de Lyon, Lyon, France
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210
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Bauchet G, Munos S, Sauvage C, Bonnet J, Grivet L, Causse M. Genes involved in floral meristem in tomato exhibit drastically reduced genetic diversity and signature of selection. BMC PLANT BIOLOGY 2014; 14:279. [PMID: 25325924 PMCID: PMC4210547 DOI: 10.1186/s12870-014-0279-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Accepted: 10/06/2014] [Indexed: 05/12/2023]
Abstract
BACKGROUND Domestication and selection of crops have notably reshaped fruit morphology. With its large phenotypic diversity, tomato (Solanum lycopersicum) illustrates this evolutive trend. Genes involved in flower meristem development are known to regulate also fruit morphology. To decipher the genetic variation underlying tomato fruit morphology, we assessed the nucleotide diversity and selection footprints of candidate genes involved in flower and fruit development and performed genome-wide association studies. RESULTS Thirty candidate genes were selected according to their similarity with genes involved in meristem development or their known causal function in Arabidopsis thaliana. In tomato, these genes and flanking regions were sequenced in a core collection of 96 accessions (including cultivated, cherry-type and wild relative accessions) maximizing the molecular diversity, using the Roche 454 technology. A total amount of 17 Mb was sequenced allowing the discovery of 6,106 single nucleotide polymorphisms (SNPs). The annotation of the 30 gene regions identified 231 exons carrying 517 SNPs. Subsequently, the nucleotide diversity (π) and the neutral evolution of each region were compared against genome-wide values within the collection, using a SNP array carrying 7,667 SNPs mainly distributed in coding sequences.About half of the genes revealed footprints of selection and polymorphisms putatively involved in fruit size variation by showing negative Tajima's D and nucleotide diversity reduction in cultivated tomato compared to its wild relative. Among the candidates, FW2.2 and BAM1 sequences revealed selection footprints within their promoter regions suggesting their potential involvement in their regulation. Two associations co-localized with previously identified loci: LC (locule number) and Ovate (fruit shape). CONCLUSION Compared to whole genome genotypic data, a drastic reduction of nucleotide diversity was shown for several candidate genes. Strong selection patterns were identified in 15 candidates highlighting the critical role of meristem maintenance genes as well as the impact of domestication on candidates. The study highlighted a set of polymorphisms putatively important in the evolution of these genes.
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Affiliation(s)
- Guillaume Bauchet
- />INRA, UR1052, Génétique et Amélioration des Fruits et Légumes (GAFL), 67 Allée des Chênes Domaine Saint Maurice – CS60094, 84143 Montfavet Cedex, France
- />Syngenta Seeds, 12 chemin de l’Hobit, 31790 Saint Sauveur, France
| | - Stéphane Munos
- />INRA, UR1052, Génétique et Amélioration des Fruits et Légumes (GAFL), 67 Allée des Chênes Domaine Saint Maurice – CS60094, 84143 Montfavet Cedex, France
- />Present address: INRA, UMR CNRS-INRA 441-2594, 24 Chemin de Borde Rouge – Auzeville - CS 52627, 31326 Castanet Tolosan Cedex, France
| | - Christopher Sauvage
- />INRA, UR1052, Génétique et Amélioration des Fruits et Légumes (GAFL), 67 Allée des Chênes Domaine Saint Maurice – CS60094, 84143 Montfavet Cedex, France
| | - Julien Bonnet
- />Syngenta Seeds, 12 chemin de l’Hobit, 31790 Saint Sauveur, France
| | - Laurent Grivet
- />Syngenta Seeds, 12 chemin de l’Hobit, 31790 Saint Sauveur, France
| | - Mathilde Causse
- />INRA, UR1052, Génétique et Amélioration des Fruits et Légumes (GAFL), 67 Allée des Chênes Domaine Saint Maurice – CS60094, 84143 Montfavet Cedex, France
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211
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Wang R, Estelle M. Diversity and specificity: auxin perception and signaling through the TIR1/AFB pathway. CURRENT OPINION IN PLANT BIOLOGY 2014; 21:51-58. [PMID: 25032902 PMCID: PMC4294414 DOI: 10.1016/j.pbi.2014.06.006] [Citation(s) in RCA: 165] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Accepted: 06/15/2014] [Indexed: 05/19/2023]
Abstract
Auxin is a versatile plant hormone that plays an essential role in most aspects of plant growth and development. Auxin regulates various growth processes by modulating gene transcription through a SCF(TIR1/AFB)-Aux/IAA-ARF nuclear signaling module. Recent work has generated clues as to how multiple layers of regulation of the auxin signaling components may result in diverse and specific response outputs. In particular, interaction and structural studies of key auxin signaling proteins have produced novel insights into the molecular basis of auxin-regulated transcription and may lead to a refined auxin signaling model.
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Affiliation(s)
- Renhou Wang
- Section of Cell and Developmental Biology and Howard Hughes Medical Institute, UCSD, La Jolla, CA 92093, United States
| | - Mark Estelle
- Section of Cell and Developmental Biology and Howard Hughes Medical Institute, UCSD, La Jolla, CA 92093, United States.
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212
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Wang JW. Regulation of flowering time by the miR156-mediated age pathway. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:4723-30. [PMID: 24958896 DOI: 10.1093/jxb/eru246] [Citation(s) in RCA: 195] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Precise flowering time is critical to reproductive success. In response to diverse exogenous and endogenous cues including age, hormones, photoperiod, and temperature, the floral transition is controlled by a complex regulatory network, which involves extensive crosstalks, feedback, or feedforward loops between the components within flowering time pathways. The newly identified age pathway, which is controlled by microRNA156 (miR156) and its target SQUAMOSA PROMOTER BINDING-LIKE (SPL) transcription factors, ensures plants flower under non-inductive conditions. In this review, I summarize the recent advance in understanding of the age pathway, focusing on the regulatory basis of the developmental decline in miR156 level by age and the molecular mechanism by which the age pathway is integrated into other flowering time pathways.
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Affiliation(s)
- Jia-Wei Wang
- National Key Laboratory of Plant Molecular Genetics (NKLPMG), Institute of Plant Physiology and Ecology (SIPPE), Shanghai Institutes for Biological Sciences (SIBS), Shanghai 200032, P. R. China
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213
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Somatic embryogenesis - Stress-induced remodeling of plant cell fate. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1849:385-402. [PMID: 25038583 DOI: 10.1016/j.bbagrm.2014.07.005] [Citation(s) in RCA: 211] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Revised: 07/08/2014] [Accepted: 07/10/2014] [Indexed: 01/13/2023]
Abstract
Plants as sessile organisms have remarkable developmental plasticity ensuring heir continuous adaptation to the environment. An extreme example is somatic embryogenesis, the initiation of autonomous embryo development in somatic cells in response to exogenous and/or endogenous signals. In this review I briefly overview the various pathways that can lead to embryo development in plants in addition to the fertilization of the egg cell and highlight the importance of the interaction of stress- and hormone-regulated pathways during the induction of somatic embryogenesis. Somatic embryogenesis can be initiated in planta or in vitro, directly or indirectly, and the requirement for dedifferentiation as well as the way to achieve developmental totipotency in the various systems is discussed in light of our present knowledge. The initiation of all forms of the stress/hormone-induced in vitro as well as the genetically provoked in planta somatic embryogenesis requires extensive and coordinated genetic reprogramming that has to take place at the chromatin level, as the embryogenic program is under strong epigenetic repression in vegetative plant cells. Our present knowledge on chromatin-based mechanisms potentially involved in the somatic-to-embryogenic developmental transition is summarized emphasizing the potential role of the chromatin to integrate stress, hormonal, and developmental pathways leading to the activation of the embryogenic program. The role of stress-related chromatin reorganization in the genetic instability of in vitro cultures is also discussed. This article is part of a Special Issue entitled: Stress as a fundamental theme in cell plasticity.
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Wolny E, Braszewska-Zalewska A, Hasterok R. Spatial distribution of epigenetic modifications in Brachypodium distachyon embryos during seed maturation and germination. PLoS One 2014; 9:e101246. [PMID: 25006668 PMCID: PMC4090163 DOI: 10.1371/journal.pone.0101246] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Accepted: 06/04/2014] [Indexed: 11/18/2022] Open
Abstract
Seed development involves a plethora of spatially and temporally synchronised genetic and epigenetic processes. Although it has been shown that epigenetic mechanisms, such as DNA methylation and chromatin remodelling, act on a large number of genes during seed development and germination, to date the global levels of histone modifications have not been studied in a tissue-specific manner in plant embryos. In this study we analysed the distribution of three epigenetic markers, i.e. H4K5ac, H3K4me2 and H3K4me1 in ‘matured’, ‘dry’ and ‘germinating’ embryos of a model grass, Brachypodium distachyon (Brachypodium). Our results indicate that the abundance of these modifications differs considerably in various organs and tissues of the three types of Brachypodium embryos. Embryos from matured seeds were characterised by the highest level of H4K5ac in RAM and epithelial cells of the scutellum, whereas this modification was not observed in the coleorhiza. In this type of embryos H3K4me2 was most evident in epithelial cells of the scutellum. In ‘dry’ embryos H4K5ac was highest in the coleorhiza but was not present in the nuclei of the scutellum. H3K4me1 was the most elevated in the coleoptile but absent from the coleorhiza, whereas H3K4me2 was the most prominent in leaf primordia and RAM. In embryos from germinating seeds H4K5ac was the most evident in the scutellum but not present in the coleoptile, similarly H3K4me1 was the highest in the scutellum and very low in the coleoptile, while the highest level of H3K4me2 was observed in the coleoptile and the lowest in the coleorhiza. The distinct patterns of epigenetic modifications that were observed may be involved in the switch of the gene expression profiles in specific organs of the developing embryo and may be linked with the physiological changes that accompany seed desiccation, imbibition and germination.
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Affiliation(s)
- Elzbieta Wolny
- Department of Plant Anatomy and Cytology, Faculty of Biology and Environmental Protection, University of Silesia in Katowice, Katowice, Poland
| | - Agnieszka Braszewska-Zalewska
- Department of Plant Anatomy and Cytology, Faculty of Biology and Environmental Protection, University of Silesia in Katowice, Katowice, Poland
| | - Robert Hasterok
- Department of Plant Anatomy and Cytology, Faculty of Biology and Environmental Protection, University of Silesia in Katowice, Katowice, Poland
- * E-mail:
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215
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Retzer K, Butt H, Korbei B, Luschnig C. The far side of auxin signaling: fundamental cellular activities and their contribution to a defined growth response in plants. PROTOPLASMA 2014; 251:731-46. [PMID: 24221297 PMCID: PMC4059964 DOI: 10.1007/s00709-013-0572-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Accepted: 10/15/2013] [Indexed: 05/04/2023]
Abstract
Recent years have provided us with spectacular insights into the biology of the plant hormone auxin, leaving the impression of a highly versatile molecule involved in virtually every aspect of plant development. A combination of genetics, biochemistry, and cell biology has established auxin signaling pathways, leading to the identification of two distinct modes of auxin perception and downstream regulatory cascades. Major targets of these signaling modules are components of the polar auxin transport machinery, mediating directional distribution of the phytohormone throughout the plant body, and decisively affecting plant development. Alterations in auxin transport, metabolism, or signaling that occur as a result of intrinsic as well as environmental stimuli, control adjustments in morphogenetic programs, giving rise to defined growth responses attributed to the activity of the phytohormone. Some of the results obtained from the analysis of auxin, however, do not fit coherently into a picture of highly specific signaling events, but rather suggest mutual interactions between auxin and fundamental cellular pathways, like the control of intracellular protein sorting or translation. Crosstalk between auxin and these basic determinants of cellular activity and how they might shape auxin effects in the control of morphogenesis are the subject of this review.
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Affiliation(s)
- Katarzyna Retzer
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, BOKU, Wien Muthgasse 18, 1190 Wien, Austria
| | - Haroon Butt
- Department of Biological Sciences, Forman Christian College, Ferozepur Road, Lahore, 54600 Pakistan
| | - Barbara Korbei
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, BOKU, Wien Muthgasse 18, 1190 Wien, Austria
| | - Christian Luschnig
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, BOKU, Wien Muthgasse 18, 1190 Wien, Austria
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216
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Fukazawa J, Teramura H, Murakoshi S, Nasuno K, Nishida N, Ito T, Yoshida M, Kamiya Y, Yamaguchi S, Takahashi Y. DELLAs function as coactivators of GAI-ASSOCIATED FACTOR1 in regulation of gibberellin homeostasis and signaling in Arabidopsis. THE PLANT CELL 2014; 26:2920-38. [PMID: 25035403 PMCID: PMC4145123 DOI: 10.1105/tpc.114.125690] [Citation(s) in RCA: 124] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Revised: 06/11/2014] [Accepted: 06/25/2014] [Indexed: 05/19/2023]
Abstract
Gibberellins (GAs) are essential regulators of plant development, and DELLAs are negative regulators of GA signaling. The mechanism of GA-dependent transcription has been explained by DELLA-mediated titration of transcriptional activators and their release through the degradation of DELLAs in response to GA. However, the effect of GA on genome-wide expression is predominantly repression, suggesting the existence of unknown mechanisms of GA function. In this study, we identified an Arabidopsis thaliana DELLA binding transcription factor, GAI-ASSOCIATED FACTOR1 (GAF1). GAF1 shows high homology to INDETERMINATE DOMAIN1 (IDD1)/ENHYDROUS. GA responsiveness was decreased in the double mutant gaf1 idd1, whereas it was enhanced in a GAF1 overexpressor. GAF1 binds to genes that are subject to GA feedback regulation. Furthermore, we found that GAF1 interacts with the corepressor TOPLESS RELATED (TPR) and that DELLAs and TPR act as coactivators and a corepressor of GAF1, respectively. GA converts the GAF1 complex from transcriptional activator to repressor via the degradation of DELLAs. These results indicate that DELLAs turn on or off two sets of GA-regulated genes via dual functions, namely titration and coactivation, providing a mechanism for the integrative regulation of plant growth and GA homeostasis.
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Affiliation(s)
- Jutarou Fukazawa
- Department of Biological Science, Graduate School of Science, Hiroshima University, Kagamiyama, Higashi-Hiroshima 739-8526, Japan RIKEN Plant Science Center, Tsurumi, Yokohama, Kanagawa 230-0045, Japan Department of Biological Science and Technology, Tokyo University of Science, Noda, Chiba 278-8510, Japan
| | - Hiroshi Teramura
- Department of Biological Science and Technology, Tokyo University of Science, Noda, Chiba 278-8510, Japan
| | - Satoru Murakoshi
- Department of Biological Science and Technology, Tokyo University of Science, Noda, Chiba 278-8510, Japan
| | - Kei Nasuno
- Department of Biological Science and Technology, Tokyo University of Science, Noda, Chiba 278-8510, Japan
| | - Naotaka Nishida
- Department of Biological Science and Technology, Tokyo University of Science, Noda, Chiba 278-8510, Japan
| | - Takeshi Ito
- Department of Biological Science, Graduate School of Science, Hiroshima University, Kagamiyama, Higashi-Hiroshima 739-8526, Japan
| | - Michiteru Yoshida
- Department of Biological Science and Technology, Tokyo University of Science, Noda, Chiba 278-8510, Japan
| | - Yuji Kamiya
- RIKEN Plant Science Center, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | | | - Yohsuke Takahashi
- Department of Biological Science, Graduate School of Science, Hiroshima University, Kagamiyama, Higashi-Hiroshima 739-8526, Japan
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217
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Shi G, Huang F, Gong Y, Xu G, Yu J, Hu Z, Cai Q, Yu D. RNA-Seq analysis reveals that multiple phytohormone biosynthesis and signal transduction pathways are reprogrammed in curled-cotyledons mutant of soybean [Glycine max (L.) Merr]. BMC Genomics 2014; 15:510. [PMID: 24952381 PMCID: PMC4078243 DOI: 10.1186/1471-2164-15-510] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2014] [Accepted: 06/18/2014] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND Soybean is one of the most economically important crops in the world. The cotyledon is the nutrient storage area in seeds, and it is critical for seed quality and yield. Cotyledon mutants are important for the genetic dissection of embryo patterning and seed development. However, the molecular mechanisms underlying soybean cotyledon development are largely unexplored. RESULTS In this study, we characterised a soybean curled-cotyledon (cco) mutant. Compared with wild-type (WT), anatomical analysis revealed that the cco cotyledons at the torpedo stage became more slender and grew outward. The entire embryos of cco mutant resembled the "tail of swallow". In addition, cco seeds displayed reduced germination rate and gibberellic acid (GA3) level, whereas the abscisic acid (ABA) and auxin (IAA) levels were increased. RNA-seq identified 1,093 differentially expressed genes (DEGs) between WT and the cco mutant. The KEGG pathway analysis showed many DEGs were mapped to the hormone biosynthesis and signal transduction pathways. Consistent with assays of hormones in seeds, the results of RNA-seq indicated auxin and ABA biosynthesis and signal transduction in cco were more active than in WT, while an early step in GA biosynthesis was blocked, as well as conversion rate of inactive GAs to bioactive GAs in GA signaling. Furthermore, genes participated in other hormone biosynthesis and signalling pathways such as cytokinin (CK), ethylene (ET), brassinosteroid (BR), and jasmonate acid (JA) were also affected in the cco mutant. CONCLUSIONS Our data suggest that multiple phytohormone biosynthesis and signal transduction pathways are reprogrammed in cco, and changes in these pathways may partially contribute to the cco mutant phenotype, suggesting the involvement of multiple hormones in the coordination of soybean cotyledon development.
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Affiliation(s)
- Guixia Shi
- />College of Life Sciences, Nanjing Agricultural University, Nanjing, China
- />National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
| | - Fang Huang
- />National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
| | - Yu Gong
- />National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
| | - Guangli Xu
- />National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
| | - Jingjing Yu
- />National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
| | - Zhenbin Hu
- />National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
| | - Qingsheng Cai
- />College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Deyue Yu
- />National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
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218
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Ryu H, Cho H, Bae W, Hwang I. Control of early seedling development by BES1/TPL/HDA19-mediated epigenetic regulation of ABI3. Nat Commun 2014; 5:4138. [PMID: 24938150 DOI: 10.1038/ncomms5138] [Citation(s) in RCA: 132] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Accepted: 05/16/2014] [Indexed: 12/23/2022] Open
Abstract
Seed germination and young seedling establishment should be tightly regulated to maximize plant survival and thereby enable successful propagation. Plants have evolved developmental signalling networks to integrate environmental cues for proper control of these critical processes, in which brassinosteroids are known to attenuate ABA-mediated arrest of early seedling development; however, the underlying regulatory mechanism remains elusive. Here we reveal that a BES1/TPL/HDA19 repressor complex mediates the inhibitory action of brassinosteroids on ABA responses during early seedling development. BR-activated BES1 forms a transcriptional repressor complex with TPL-HDA19, which directly facilitates the histone deacetylation of ABI3 chromatin. This event leads to the transcriptional repression of ABI3 and consequently ABI5, major ABA signalling regulators in early seedling development. Our data reveal that the BR-activated BES1-TPL-HDA19 repressor complex controls epigenetic silencing of ABI3 and thereby suppresses the ABA signalling output during early seedling development.
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Affiliation(s)
- Hojin Ryu
- 1] Department of Life Sciences, POSTECH Biotech Center, Pohang University of Science and Technology, Pohang 790-784, Korea [2] Division of Agricultural Microbiology, National Academy of Agricultural Science, RDA, Suwon 441-707, South Korea
| | - Hyunwoo Cho
- Department of Life Sciences, POSTECH Biotech Center, Pohang University of Science and Technology, Pohang 790-784, Korea
| | - Wonsil Bae
- Department of Life Sciences, POSTECH Biotech Center, Pohang University of Science and Technology, Pohang 790-784, Korea
| | - Ildoo Hwang
- Department of Life Sciences, POSTECH Biotech Center, Pohang University of Science and Technology, Pohang 790-784, Korea
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219
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Weiste C, Dröge-Laser W. The Arabidopsis transcription factor bZIP11 activates auxin-mediated transcription by recruiting the histone acetylation machinery. Nat Commun 2014; 5:3883. [DOI: 10.1038/ncomms4883] [Citation(s) in RCA: 112] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Accepted: 04/15/2014] [Indexed: 01/05/2023] Open
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220
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Liu X, Yang S, Zhao M, Luo M, Yu CW, Chen CY, Tai R, Wu K. Transcriptional repression by histone deacetylases in plants. MOLECULAR PLANT 2014; 7:764-72. [PMID: 24658416 DOI: 10.1093/mp/ssu033] [Citation(s) in RCA: 150] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Reversible histone acetylation and deacetylation at the N-terminus of histone tails play crucial roles in regulation of eukaryotic gene activity. Acetylation of core histones usually induces an 'open' chromatin structure and is associated with gene activation, whereas deacetylation of histone is often correlated with 'closed' chromatin and gene repression. Histone deacetylation is catalyzed by histone deacetylases (HDACs). A growing number of studies have demonstrated the importance of histone deacetylation/acetylation on genome stability, transcriptional regulation, and development in plants. Furthermore, HDACs were shown to interact with various chromatin remolding factors and transcription factors involved in transcriptional repression in multiple developmental processes. In this review, we summarized recent findings on the transcriptional repression mediated by HDACs in plants.
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Affiliation(s)
- Xuncheng Liu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
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221
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Boycheva I, Vassileva V, Iantcheva A. Histone acetyltransferases in plant development and plasticity. Curr Genomics 2014; 15:28-37. [PMID: 24653661 PMCID: PMC3958957 DOI: 10.2174/138920291501140306112742] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Revised: 10/15/2013] [Accepted: 10/21/2013] [Indexed: 12/16/2022] Open
Abstract
In eukaryotes, transcriptional regulation is determined by dynamic and reversible chromatin modifications, such as acetylation, methylation, phosphorylation, ubiquitination, glycosylation, that are essential for the processes of DNA replication, DNA-repair, recombination and gene transcription. The reversible and rapid changes in histone acetylation induce genome-wide and specific alterations in gene expression and play a key role in chromatin modification. Because of their sessile lifestyle, plants cannot escape environmental stress, and hence have evolved a number of adaptations to survive in stress surroundings. Chromatin modifications play a major role in regulating plant gene expression following abiotic and biotic stress. Plants are also able to respond to signals that affect the maintaince of genome integrity. All these factors are associated with changes in gene expression levels through modification of histone acetylation. This review focuses on the major types of genes encoding for histone acetyltransferases, their structure, function, interaction with other genes, and participation in plant responses to environmental stimuli, as well as their role in cell cycle progression. We also bring together the most recent findings on the study of the histone acetyltransferase HAC1 in the model legumes Medicago truncatula and Lotus japonicus.
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Affiliation(s)
- Irina Boycheva
- AgroBioInstitute, Blvd. Dragan Tzankov 8, 1164 Sofia, Bulgaria
| | - Valya Vassileva
- Institute of Plant Physiology and Genetics, Acad. Georgi Bonchev str. Bl. 21 1113, Sofia, Bulgaria
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222
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Abstract
Plants can grow complex and elaborate structures, in some species for thousands of years. Despite the diversity in form and shape, plants are built from a limited number of fundamental tissue types, and their arrangement is deeply conserved in the plant kingdom. A key question in biology is how these fundamental tissues, i.e. epidermal, ground and vascular tissue, are specified and organized in time and space. In the present paper, I discuss the use of the early Arabidopsis embryo as a model system to dissect the control of tissue formation and patterning, as well as the specification of the stem cells that sustain post-embryonic growth. I present recent insights into the molecules and mechanisms that control both the specification and the subsequent growth of the different cell types within the embryonic root. Finally, I discuss major unanswered questions and future challenges in using the embryo as a model to decipher the regulatory logic of plant development.
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223
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Rayapuram N, Bonhomme L, Bigeard J, Haddadou K, Przybylski C, Hirt H, Pflieger D. Identification of novel PAMP-triggered phosphorylation and dephosphorylation events in Arabidopsis thaliana by quantitative phosphoproteomic analysis. J Proteome Res 2014; 13:2137-51. [PMID: 24601666 DOI: 10.1021/pr401268v] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Signaling cascades rely strongly on protein kinase-mediated substrate phosphorylation. Currently a major challenge in signal transduction research is to obtain high confidence substrate phosphorylation sites and assign them to specific kinases. In response to bacterial flagellin, a pathogen-associated molecular pattern (PAMP), we searched for rapidly phosphorylated proteins in Arabidopsis thaliana by combining multistage activation (MSA) and electron transfer dissociation (ETD) fragmentation modes, which generate complementary spectra and identify phosphopeptide sites with increased reliability. Of a total of 825 phosphopeptides, we identified 58 to be differentially phosphorylated. These peptides harbor kinase motifs of mitogen-activated protein kinases (MAPKs) and calcium-dependent protein kinases (CDPKs), as well as yet unknown protein kinases. Importantly, 12 of the phosphopeptides show reduced phosphorylation upon flagellin treatment. Since protein abundance levels did not change, these results indicate that flagellin induces not only various protein kinases but also protein phosphatases, even though a scenario of inhibited kinase activity may also be possible.
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224
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Horstman A, Willemsen V, Boutilier K, Heidstra R. AINTEGUMENTA-LIKE proteins: hubs in a plethora of networks. TRENDS IN PLANT SCIENCE 2014; 19:146-57. [PMID: 24280109 DOI: 10.1016/j.tplants.2013.10.010] [Citation(s) in RCA: 106] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Revised: 10/24/2013] [Accepted: 10/27/2013] [Indexed: 05/18/2023]
Abstract
Members of the AINTEGUMENTA-LIKE (AIL) family of APETALA 2/ETHYLENE RESPONSE FACTOR (AP2/ERF) domain transcription factors are expressed in all dividing tissues in the plant, where they have central roles in developmental processes such as embryogenesis, stem cell niche specification, meristem maintenance, organ positioning, and growth. When overexpressed, AIL proteins induce adventitious growth, including somatic embryogenesis and ectopic organ formation. The Arabidopsis (Arabidopsis thaliana) genome contains eight AIL genes, including AINTEGUMENTA, BABY BOOM, and the PLETHORA genes. Studies on these transcription factors have revealed their intricate relationship with auxin as well as their involvement in an increasing number of gene regulatory networks, in which extensive crosstalk and feedback loops have a major role.
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Affiliation(s)
- Anneke Horstman
- Plant Research International, Wageningen University and Research Centre, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Viola Willemsen
- Plant Developmental Biology, Wageningen University and Research Centre, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Kim Boutilier
- Plant Research International, Wageningen University and Research Centre, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Renze Heidstra
- Plant Developmental Biology, Wageningen University and Research Centre, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands.
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225
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Hao Y, Wang X, Li X, Bassa C, Mila I, Audran C, Maza E, Li Z, Bouzayen M, van der Rest B, Zouine M. Genome-wide identification, phylogenetic analysis, expression profiling, and protein-protein interaction properties of TOPLESS gene family members in tomato. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:1013-23. [PMID: 24399174 PMCID: PMC3935560 DOI: 10.1093/jxb/ert440] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Members of the TOPLESS gene family emerged recently as key players in gene repression in several mechanisms, especially in auxin perception. The TOPLESS genes constitute, in 'higher-plant' genomes, a small multigenic family comprising four to 11 members. In this study, this family was investigated in tomato, a model plant for Solanaceae species and fleshy fruits. Six open reading frames predicted to encode topless-like proteins (SlTPLs) containing the canonical domains (LisH, CTLH, and two WD40 repeats) were identified in the tomato genome. Nuclear localization was confirmed for all members of the SlTPL family with the exception SlTPL6, which localized at the cytoplasm and was excluded from the nucleus. SlTPL genes displayed distinctive expression patterns in different tomato organs, with SlTPL1 showing the highest levels of transcript accumulation in all tissues tested except in ripening fruit where SlTPL3 and SlTPL4 were the most prominently expressed. To gain insight into the specificity of the different TOPLESS paralogues, a protein-protein interaction map between TOPLESS and auxin/indole-3-acetic acid (Aux/IAA) proteins was built using a yeast two-hybrid approach. The PPI map enabled the distinction of two patterns: TOPLESS isoforms interacting with the majority of Aux/IAA, and isoforms with limited capacity for interaction with these protein partners. Interestingly, evolutionary analyses of the TOPLESS gene family revealed that the highly expressed isoforms (SlTPL1, SlTPL3, and SlTPL4) corresponded to the three TPL-related genes undergoing the strongest purifying selection, while the selection was much weaker for SlTPL6, which was expressed at a low level and encoded a protein lacking the capacity to interact with Aux/IAAs.
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Affiliation(s)
- Yanwei Hao
- University of Toulouse, INPT, Laboratory of Genomics and Biotechnology of Fruit, Avenue de l’Agrobiopole BP 32607, Castanet-Tolosan F-31326, France
- INRA, UMR990 Génomique et Biotechnologie des Fruits, Chemin de Borde Rouge, Castanet-Tolosan, F-31326, France
| | - Xinyu Wang
- University of Toulouse, INPT, Laboratory of Genomics and Biotechnology of Fruit, Avenue de l’Agrobiopole BP 32607, Castanet-Tolosan F-31326, France
- INRA, UMR990 Génomique et Biotechnologie des Fruits, Chemin de Borde Rouge, Castanet-Tolosan, F-31326, France
| | - Xian Li
- University of Toulouse, INPT, Laboratory of Genomics and Biotechnology of Fruit, Avenue de l’Agrobiopole BP 32607, Castanet-Tolosan F-31326, France
- Laboratory of Fruit Quality Biology, The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Zijingang Campus, Hangzhou, PR China
| | - Carole Bassa
- University of Toulouse, INPT, Laboratory of Genomics and Biotechnology of Fruit, Avenue de l’Agrobiopole BP 32607, Castanet-Tolosan F-31326, France
- INRA, UMR990 Génomique et Biotechnologie des Fruits, Chemin de Borde Rouge, Castanet-Tolosan, F-31326, France
- Université de Toulouse, UPS, UMR 5546, Laboratoire de Recherche en Sciences Végétales, Castanet-Tolosan, France
- CNRS, UMR 5546, 31326 Castanet-Tolosan, France
| | - Isabelle Mila
- University of Toulouse, INPT, Laboratory of Genomics and Biotechnology of Fruit, Avenue de l’Agrobiopole BP 32607, Castanet-Tolosan F-31326, France
- INRA, UMR990 Génomique et Biotechnologie des Fruits, Chemin de Borde Rouge, Castanet-Tolosan, F-31326, France
| | - Corinne Audran
- University of Toulouse, INPT, Laboratory of Genomics and Biotechnology of Fruit, Avenue de l’Agrobiopole BP 32607, Castanet-Tolosan F-31326, France
- INRA, UMR990 Génomique et Biotechnologie des Fruits, Chemin de Borde Rouge, Castanet-Tolosan, F-31326, France
| | - Elie Maza
- University of Toulouse, INPT, Laboratory of Genomics and Biotechnology of Fruit, Avenue de l’Agrobiopole BP 32607, Castanet-Tolosan F-31326, France
- INRA, UMR990 Génomique et Biotechnologie des Fruits, Chemin de Borde Rouge, Castanet-Tolosan, F-31326, France
| | - Zhengguo Li
- School of Life Sciences, Chongqing University, Chongqing 400044, China
| | - Mondher Bouzayen
- University of Toulouse, INPT, Laboratory of Genomics and Biotechnology of Fruit, Avenue de l’Agrobiopole BP 32607, Castanet-Tolosan F-31326, France
- INRA, UMR990 Génomique et Biotechnologie des Fruits, Chemin de Borde Rouge, Castanet-Tolosan, F-31326, France
| | - Benoit van der Rest
- University of Toulouse, INPT, Laboratory of Genomics and Biotechnology of Fruit, Avenue de l’Agrobiopole BP 32607, Castanet-Tolosan F-31326, France
- INRA, UMR990 Génomique et Biotechnologie des Fruits, Chemin de Borde Rouge, Castanet-Tolosan, F-31326, France
| | - Mohamed Zouine
- University of Toulouse, INPT, Laboratory of Genomics and Biotechnology of Fruit, Avenue de l’Agrobiopole BP 32607, Castanet-Tolosan F-31326, France
- INRA, UMR990 Génomique et Biotechnologie des Fruits, Chemin de Borde Rouge, Castanet-Tolosan, F-31326, France
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226
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Zhang F, Wang Y, Li G, Tang Y, Kramer EM, Tadege M. STENOFOLIA recruits TOPLESS to repress ASYMMETRIC LEAVES2 at the leaf margin and promote leaf blade outgrowth in Medicago truncatula. THE PLANT CELL 2014; 26:650-64. [PMID: 24585835 PMCID: PMC3967031 DOI: 10.1105/tpc.113.121947] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2013] [Revised: 01/28/2014] [Accepted: 02/03/2014] [Indexed: 05/22/2023]
Abstract
The Medicago truncatula WUSCHEL-related homeobox (WOX) gene, STENOFOLIA (STF), plays a key role in leaf blade outgrowth by promoting cell proliferation at the adaxial-abaxial junction. STF functions primarily as a transcriptional repressor, but the underlying molecular mechanism is unknown. Here, we report the identification of a protein interaction partner and a direct target, shedding light on the mechanism of STF function. Two highly conserved motifs in the C-terminal domain of STF, the WUSCHEL (WUS) box and the STF box, cooperatively recruit TOPLESS (Mt-TPL) family corepressors, and this recruitment is required for STF function, as deletion of these two domains (STFdel) impaired blade outgrowth whereas fusing Mt-TPL to STFdel restored function. The homeodomain motif is required for direct repression of ASYMMETRIC LEAVES2 (Mt-AS2), silencing of which partially rescues the stf mutant phenotype. STF and LAMINALESS1 (LAM1) are functional orthologs. A single amino acid (Asn to Ile) substitution in the homeodomain abolished the repression of Mt-AS2 and STF's ability to complement the lam1 mutant of Nicotiana sylvestris. Our data together support a model in which STF recruits corepressors to transcriptionally repress its targets during leaf blade morphogenesis. We propose that recruitment of TPL/TPL-related proteins may be a common mechanism in the repressive function of modern/WUS clade WOX genes.
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Affiliation(s)
- Fei Zhang
- Department of Plant and Soil Sciences, Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, Oklahoma 73401
| | - Yewei Wang
- Department of Plant and Soil Sciences, Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, Oklahoma 73401
| | - Guifen Li
- Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401
| | - Yuhong Tang
- Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401
| | - Elena M. Kramer
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138
| | - Million Tadege
- Department of Plant and Soil Sciences, Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, Oklahoma 73401
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227
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Motte H, Vereecke D, Geelen D, Werbrouck S. The molecular path to in vitro shoot regeneration. Biotechnol Adv 2014; 32:107-21. [DOI: 10.1016/j.biotechadv.2013.12.002] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Revised: 11/20/2013] [Accepted: 12/08/2013] [Indexed: 10/25/2022]
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228
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Abstract
The grass family is one of the largest families in angiosperms and has evolved a characteristic inflorescence morphology, with complex branches and specialized spikelets. The origin and development of the highly divergent inflorescence architecture in grasses have recently received much attention. Increasing evidence has revealed that numerous factors, such as transcription factors and plant hormones, play key roles in determining reproductive meristem fate and inflorescence patterning in grasses. Moreover, some molecular switches that have been implicated in specifying inflorescence shapes contribute significantly to grain yields in cereals. Here, we review key genetic and molecular switches recently identified from two model grass species, rice (Oryza sativa) and maize (Zea mays), that regulate inflorescence morphology specification, including meristem identity, meristem size and maintenance, initiation and outgrowth of axillary meristems, and organogenesis. Furthermore, we summarize emerging networks of genes and pathways in grass inflorescence morphogenesis and emphasize their evolutionary divergence in comparison with the model eudicot Arabidopsis thaliana. We also discuss the agricultural application of genes controlling grass inflorescence development.
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Affiliation(s)
- Dabing Zhang
- State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China;
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229
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Zhao L, Lu J, Zhang J, Wu PY, Yang S, Wu K. Identification and characterization of histone deacetylases in tomato (Solanum lycopersicum). FRONTIERS IN PLANT SCIENCE 2014; 5:760. [PMID: 25610445 PMCID: PMC4285013 DOI: 10.3389/fpls.2014.00760] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Accepted: 12/10/2014] [Indexed: 05/19/2023]
Abstract
Histone acetylation and deacetylation at the N-terminus of histone tails play crucial roles in the regulation of eukaryotic gene activity. Histone acetylation and deacetylation are catalyzed by histone acetyltransferases and histone deacetylases (HDACs), respectively. A growing number of studies have demonstrated the importance of histone deacetylation/acetylation on genome stability, transcriptional regulation, development and response to stress in Arabidopsis. However, the biological functions of HDACs in tomato have not been investigated previously. Fifteen HDACs identified from tomato (Solanum lycopersicum) can be grouped into RPD3/HDA1, SIR2 and HD2 families based on phylogenetic analysis. Meanwhile, 10 members of the RPD3/HDA1 family can be further subdivided into four groups, namely Class I, Class II, Class III, and Class IV. High similarities of protein sequences and conserved domains were identified among SlHDACs and their homologs in Arabidopsis. Most SlHDACs were expressed in all tissues examined with different transcript abundance. Transient expression in Arabidopsis protoplasts showed that SlHDA8, SlHDA1, SlHDA5, SlSRT1 and members of the HD2 family were localized to the nucleus, whereas SlHDA3 and SlHDA4 were localized in both the cytoplasm and nucleus. The difference in the expression patterns and subcellular localization of SlHDACs suggest that they may play distinct functions in tomato. Furthermore, we found that three members of the RPD3/HDA1 family, SlHDA1, SIHDA3 and SlHDA4, interacted with TAG1 (TOMATO AGAMOUS1) and TM29 (TOMATO MADS BOX29), two MADS-box proteins associated with tomato reproductive development, indicating that these HDACs may be involved in gene regulation in reproductive development.
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Affiliation(s)
- Linmao Zhao
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of SciencesGuangzhou, China
- College of Life Sciences, University of Chinese Academy of SciencesBeijing, China
| | - Jingxia Lu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of SciencesGuangzhou, China
- College of Life Sciences, University of Chinese Academy of SciencesBeijing, China
| | - Jianxia Zhang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of SciencesGuangzhou, China
- Institute of Plant Biology, National Taiwan UniversityTaipei, Taiwan
| | - Pei-Ying Wu
- Institute of Plant Biology, National Taiwan UniversityTaipei, Taiwan
| | - Songguang Yang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of SciencesGuangzhou, China
- *Correspondence: Songguang Yang, Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Xingke Road 723, Tianhe District, Guangzhou 510650, China e-mail:
| | - Keqiang Wu
- Institute of Plant Biology, National Taiwan UniversityTaipei, Taiwan
- Keqiang Wu, Institute of Plant Biology, National Taiwan University, Taipei 106, No. 1, Sec. 4, Roosevelt Road, 10617 Taipei, Taiwan e-mail:
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230
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Abstract
Grasses bear unique flowers lacking obvious petals and sepals in special inflorescence units, the florets and the spikelet. Despite this, grass floral organs such as stamens and lodicules (petal homologs) are specified by ABC homeotic genes encoding MADS domain transcription factors, suggesting that the ABC model of eudicot flower development is largely applicable to grass flowers. However, some modifications need to be made for the model to fit grasses well: for example, a YABBY gene plays an important role in carpel specification. In addition, a number of genes are involved in the development of the lateral organs that constitute the spikelet. In this review, we discuss recent progress in elucidating the genes required for flower and spikelet development in grasses, together with those involved in fate determination of the spikelet and flower meristems.
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Affiliation(s)
- Hiro-Yuki Hirano
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, Japan,
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231
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Prunet N, Jack TP. Flower development in Arabidopsis: there is more to it than learning your ABCs. Methods Mol Biol 2014; 1110:3-33. [PMID: 24395250 DOI: 10.1007/978-1-4614-9408-9_1] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The field of Arabidopsis flower development began in the early 1980s with the initial description of several mutants including apetala1, apetala2, and agamous that altered floral organ identity (Koornneef and van der Veen, Theor Appl Genet 58:257-263, 1980; Koornneef et al., J Hered 74:265-272, 1983). By the end of the 1980s, these mutants were receiving more focused attention to determine precisely how they affected flower development (Komaki et al., Development 104:195-203, 1988; Bowman et al., Plant Cell 1:37-52, 1989). In the last quarter century, impressive progress has been made in characterizing the gene products and molecular mechanisms that control the key events in flower development. In this review, we briefly summarize the highlights of work from the past 25 years but focus on advances in the field in the last several years.
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Affiliation(s)
- Nathanaël Prunet
- Department of Biological Sciences, Dartmouth College, Hanover, NH, USA
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232
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DWARF 53 acts as a repressor of strigolactone signalling in rice. Nature 2013; 504:401-5. [PMID: 24336200 DOI: 10.1038/nature12870] [Citation(s) in RCA: 527] [Impact Index Per Article: 47.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Accepted: 11/06/2013] [Indexed: 01/05/2023]
Abstract
Strigolactones (SLs) are a group of newly identified plant hormones that control plant shoot branching. SL signalling requires the hormone-dependent interaction of DWARF 14 (D14), a probable candidate SL receptor, with DWARF 3 (D3), an F-box component of the Skp-Cullin-F-box (SCF) E3 ubiquitin ligase complex. Here we report the characterization of a dominant SL-insensitive rice (Oryza sativa) mutant dwarf 53 (d53) and the cloning of D53, which encodes a substrate of the SCF(D3) ubiquitination complex and functions as a repressor of SL signalling. Treatments with GR24, a synthetic SL analogue, cause D53 degradation via the proteasome in a manner that requires D14 and the SCF(D3) ubiquitin ligase, whereas the dominant form of D53 is resistant to SL-mediated degradation. Moreover, D53 can interact with transcriptional co-repressors known as TOPLESS-RELATED PROTEINS. Our results suggest a model of SL signalling that involves SL-dependent degradation of the D53 repressor mediated by the D14-D3 complex.
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233
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Pérez AC, Goossens A. Jasmonate signalling: a copycat of auxin signalling? PLANT, CELL & ENVIRONMENT 2013; 36:2071-84. [PMID: 23611666 DOI: 10.1111/pce.12121] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Accepted: 04/15/2013] [Indexed: 05/22/2023]
Abstract
Plant hormones regulate almost all aspects of plant growth and development. The past decade has provided breakthrough discoveries in phytohormone sensing and signal transduction, and highlighted the striking mechanistic similarities between the auxin and jasmonate (JA) signalling pathways. Perception of auxin and JA involves the formation of co-receptor complexes in which hormone-specific E3-ubiquitin ligases of the SKP1-Cullin-F-box protein (SCF) type interact with specific repressor proteins. Across the plant kingdom, the Aux/IAA and the JASMONATE-ZIM DOMAIN (JAZ) proteins correspond to the auxin- and JA-specific repressors, respectively. In the absence of the hormones, these repressors form a complex with transcription factors (TFs) specific for both pathways. They also recruit several proteins, among which the general co-repressor TOPLESS, and thereby prevent the TFs from activating gene expression. The hormone-mediated interaction between the SCF and the repressors targets the latter for 26S proteasome-mediated degradation, which, in turn, releases the TFs to allow modulating hormone-dependent gene expression. In this review, we describe the similarities and differences in the auxin and JA signalling cascades with respect to the protein families and the protein domains involved in the formation of the pathway-specific complexes.
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Affiliation(s)
- A Cuéllar Pérez
- Department of Plant Systems Biology, VIB, B-9052, Gent, Belgium; Department of Plant Biotechnology & Bioinformatics, Ghent University, B-9052, Gent, Belgium
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234
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Li Q, Zhao P, Li J, Zhang C, Wang L, Ren Z. Genome-wide analysis of the WD-repeat protein family in cucumber and Arabidopsis. Mol Genet Genomics 2013; 289:103-24. [DOI: 10.1007/s00438-013-0789-x] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Accepted: 10/19/2013] [Indexed: 12/31/2022]
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235
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Lyons R, Iwase A, Gänsewig T, Sherstnev A, Duc C, Barton GJ, Hanada K, Higuchi-Takeuchi M, Matsui M, Sugimoto K, Kazan K, Simpson GG, Shirasu K. The RNA-binding protein FPA regulates flg22-triggered defense responses and transcription factor activity by alternative polyadenylation. Sci Rep 2013; 3:2866. [PMID: 24104185 PMCID: PMC3793224 DOI: 10.1038/srep02866] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Accepted: 09/17/2013] [Indexed: 12/21/2022] Open
Abstract
RNA-binding proteins (RBPs) play an important role in plant host-microbe interactions. In this study, we show that the plant RBP known as FPA, which regulates 3′-end mRNA polyadenylation, negatively regulates basal resistance to bacterial pathogen Pseudomonas syringae in Arabidopsis. A custom microarray analysis reveals that flg22, a peptide derived from bacterial flagellins, induces expression of alternatively polyadenylated isoforms of mRNA encoding the defence-related transcriptional repressor ETHYLENE RESPONSE FACTOR 4 (ERF4), which is regulated by FPA. Flg22 induces expression of a novel isoform of ERF4 that lacks the ERF-associated amphiphilic repression (EAR) motif, while FPA inhibits this induction. The EAR-lacking isoform of ERF4 acts as a transcriptional activator in vivo and suppresses the flg22-dependent reactive oxygen species burst. We propose that FPA controls use of proximal polyadenylation sites of ERF4, which quantitatively limit the defence response output.
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Affiliation(s)
- Rebecca Lyons
- 1] RIKEN Plant Science Center, Tsurumi-ku, Yokohama, 230-0045, Japan [2] Commonwealth Scientific and Industrial Research Organization Plant Industry, Queensland Bioscience Precinct, St. Lucia, Queensland 4067, Australia
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236
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Braszewska-Zalewska AJ, Wolny EA, Smialek L, Hasterok R. Tissue-specific epigenetic modifications in root apical meristem cells of Hordeum vulgare. PLoS One 2013; 8:e69204. [PMID: 23935955 PMCID: PMC3729647 DOI: 10.1371/journal.pone.0069204] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Accepted: 06/05/2013] [Indexed: 11/18/2022] Open
Abstract
Epigenetic modifications of chromatin structure are essential for many biological processes, including growth and reproduction. Patterns of DNA and histone modifications have recently been widely studied in many plant species, although there is virtually no data on the spatial and temporal distribution of epigenetic markers during plant development. Accordingly, we have used immunostaining techniques to investigate epigenetic modifications in the root apical meristem of Hordeum vulgare. Histone H4 acetylation (H4K5ac), histone H3 dimethylation (H3K4me2, H3K9me2) and DNA methylation (5mC) patterns were established for various root meristem tissues. Distinct levels of those modifications were visualised in the root cap, epidermis, cortex and vascular tissues. The lateral root cap cells seem to display the highest level of H3K9me2 and 5mC. In the epidermis, the highest level of 5mC and H3K9me2 was detected in the nuclei from the boundary of the proximal meristem and the elongation zone, while the vascular tissues were characterized by the highest level of H4K5ac. Some of the modified histones were also detectable in the cytoplasm in a highly tissue-specific manner. Immunolocalisation of epigenetic modifications of chromatin carried out in this way, on longitudinal or transverse sections, provides a unique topographic context within the organ, and will provide some answers to the significant biological question of tissue differentiation processes during root development in a monocotyledon plant species.
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Affiliation(s)
- Agnieszka J. Braszewska-Zalewska
- Department of Plant Anatomy and Cytology, Faculty of Biology and Environmental Protection, University of Silesia, Katowice, Poland
| | - Elzbieta A. Wolny
- Department of Plant Anatomy and Cytology, Faculty of Biology and Environmental Protection, University of Silesia, Katowice, Poland
| | - Lukasz Smialek
- Department of Plant Anatomy and Cytology, Faculty of Biology and Environmental Protection, University of Silesia, Katowice, Poland
| | - Robert Hasterok
- Department of Plant Anatomy and Cytology, Faculty of Biology and Environmental Protection, University of Silesia, Katowice, Poland
- * E-mail:
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237
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Santino A, Taurino M, De Domenico S, Bonsegna S, Poltronieri P, Pastor V, Flors V. Jasmonate signaling in plant development and defense response to multiple (a)biotic stresses. PLANT CELL REPORTS 2013; 32:1085-98. [PMID: 23584548 DOI: 10.1007/s00299-013-1441-2] [Citation(s) in RCA: 157] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2013] [Revised: 03/25/2013] [Accepted: 03/28/2013] [Indexed: 05/23/2023]
Abstract
Plants frequently live in environments characterized by the presence of simultaneous and different stresses. The intricate and finely tuned molecular mechanisms activated by plants in response to abiotic and biotic environmental factors are not well understood, and less is known about the integrative signals and convergence points activated by plants in response to multiple (a)biotic stresses. Phytohormones play a key role in plant development and response to (a)biotic stresses. Among these, one of the most important signaling molecules is an oxylipin, the plant hormone jasmonic acid. Oxylipins are derived from oxygenation of polyunsaturated fatty acids. Jasmonic acid and its volatile derivative methyl jasmonate have been considered for a long time to be the bioactive forms due to their physiological effects and abundance in the plant. However, more recent studies showed unambiguously that they are only precursors of the active forms represented by some amino acid conjugates. Upon developmental or environmental stimuli, jasmonates are synthesized and accumulate transiently. Upon perception, jasmonate signal transduction process is finely tuned by a complex mechanism comprising specific repressor proteins which in turn control a number of transcription factors regulating the expression of jasmonate responsive genes. We discuss the latest discoveries about the role of jasmonates in plants resistance mechanism against biotic and abiotic stresses. Finally, the deep interplay of different phytohormones in stresses signaling will be also discussed.
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Affiliation(s)
- Angelo Santino
- Institute of Sciences of Food Production C.N.R. Unit of Lecce, via Monteroni, 73100 Lecce, Italy.
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238
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Pierre-Jerome E, Moss BL, Nemhauser JL. Tuning the auxin transcriptional response. JOURNAL OF EXPERIMENTAL BOTANY 2013; 64:2557-63. [PMID: 23630231 DOI: 10.1093/jxb/ert100] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
How does auxin provoke such a diverse array of responses? This long-standing question is further complicated by a remarkably short nuclear auxin signalling pathway. To crack the auxin code, several potential sources of specificity need to be evaluated. These include: specificity of interactions among the core auxin response components, specificity resulting from higher order complex dynamics, and specificity in interactions with global factors controlling protein turnover and transcriptional repression. Here, we review recent progress towards characterizing and quantifying these interactions and highlight key gaps that remain.
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239
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Gallavotti A. The role of auxin in shaping shoot architecture. JOURNAL OF EXPERIMENTAL BOTANY 2013; 64:2593-608. [PMID: 23709672 DOI: 10.1093/jxb/ert141] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The variety of plant architectures observed in nature is predominantly determined by vegetative and reproductive branching patterns, the positioning of lateral organs, and differential stem elongation. Branches, lateral organs, and stems are the final products of the activity of meristems, groups of stem cells whose function is genetically determined and environmentally influenced. Several decades of studies in different plant species have shed light on the essential role of the hormone auxin in plant growth and development. Auxin influences stem elongation and regulates the formation, activity, and fate of meristems, and has therefore been recognized as a major hormone shaping plant architecture. Increasing our knowledge of the molecular mechanisms that regulate auxin function is necessary to understand how different plant species integrate a genetically determined developmental programme, the establishment of a body plan, with constant inputs from the surrounding environment. This information will allow us to develop the molecular tools needed to modify plant architecture in several crop species and in rapidly changing environments.
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Affiliation(s)
- Andrea Gallavotti
- Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854-8020, USA.
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240
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Abstract
Jasmonates (JAs) are plant hormones with essential roles in plant defense and development. The basic-helix-loop-helix (bHLH) transcription factor (TF) MYC2 has recently emerged as a master regulator of most aspects of the jasmonate (JA) signaling pathway in Arabidopsis. MYC2 coordinates JA-mediated defense responses by antagonistically regulating two different branches of the JA signaling pathway that determine resistance to pests and pathogens, respectively. MYC2 is required for induced systemic resistance (ISR) triggered by beneficial soil microbes while MYC2 function is targeted by pathogens during effector-mediated suppression of innate immunity in roots. Another notable function of MYC2 is the regulation of crosstalk between the signaling pathways of JA and those of other phytohormones such as abscisic acid (ABA), salicylic acid (SA), gibberellins (GAs), and auxin (IAA). MYC2 also regulates interactions between JA signaling and light, phytochrome signaling, and the circadian clock. MYC2 is involved in JA-regulated plant development, lateral and adventitious root formation, flowering time, and shade avoidance syndrome. Related bHLH TFs MYC3 and MYC4 also regulate both overlapping and distinct MYC2-regulated functions in Arabidopsis while MYC2 orthologs act as 'master switches' that regulate JA-mediated biosynthesis of secondary metabolites. Here, we briefly review recent studies that revealed mechanistic new insights into the mode of action of this versatile TF.
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Affiliation(s)
- Kemal Kazan
- Commonwealth Scientific and Industrial Research Organization Plant Industry, Queensland Bioscience Precinct, Brisbane, Queensland 4067, Australia.
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241
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Turchi L, Carabelli M, Ruzza V, Possenti M, Sassi M, Peñalosa A, Sessa G, Salvi S, Forte V, Morelli G, Ruberti I. Arabidopsis HD-Zip II transcription factors control apical embryo development and meristem function. Development 2013; 140:2118-29. [PMID: 23578926 DOI: 10.1242/dev.092833] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The Arabidopsis genome encodes ten Homeodomain-Leucine zipper (HD-Zip) II proteins. ARABIDOPSIS THALIANA HOMEOBOX 2 (ATHB2), HOMEOBOX ARABIDOPSIS THALIANA 1 (HAT1), HAT2, HAT3 and ATHB4 are regulated by changes in the red/far red light ratio that induce shade avoidance in most of the angiosperms. Here, we show that progressive loss of HAT3, ATHB4 and ATHB2 activity causes developmental defects from embryogenesis onwards in white light. Cotyledon development and number are altered in hat3 athb4 embryos, and these defects correlate with changes in auxin distribution and response. athb2 gain-of-function mutation and ATHB2 expression driven by its promoter in hat3 athb4 result in significant attenuation of phenotypes, thus demonstrating that ATHB2 is functionally redundant to HAT3 and ATHB4. In analogy to loss-of-function mutations in HD-Zip III genes, loss of HAT3 and ATHB4 results in organ polarity defects, whereas triple hat3 athb4 athb2 mutants develop one or two radialized cotyledons and lack an active shoot apical meristem (SAM). Consistent with overlapping expression pattern of HD-Zip II and HD-Zip III gene family members, bilateral symmetry and SAM defects are enhanced when hat3 athb4 is combined with mutations in PHABULOSA (PHB), PHAVOLUTA (PHV) or REVOLUTA (REV). Finally, we show that ATHB2 is part of a complex regulatory circuit directly involving both HD-Zip II and HD-Zip III proteins. Taken together, our study provides evidence that a genetic system consisting of HD-Zip II and HD-Zip III genes cooperates in establishing bilateral symmetry and patterning along the adaxial-abaxial axis in the embryo as well as in controlling SAM activity.
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Affiliation(s)
- Luana Turchi
- Institute of Molecular Biology and Pathology, National Research Council, P.le A. Moro 5, 00185 Rome, Italy
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242
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Elhiti M, Wally OSD, Belmonte MF, Chan A, Cao Y, Xiang D, Datla R, Stasolla C. Gene expression analysis in microdissected shoot meristems of Brassica napus microspore-derived embryos with altered SHOOTMERISTEMLESS levels. PLANTA 2013; 237:1065-1082. [PMID: 23242073 DOI: 10.1007/s00425-012-1814-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2012] [Accepted: 11/12/2012] [Indexed: 05/28/2023]
Abstract
Altered expression of Brassica napus (Bn) SHOOTMERISTEMLESS (STM) affects the morphology and behaviour of microspore-derived embryos (MDEs). While down-regulation of BnSTM repressed the formation of the shoot meristem (SAM) and reduced the number of Brassica MDEs able to regenerate viable plants at germination, over-expression of BnSTM enhanced the structure of the SAM and improved regeneration frequency. Within dissected SAMs, the induction of BnSTM up-regulated the expression of many transcription factors (TFs) some of which directly involved in the formation of the meristem, i.e. CUP-SHAPED COTYLEDON1 and WUSCHEL, and regulatory components of the antioxidant response, hormone signalling, and cell wall synthesis and modification. Opposite expression patterns for some of these genes were observed in the SAMs of MDEs down-regulating BnSTM. Altered expression of BnSTM affected transcription of cell wall and lignin biosynthetic genes. The expression of PHENYLALANINE AMMONIA LYASE2, CINNAMATE 4-4HYDROXYLASE, and CINNAMYL ALCOHOL DEHYDROGENASE were repressed in SAMs over-expressing BnSTM. Since lignin formation is a feature of irreversible cell differentiation, these results suggest that one way in which BnSTM promotes indeterminate cell fate may be by preventing the expression of components of biochemical pathways involved in the accumulation of lignin in the meristematic cells. Overall, these studies provide evidence for a novel function of BnSTM in enhancing the quality of in vitro produced meristems, and propose that this gene can be used as a potential target to improve regeneration of cultured embryos.
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Affiliation(s)
- Mohamed Elhiti
- Department of Botany, Faculty of Science, Tanta University, Tanta, 31527, Egypt
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Ma X, Lv S, Zhang C, Yang C. Histone deacetylases and their functions in plants. PLANT CELL REPORTS 2013; 32:465-78. [PMID: 23408190 DOI: 10.1007/s00299-013-1393-6] [Citation(s) in RCA: 92] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2012] [Revised: 01/12/2013] [Accepted: 01/24/2013] [Indexed: 05/07/2023]
Abstract
Histone deacetylases (HDACs) mediate histone deacetylation and act in concert with histone acetyltransferases to regulate dynamic and reversible histone acetylation which modifies chromatin structure and function, affects gene transcription, thus, controlling multiple cellular processes. HDACs are widely distributed in almost all eukaryotes, and there have been many researches focusing on plant HDACs recently. An increasing number of HDAC genes have been identified and characterized in a variety of plant species and the functions of certain HDACs have been studied. The present studies indicate that HDACs play a key role in regulating plant growth, development and stress responses. This paper reviews recent findings on HDACs and their functions in plants, especially their roles in development and stress responses.
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Affiliation(s)
- Xujun Ma
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), 26 Hexing Road, Harbin, 150040, China
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244
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Xiao J, Zhang H, Xing L, Xu S, Liu H, Chong K, Xu Y. Requirement of histone acetyltransferases HAM1 and HAM2 for epigenetic modification of FLC in regulating flowering in Arabidopsis. JOURNAL OF PLANT PHYSIOLOGY 2013; 170:444-51. [PMID: 23273925 DOI: 10.1016/j.jplph.2012.11.007] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Revised: 10/29/2012] [Accepted: 11/05/2012] [Indexed: 05/03/2023]
Abstract
Histone acetylation is an important posttranslational modification associated with gene activation. In Arabidopsis, two MYST histone acetyltransferases HAM1 and HAM2 work redundantly to acetylate histone H4 lysine 5 (H4K5ace) in vitro. The double mutant ham1/ham2 is lethal, which suggests the critical role of HAM1 and HAM2 in development. Here, we used an artificial microRNA (amiRNA) strategy in Arabidopsis to uncover a novel function of HAM1 and HAM2. The amiRNA-HAM1/2 transgenic plants showed early flowering and reduced fertility. In addition, they responded normally to photoperiod, gibberellic acid treatment, and vernalization. The expression of flowering-repressor FLOWERING LOCUS C (FLC) and its homologues, MADS-box Affecting Flowering genes 3/4 (MAF3/4), were decreased in amiRNA-HAM1/2 lines. HAM1 overexpression caused late flowering and elevated expression of FLC and MAF3/4. Mutation of FLC almost rescued the late flowering with HAM1 overexpression, which suggests that HAM1 regulation of flowering time depended on FLC. Global H4 acetylation was decreased in amiRNA-HAM1/2 lines, but increased in HAM1-OE lines, which further confirmed the acetyltransferase activity of HAM1 in vivo. Chromatin immunoprecipitation revealed that H4 hyperacetylation and H4K5ace at FLC and MAF3/4 were less abundant in amiRNA-HAM1/2 lines than the wild type, but were enriched in HAM1-OE lines. Thus, HAM1 and HAM2 may affect flowering time by epigenetic modification of FLC and MAF3/4 chromatins at H4K5 acetylation.
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Affiliation(s)
- Jun Xiao
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
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245
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Tao Q, Guo D, Wei B, Zhang F, Pang C, Jiang H, Zhang J, Wei T, Gu H, Qu LJ, Qin G. The TIE1 transcriptional repressor links TCP transcription factors with TOPLESS/TOPLESS-RELATED corepressors and modulates leaf development in Arabidopsis. THE PLANT CELL 2013; 25:421-37. [PMID: 23444332 PMCID: PMC3608769 DOI: 10.1105/tpc.113.109223] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2013] [Revised: 02/06/2013] [Accepted: 02/11/2013] [Indexed: 05/18/2023]
Abstract
Leaf size and shape are mainly determined by coordinated cell division and differentiation in lamina. The CINCINNATA (CIN)-like TEOSINTE BRANCHED1/CYCLOIDEA/PCF (TCP) transcription factors are key regulators of leaf development. However, the mechanisms that control TCP activities during leaf development are largely unknown. We identified the TCP Interactor containing EAR motif protein1 (TIE1), a novel transcriptional repressor, as a major modulator of TCP activities during leaf development. Overexpression of TIE1 leads to hyponastic and serrated leaves, whereas disruption of TIE1 causes epinastic leaves. TIE1 is expressed in young leaves and encodes a transcriptional repressor containing a C-terminal EAR motif, which mediates interactions with the TOPLESS (TPL)/TOPLESS-RELATED (TPR) corepressors. In addition, TIE1 physically interacts with CIN-like TCPs. We propose that TIE1 regulates leaf size and morphology by inhibiting the activities of TCPs through recruiting the TPL/TPR corepressors to form a tertiary complex at early stages of leaf development.
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Affiliation(s)
- Qing Tao
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, People’s Republic of China
| | - Dongshu Guo
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, People’s Republic of China
| | - Baoye Wei
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, People’s Republic of China
| | - Fan Zhang
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, People’s Republic of China
| | - Changxu Pang
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, People’s Republic of China
| | - Hao Jiang
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, People’s Republic of China
| | - Jinzhe Zhang
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, People’s Republic of China
| | - Tong Wei
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, People’s Republic of China
| | - Hongya Gu
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, People’s Republic of China
- The National Plant Gene Research Center, Beijing 100101, People’s Republic of China
| | - Li-Jia Qu
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, People’s Republic of China
- The National Plant Gene Research Center, Beijing 100101, People’s Republic of China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, People’s Republic of China
| | - Genji Qin
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, People’s Republic of China
- Address correspondence to
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246
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Aiese Cigliano R, Sanseverino W, Cremona G, Ercolano MR, Conicella C, Consiglio FM. Genome-wide analysis of histone modifiers in tomato: gaining an insight into their developmental roles. BMC Genomics 2013; 14:57. [PMID: 23356725 PMCID: PMC3567966 DOI: 10.1186/1471-2164-14-57] [Citation(s) in RCA: 82] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2012] [Accepted: 01/22/2013] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Histone post-translational modifications (HPTMs) including acetylation and methylation have been recognized as playing a crucial role in epigenetic regulation of plant growth and development. Although Solanum lycopersicum is a dicot model plant as well as an important crop, systematic analysis and expression profiling of histone modifier genes (HMs) in tomato are sketchy. RESULTS Based on recently released tomato whole-genome sequences, we identified in silico 32 histone acetyltransferases (HATs), 15 histone deacetylases (HDACs), 52 histone methytransferases (HMTs) and 26 histone demethylases (HDMs), and compared them with those detected in Arabidopsis (Arabidopsis thaliana), maize (Zea mays) and rice (Oryza sativa) orthologs. Comprehensive analysis of the protein domain architecture and phylogeny revealed the presence of non-canonical motifs and new domain combinations, thereby suggesting for HATs the existence of a new family in plants. Due to species-specific diversification during evolutionary history tomato has fewer HMs than Arabidopsis. The transcription profiles of HMs within tomato organs revealed a broad functional role for some HMs and a more specific activity for others, suggesting key HM regulators in tomato development. Finally, we explored S. pennellii introgression lines (ILs) and integrated the map position of HMs, their expression profiles and the phenotype of ILs. We thereby proved that the strategy was useful to identify HM candidates involved in carotenoid biosynthesis in tomato fruits. CONCLUSIONS In this study, we reveal the structure, phylogeny and spatial expression of members belonging to the classical families of HMs in tomato. We provide a framework for gene discovery and functional investigation of HMs in other Solanaceae species.
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Affiliation(s)
- Riccardo Aiese Cigliano
- CNR, National Research Council of Italy, Institute of Plant Genetics, Research Division Portici, Via Università 133, 80055 Portici, Italy
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247
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Abstract
Organogenesis is the developmental process for producing new organs from undifferentiated cells. In plants, most organs are formed during postembryonic development. Shoot lateral organs are generated in the shoot apical meristem whereas lateral roots develop outside the root apical meristem. While lateral organ formation at the shoot and root might seem quite different, recent genetic studies have highlighted numerous parallels between these processes. In particular, the dynamic accumulation of auxin has been shown to play a crucial role both as a "morphogenetic trigger" and as a morphogen in both phenomena. This suggests that a unique model system could be adopted to study organogenesis in plants. In this chapter we describe the conceptual and technical advantages that support lateral root development as a good model system for studying organogenesis in plants.
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248
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Di Giacomo E, Serino G, Frugis G. Emerging role of the ubiquitin proteasome system in the control of shoot apical meristem function(f). JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2013; 55:7-20. [PMID: 23164365 DOI: 10.1111/jipb.12010] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The shoot apical meristem (SAM) is a population of undifferentiated cells at the tip of the shoot axis that establishes early during plant embryogenesis and gives rise to all shoot organs throughout the plant's life. A plethora of different families of transcription factors (TFs) play a key role in establishing the equilibrium between cell differentiation and stem cell maintenance in the SAM. Fine tuning of these regulatory proteins is crucial for a proper and fast SAM response to environmental and hormonal cues, and for development progression. One effective way to rapidly inactivate TFs involves regulated proteolysis by the ubiquitin/26S proteasome system (UPS). However, a possible role of UPS-dependent protein degradation in the regulation of key SAM TFs has not been thoroughly investigated. Here, we summarize recent evidence supporting a role for the UPS in SAM maintenance and function. We integrate this survey with an in silico analysis of publicly-available microarray databases which identified ubiquitin ligases that are expressed in specific areas within the SAM, suggesting that they may regulate or act downstream of meristem-specific factors.
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Affiliation(s)
- Elisabetta Di Giacomo
- Istituto di Biologia e Biotecnologia Agraria, UOS Roma, Consiglio Nazionale delle Ricerche, Monterotondo Scalo, Roma 00015, Italy
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249
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Wang Z, Cao H, Sun Y, Li X, Chen F, Carles A, Li Y, Ding M, Zhang C, Deng X, Soppe WJ, Liu YX. Arabidopsis paired amphipathic helix proteins SNL1 and SNL2 redundantly regulate primary seed dormancy via abscisic acid-ethylene antagonism mediated by histone deacetylation. THE PLANT CELL 2013; 25:149-66. [PMID: 23371947 PMCID: PMC3584531 DOI: 10.1105/tpc.112.108191] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2013] [Revised: 01/09/2013] [Accepted: 01/15/2013] [Indexed: 05/18/2023]
Abstract
Histone (de)acetylation is a highly conserved chromatin modification that is vital for development and growth. In this study, we identified a role in seed dormancy for two members of the histone deacetylation complex in Arabidopsis thaliana, SIN3-LIKE1 (SNL1) and SNL2. The double mutant snl1 snl2 shows reduced dormancy and hypersensitivity to the histone deacetylase inhibitors trichostatin A and diallyl disulfide compared with the wild type. SNL1 interacts with HISTONE DEACETYLASE19 in vitro and in planta, and loss-of-function mutants of SNL1 and SNL2 show increased acetylation levels of histone 3 lysine 9/18 (H3K9/18) and H3K14. Moreover, SNL1 and SNL2 regulate key genes involved in the ethylene and abscisic acid (ABA) pathways by decreasing their histone acetylation levels. Taken together, we showed that SNL1 and SNL2 regulate seed dormancy by mediating the ABA-ethylene antagonism in Arabidopsis. SNL1 and SNL2 could represent a cross-link point of the ABA and ethylene pathways in the regulation of seed dormancy.
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Affiliation(s)
- Zhi Wang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Hong Cao
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Yongzhen Sun
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Xiaoying Li
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fengying Chen
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Annaick Carles
- Center for Biological Systems Analysis, University of Freiburg, 79104 Freiburg, Germany
| | - Yong Li
- Center for Biological Systems Analysis, University of Freiburg, 79104 Freiburg, Germany
| | - Meng Ding
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Cun Zhang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xin Deng
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Wim J.J. Soppe
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Yong-Xiu Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- Address correspondence to
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250
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Transcriptional corepressor TOPLESS complexes with pseudoresponse regulator proteins and histone deacetylases to regulate circadian transcription. Proc Natl Acad Sci U S A 2012; 110:761-6. [PMID: 23267111 DOI: 10.1073/pnas.1215010110] [Citation(s) in RCA: 186] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Circadian clocks are ubiquitous molecular time-keeping mechanisms that coordinate physiology and metabolism and provide an adaptive advantage to higher plants. The central oscillator of the plant clock is composed of interlocked feedback loops that involve multiple repressive factors acting throughout the circadian cycle. Pseudo response regulators (PRRs) comprise a five-member family that is essential to the function of the central oscillator. PRR5, PRR7, and PRR9 can bind the promoters of the core clock genes circadian clock associated 1 (CCA1) and late elongated hypocotyl (LHY) to restrict their expression to near dawn, but the mechanism has been unclear. Here we report that members of the plant Groucho/Tup1 corepressor family, topless/topless-related (TPL/TPR), interact with these three PRR proteins at the CCA1 and LHY promoters to repress transcription and alter circadian period. This activity is diminished in the presence of the inhibitor trichostatin A, indicating the requirement of histone deacetylase for full TPL activity. Additionally, a complex of PRR9, TPL, and histone deacetylase 6, can form in vivo, implicating this tripartite association as a central repressor of circadian gene expression. Our findings show that the TPL/TPR corepressor family are components of the central circadian oscillator mechanism and reinforces the role of this family as central to multiple signaling pathways in higher plants.
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