51
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Kim JY, Oh JE, Noh YS, Noh B. Epigenetic control of juvenile-to-adult phase transition by the Arabidopsis SAGA-like complex. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 83:537-45. [PMID: 26095998 DOI: 10.1111/tpj.12908] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Revised: 06/03/2015] [Accepted: 06/04/2015] [Indexed: 05/18/2023]
Abstract
During growth and development, plants undergo a series of phase transitions from the juvenile-to-adult vegetative phase to the reproductive phase. In Arabidopsis, vegetative phase transitions and flowering are regulated by SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) factors. SPL mRNAs are post-transcriptionally regulated by miR156 in an age-dependent manner; however, the role of other mechanisms in this process is not known. In this study, we demonstrate that the HAG1/GCN5- and PRZ1/ADA2b-containing SAGA-like histone acetyltransferase (HAT) complex directly controls the transcription of SPLs and determines the time for juvenile-to-adult phase transition. Thus, epigenetic control by the SAGA-like HAT complex determines the transcriptional output of SPLs, which might be a prerequisite for the subsequent post-transcriptional regulation by miR156. Importantly, this epigenetic control mechanism is also crucial for miR156-independent induction of SPLs and acceleration of phase transition by light and photoperiod or during post-embryonic growth.
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Affiliation(s)
- Ji-Yun Kim
- School of Biological Sciences, Seoul National University, Seoul, 151-747, Korea
| | - Jee Eun Oh
- School of Biological Sciences, Seoul National University, Seoul, 151-747, Korea
| | - Yoo-Sun Noh
- School of Biological Sciences, Seoul National University, Seoul, 151-747, Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, 151-742, Korea
| | - Bosl Noh
- Research Institute of Basic Sciences, Seoul National University, Seoul, 151-747, Korea
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52
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Sénéchal F, L'Enfant M, Domon JM, Rosiau E, Crépeau MJ, Surcouf O, Esquivel-Rodriguez J, Marcelo P, Mareck A, Guérineau F, Kim HR, Mravec J, Bonnin E, Jamet E, Kihara D, Lerouge P, Ralet MC, Pelloux J, Rayon C. Tuning of Pectin Methylesterification: PECTIN METHYLESTERASE INHIBITOR 7 MODULATES THE PROCESSIVE ACTIVITY OF CO-EXPRESSED PECTIN METHYLESTERASE 3 IN A pH-DEPENDENT MANNER. J Biol Chem 2015; 290:23320-35. [PMID: 26183897 DOI: 10.1074/jbc.m115.639534] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Indexed: 11/06/2022] Open
Abstract
Pectin methylesterases (PMEs) catalyze the demethylesterification of homogalacturonan domains of pectin in plant cell walls and are regulated by endogenous pectin methylesterase inhibitors (PMEIs). In Arabidopsis dark-grown hypocotyls, one PME (AtPME3) and one PMEI (AtPMEI7) were identified as potential interacting proteins. Using RT-quantitative PCR analysis and gene promoter::GUS fusions, we first showed that AtPME3 and AtPMEI7 genes had overlapping patterns of expression in etiolated hypocotyls. The two proteins were identified in hypocotyl cell wall extracts by proteomics. To investigate the potential interaction between AtPME3 and AtPMEI7, both proteins were expressed in a heterologous system and purified by affinity chromatography. The activity of recombinant AtPME3 was characterized on homogalacturonans (HGs) with distinct degrees/patterns of methylesterification. AtPME3 showed the highest activity at pH 7.5 on HG substrates with a degree of methylesterification between 60 and 80% and a random distribution of methyl esters. On the best HG substrate, AtPME3 generates long non-methylesterified stretches and leaves short highly methylesterified zones, indicating that it acts as a processive enzyme. The recombinant AtPMEI7 and AtPME3 interaction reduces the level of demethylesterification of the HG substrate but does not inhibit the processivity of the enzyme. These data suggest that the AtPME3·AtPMEI7 complex is not covalently linked and could, depending on the pH, be alternately formed and dissociated. Docking analysis indicated that the inhibition of AtPME3 could occur via the interaction of AtPMEI7 with a PME ligand-binding cleft structure. All of these data indicate that AtPME3 and AtPMEI7 could be partners involved in the fine tuning of HG methylesterification during plant development.
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Affiliation(s)
- Fabien Sénéchal
- From the EA3900-BIOPI, Biologie des Plantes et Innovation and
| | | | - Jean-Marc Domon
- From the EA3900-BIOPI, Biologie des Plantes et Innovation and
| | - Emeline Rosiau
- From the EA3900-BIOPI, Biologie des Plantes et Innovation and
| | - Marie-Jeanne Crépeau
- INRA, UMR 1268, Biopolymères-Interactions-Assemblages, BP 71627, 44316 Nantes, France
| | - Ogier Surcouf
- the Laboratoire de Glycobiologie et Matrice Extracellulaire Végétale, UPRES EA 4358, Institut de Recherche et d'Innovation Biomédicale, Grand Réseau de Recherche-Végétal, Agronomie, Sol, Innovation, UFR des Sciences et Techniques, Normandie Université-Université de Rouen, 76821 Mont-Saint-Aignan Cedex 1, France
| | | | - Paulo Marcelo
- Plateforme d'Ingénierie Cellulaire and Analyses des Protéines (ICAP), Université de Picardie Jules Verne, 80039 Amiens, France
| | - Alain Mareck
- the Laboratoire de Glycobiologie et Matrice Extracellulaire Végétale, UPRES EA 4358, Institut de Recherche et d'Innovation Biomédicale, Grand Réseau de Recherche-Végétal, Agronomie, Sol, Innovation, UFR des Sciences et Techniques, Normandie Université-Université de Rouen, 76821 Mont-Saint-Aignan Cedex 1, France
| | | | - Hyung-Rae Kim
- Biological Sciences, Purdue University, West Lafayette, Indiana 47907
| | - Jozef Mravec
- the Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg, Denmark, and
| | - Estelle Bonnin
- INRA, UMR 1268, Biopolymères-Interactions-Assemblages, BP 71627, 44316 Nantes, France
| | - Elisabeth Jamet
- the LRSV, UMR 5546 Université Toulouse 3/CNRS, 31326 Castanet-Tolosan, France
| | - Daisuke Kihara
- the Departments of Computer Sciences and Biological Sciences, Purdue University, West Lafayette, Indiana 47907
| | - Patrice Lerouge
- the Laboratoire de Glycobiologie et Matrice Extracellulaire Végétale, UPRES EA 4358, Institut de Recherche et d'Innovation Biomédicale, Grand Réseau de Recherche-Végétal, Agronomie, Sol, Innovation, UFR des Sciences et Techniques, Normandie Université-Université de Rouen, 76821 Mont-Saint-Aignan Cedex 1, France
| | - Marie-Christine Ralet
- INRA, UMR 1268, Biopolymères-Interactions-Assemblages, BP 71627, 44316 Nantes, France
| | - Jérôme Pelloux
- From the EA3900-BIOPI, Biologie des Plantes et Innovation and
| | - Catherine Rayon
- From the EA3900-BIOPI, Biologie des Plantes et Innovation and
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53
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Moraga F, Aquea F. Composition of the SAGA complex in plants and its role in controlling gene expression in response to abiotic stresses. FRONTIERS IN PLANT SCIENCE 2015; 6:865. [PMID: 26528322 PMCID: PMC4604261 DOI: 10.3389/fpls.2015.00865] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 09/30/2015] [Indexed: 05/07/2023]
Abstract
Protein complexes involved in epigenetic regulation of transcription have evolved as molecular strategies to face environmental stress in plants. SAGA (Spt-Ada-Gcn5 Acetyltransferase) is a transcriptional co-activator complex that regulates numerous cellular processes through the coordination of multiple post-translational histone modifications, including acetylation, deubiquitination, and chromatin recognition. The diverse functions of the SAGA complex involve distinct modules that are highly conserved between yeast, flies, and mammals. In this review, the composition of the SAGA complex in plants is described and its role in gene expression regulation under stress conditions summarized. Some of these proteins are likely involved in the regulation of the inducible expression of genes under light, cold, drought, salt, and iron stress, although the functions of several of its components remain unknown.
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Affiliation(s)
- Felipe Moraga
- Laboratorio de Bioingeniería, Facultad de Ingeniería y Ciencias, Universidad Adolfo IbáñezSantiago, Chile
| | - Felipe Aquea
- Laboratorio de Bioingeniería, Facultad de Ingeniería y Ciencias, Universidad Adolfo IbáñezSantiago, Chile
- Center for Applied Ecology and SustainabilitySantiago, Chile
- *Correspondence: Felipe Aquea
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54
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An improved toolbox to unravel the plant cellular machinery by tandem affinity purification of Arabidopsis protein complexes. Nat Protoc 2014; 10:169-87. [DOI: 10.1038/nprot.2014.199] [Citation(s) in RCA: 114] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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55
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Guo B, Chen Y, Li C, Wang T, Wang R, Wang B, Hu S, Du X, Xing H, Song X, Yao Y, Sun Q, Ni Z. Maize (Zea mays L.) seedling leaf nuclear proteome and differentially expressed proteins between a hybrid and its parental lines. Proteomics 2014; 14:1071-87. [PMID: 24677780 DOI: 10.1002/pmic.201300147] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2013] [Revised: 01/10/2014] [Accepted: 01/24/2014] [Indexed: 12/27/2022]
Abstract
To better understand the underlying molecular basis of leaf development in maize, a reference map of nuclear proteins in basal region of seedling leaf was established using a combination of 2DE and MALDI-TOF-MS. In total, 441 reproducible protein spots in nuclear proteome of maize leaf basal region were detected with silver staining in a pH range of 3-10, among which 203 spots corresponding to 163 different proteins were identified. As expected, proteins implicated in RNA and protein-associated functions were overrepresented in nuclear proteome. Remarkably, a high percentage (10%) of proteins was identified to be involved in cell division and growth. In addition, comparative nuclear proteomic analysis in leaf basal region of highly heterotic hybrid Mo17/B73 and its parental lines was also performed and 52 of 445 (11.69%) detected protein spots were differentially expressed between the hybrid and its parental lines, among which 16 protein spots displayed nonadditively expressed pattern. These results indicated that hybridization between two parental lines can cause changes in the expression of a variety of nuclear proteins, which may be responsible for the observed leaf size heterosis.
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Affiliation(s)
- Baojian Guo
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE); Beijing Key Laboratory of Crop Genetic Improvement; China Agricultural University; Beijing China
- National Plant Gene Research Centre (Beijing); Beijing China
| | - Yanhong Chen
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE); Beijing Key Laboratory of Crop Genetic Improvement; China Agricultural University; Beijing China
- National Plant Gene Research Centre (Beijing); Beijing China
| | - Chuan Li
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE); Beijing Key Laboratory of Crop Genetic Improvement; China Agricultural University; Beijing China
- National Plant Gene Research Centre (Beijing); Beijing China
| | - Tianya Wang
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE); Beijing Key Laboratory of Crop Genetic Improvement; China Agricultural University; Beijing China
- National Plant Gene Research Centre (Beijing); Beijing China
| | - Rui Wang
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE); Beijing Key Laboratory of Crop Genetic Improvement; China Agricultural University; Beijing China
- National Plant Gene Research Centre (Beijing); Beijing China
| | - Bo Wang
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE); Beijing Key Laboratory of Crop Genetic Improvement; China Agricultural University; Beijing China
- National Plant Gene Research Centre (Beijing); Beijing China
| | - Sha Hu
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE); Beijing Key Laboratory of Crop Genetic Improvement; China Agricultural University; Beijing China
- National Plant Gene Research Centre (Beijing); Beijing China
| | - Xiaofen Du
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE); Beijing Key Laboratory of Crop Genetic Improvement; China Agricultural University; Beijing China
- National Plant Gene Research Centre (Beijing); Beijing China
| | - Hongyan Xing
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE); Beijing Key Laboratory of Crop Genetic Improvement; China Agricultural University; Beijing China
- National Plant Gene Research Centre (Beijing); Beijing China
| | - Xiao Song
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE); Beijing Key Laboratory of Crop Genetic Improvement; China Agricultural University; Beijing China
- National Plant Gene Research Centre (Beijing); Beijing China
| | - Yingyin Yao
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE); Beijing Key Laboratory of Crop Genetic Improvement; China Agricultural University; Beijing China
- National Plant Gene Research Centre (Beijing); Beijing China
| | - Qixin Sun
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE); Beijing Key Laboratory of Crop Genetic Improvement; China Agricultural University; Beijing China
- National Plant Gene Research Centre (Beijing); Beijing China
| | - Zhongfu Ni
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE); Beijing Key Laboratory of Crop Genetic Improvement; China Agricultural University; Beijing China
- National Plant Gene Research Centre (Beijing); Beijing China
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56
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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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57
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Van Lijsebettens M, Grasser KD. Transcript elongation factors: shaping transcriptomes after transcript initiation. TRENDS IN PLANT SCIENCE 2014; 19:717-26. [PMID: 25131948 DOI: 10.1016/j.tplants.2014.07.002] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Revised: 07/16/2014] [Accepted: 07/17/2014] [Indexed: 05/06/2023]
Abstract
Elongation is a dynamic and highly regulated step of eukaryotic gene transcription. A variety of transcript elongation factors (TEFs), including modulators of RNA polymerase II (RNAPII) activity, histone chaperones, and histone modifiers, have been characterized from plants. These factors control the efficiency of transcript elongation of subsets of genes in the chromatin context and thus contribute to tuning gene expression programs. We review here how genetic and biochemical analyses, primarily in Arabidopsis thaliana, have advanced our understanding of how TEFs adjust plant gene transcription. These studies have revealed that TEFs regulate plant growth and development by modulating diverse processes including hormone signaling, circadian clock, pathogen defense, responses to light, and developmental transitions.
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Affiliation(s)
- Mieke Van Lijsebettens
- Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie (VIB), Technologiepark 927, 9052 Gent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052 Gent, Belgium.
| | - Klaus D Grasser
- Department of Cell Biology and Plant Biochemistry, Biochemie-Zentrum Regensburg (BZR), University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany.
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58
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Müller-Xing R, Xing Q, Goodrich J. Footprints of the sun: memory of UV and light stress in plants. FRONTIERS IN PLANT SCIENCE 2014; 5:474. [PMID: 25278950 PMCID: PMC4165212 DOI: 10.3389/fpls.2014.00474] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Accepted: 08/28/2014] [Indexed: 05/18/2023]
Abstract
Sunlight provides the necessary energy for plant growth via photosynthesis but high light and particular its integral ultraviolet (UV) part causes stress potentially leading to serious damage to DNA, proteins, and other cellular components. Plants show adaptation to environmental stresses, sometimes referred to as "plant memory." There is growing evidence that plants memorize exposure to biotic or abiotic stresses through epigenetic mechanisms at the cellular level. UV target genes such as CHALCONE SYNTHASE (CHS) respond immediately to UV treatment and studies of the recently identified UV-B receptor UV RESISTANCE LOCUS 8 (UVR8) confirm the expedite nature of UV signaling. Considering these findings, an UV memory seems redundant. However, several lines of evidence suggest that plants may develop an epigenetic memory of UV and light stress, but in comparison to other abiotic stresses there has been relatively little investigation. Here we summarize the state of knowledge about acclimation and adaptation of plants to UV light and discuss the possibility of chromatin based epigenetic memory.
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Affiliation(s)
- Ralf Müller-Xing
- Institute of Genetics, Heinrich-Heine-UniversityDüsseldorf, Germany
| | - Qian Xing
- Institute of Genetics, Heinrich-Heine-UniversityDüsseldorf, Germany
| | - Justin Goodrich
- Institute for Molecular Plant Sciences, The University of EdinburghEdinburgh, UK
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59
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Barneche F, Malapeira J, Mas P. The impact of chromatin dynamics on plant light responses and circadian clock function. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:2895-913. [PMID: 24520020 DOI: 10.1093/jxb/eru011] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Research on the functional properties of nucleosome structure and composition dynamics has revealed that chromatin-level regulation is an essential component of light signalling and clock function in plants, two processes that rely extensively on transcriptional controls. In particular, several types of histone post-translational modifications and chromatin-bound factors act sequentially or in combination to establish transcriptional patterns and to fine-tune the transcript abundance of a large repertoire of light-responsive genes and clock components. Cytogenetic approaches have also identified light-induced higher-order chromatin changes that dynamically organize the condensation of chromosomal domains into sub-nuclear foci containing silenced repeat elements. In this review, we report recently identified molecular actors that establish chromatin state dynamics in response to light signals such as photoperiod, intensity, and spectral quality. We also highlight the chromatin-dependent mechanisms that contribute to the 24-h circadian gene expression and its impact on plant physiology and development. The commonalities and contrasts of light- and clock-associated chromatin-based mechanisms are discussed, with particular emphasis on their impact on the selective regulation and rapid modulation of responsive genes.
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Affiliation(s)
- Fredy Barneche
- Environmental and Evolutionary Genomics Section, Ecole Normale Supérieure, Institut de Biologie de l'ENS, IBENS, Paris, F-75005 France Inserm, U1024, Paris, F-75005 France CNRS, UMR 8197, Paris, F-75005 France
| | - Jordi Malapeira
- Center for Research in Agricultural Genomics (CRAG), Consortium CSIC-IRTA-UAB-UB, Parc de Recerca UAB, Bellaterra (Cerdanyola del Vallés), 08193 Barcelona, Spain
| | - Paloma Mas
- Center for Research in Agricultural Genomics (CRAG), Consortium CSIC-IRTA-UAB-UB, Parc de Recerca UAB, Bellaterra (Cerdanyola del Vallés), 08193 Barcelona, Spain
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60
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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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61
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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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62
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Müller-Xing R, Xing Q, Goodrich J. Footprints of the sun: memory of UV and light stress in plants. FRONTIERS IN PLANT SCIENCE 2014. [PMID: 25278950 DOI: 10.3389/fpls.2014.00474/abstract] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Sunlight provides the necessary energy for plant growth via photosynthesis but high light and particular its integral ultraviolet (UV) part causes stress potentially leading to serious damage to DNA, proteins, and other cellular components. Plants show adaptation to environmental stresses, sometimes referred to as "plant memory." There is growing evidence that plants memorize exposure to biotic or abiotic stresses through epigenetic mechanisms at the cellular level. UV target genes such as CHALCONE SYNTHASE (CHS) respond immediately to UV treatment and studies of the recently identified UV-B receptor UV RESISTANCE LOCUS 8 (UVR8) confirm the expedite nature of UV signaling. Considering these findings, an UV memory seems redundant. However, several lines of evidence suggest that plants may develop an epigenetic memory of UV and light stress, but in comparison to other abiotic stresses there has been relatively little investigation. Here we summarize the state of knowledge about acclimation and adaptation of plants to UV light and discuss the possibility of chromatin based epigenetic memory.
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Affiliation(s)
- Ralf Müller-Xing
- Institute of Genetics, Heinrich-Heine-University Düsseldorf, Germany
| | - Qian Xing
- Institute of Genetics, Heinrich-Heine-University Düsseldorf, Germany
| | - Justin Goodrich
- Institute for Molecular Plant Sciences, The University of Edinburgh Edinburgh, UK
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63
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Wu SH. Gene expression regulation in photomorphogenesis from the perspective of the central dogma. ANNUAL REVIEW OF PLANT BIOLOGY 2014; 65:311-33. [PMID: 24779996 DOI: 10.1146/annurev-arplant-050213-040337] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Depending on the environment a young seedling encounters, the developmental program following seed germination could be skotomorphogenesis in the dark or photomorphogenesis in the light. Light signals are interpreted by a repertoire of photoreceptors followed by sophisticated gene expression networks, eventually resulting in developmental changes. The expression and functions of photoreceptors and key signaling molecules are highly coordinated and regulated at multiple levels of the central dogma in molecular biology. Light activates gene expression through the actions of positive transcriptional regulators and the relaxation of chromatin by histone acetylation. Small regulatory RNAs help attenuate the expression of light-responsive genes. Alternative splicing, protein phosphorylation/dephosphorylation, the formation of diverse transcriptional complexes, and selective protein degradation all contribute to proteome diversity and change the functions of individual proteins.
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Affiliation(s)
- Shu-Hsing Wu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan;
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64
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Liu X, Chen CY, Wang KC, Luo M, Tai R, Yuan L, Zhao M, Yang S, Tian G, Cui Y, Hsieh HL, Wu K. PHYTOCHROME INTERACTING FACTOR3 associates with the histone deacetylase HDA15 in repression of chlorophyll biosynthesis and photosynthesis in etiolated Arabidopsis seedlings. THE PLANT CELL 2013; 25:1258-73. [PMID: 23548744 PMCID: PMC3663266 DOI: 10.1105/tpc.113.109710] [Citation(s) in RCA: 142] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2013] [Revised: 02/22/2013] [Accepted: 03/15/2013] [Indexed: 05/18/2023]
Abstract
PHYTOCHROME INTERACTING FACTOR3 (PIF3) is a key basic helix-loop-helix transcription factor of Arabidopsis thaliana that negatively regulates light responses, repressing chlorophyll biosynthesis, photosynthesis, and photomorphogenesis in the dark. However, the mechanism for the PIF3-mediated transcription regulation remains largely unknown. In this study, we found that the REDUCED POTASSIUM DEPENDENCY3/HISTONE DEACETYLASE1-type histone deacetylase HDA15 directly interacted with PIF3 in vivo and in vitro. Genome-wide transcriptome analysis revealed that HDA15 acts mainly as a transcriptional repressor and negatively regulates chlorophyll biosynthesis and photosynthesis gene expression in etiolated seedlings. HDA15 and PIF3 cotarget to the genes involved in chlorophyll biosynthesis and photosynthesis in the dark and repress gene expression by decreasing the acetylation levels and RNA Polymerase II-associated transcription. The binding of HDA15 to the target genes depends on the presence of PIF3. In addition, PIF3 and HDA15 are dissociated from the target genes upon exposure to red light. Taken together, our results indicate that PIF3 associates with HDA15 to repress chlorophyll biosynthetic and photosynthetic genes in etiolated seedlings.
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Affiliation(s)
- Xuncheng Liu
- Institute of Plant Biology, National Taiwan University, Taipei 106, Taiwan
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Chia-Yang Chen
- Institute of Plant Biology, National Taiwan University, Taipei 106, Taiwan
| | - Ko-Ching Wang
- Institute of Plant Biology, National Taiwan University, Taipei 106, Taiwan
| | - Ming Luo
- Institute of Plant Biology, National Taiwan University, Taipei 106, Taiwan
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Ready Tai
- Institute of Plant Biology, National Taiwan University, Taipei 106, Taiwan
| | - Lianyu Yuan
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Minglei Zhao
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Songguang Yang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Gang Tian
- Southern Crop Protection and Food Research Centre, Agriculture and Agri-Food Canada, Ontario N5V 4T3, Canada
| | - Yuhai Cui
- Southern Crop Protection and Food Research Centre, Agriculture and Agri-Food Canada, Ontario N5V 4T3, Canada
| | - Hsu-Liang Hsieh
- Institute of Plant Biology, National Taiwan University, Taipei 106, Taiwan
| | - Keqiang Wu
- Institute of Plant Biology, National Taiwan University, Taipei 106, Taiwan
- Address correspondence to
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Öhman D, Demedts B, Kumar M, Gerber L, Gorzsás A, Goeminne G, Hedenström M, Ellis B, Boerjan W, Sundberg B. MYB103 is required for FERULATE-5-HYDROXYLASE expression and syringyl lignin biosynthesis in Arabidopsis stems. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2013; 73:63-76. [PMID: 22967312 DOI: 10.1111/tpj.12018] [Citation(s) in RCA: 92] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2012] [Revised: 08/10/2012] [Accepted: 09/03/2012] [Indexed: 05/18/2023]
Abstract
The transcription factor MYB103 was previously identified as a member of the transcriptional network regulating secondary wall biosynthesis in xylem tissues of Arabidopsis, and was proposed to act on cellulose biosynthesis. It is a direct transcriptional target of the transcription factor SECONDARY WALL ASSOCIATED NAC DOMAIN PROTEIN 1 (SND1), and 35S-driven dominant repression or over-expression of MYB103 modifies secondary wall thickness. We identified two myb103 T-DNA insertion mutants and chemically characterized their lignocellulose by pyrolysis/GC/MS, 2D NMR, FT-IR microspectroscopy and wet chemistry. The mutants developed normally but exhibited a 70-75% decrease in syringyl (S) lignin. The level of guaiacyl (G) lignin was co-ordinately increased, so that total Klason lignin was not affected. The transcript abundance of FERULATE-5-HYDROXYLASE (F5H), the key gene in biosynthesis of S lignin, was strongly decreased in the myb103 mutants, and the metabolomes of the myb103 mutant and an F5H null mutant were very similar. Other than modification of the lignin S to G ratio, there were only very minor changes in the composition of secondary cell-wall polymers in the inflorescence stem. In conclusion, we demonstrate that F5H expression and hence biosynthesis of S lignin are dependent on MYB103.
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Affiliation(s)
- David Öhman
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, SE-90183, Umeå, Sweden
| | - Brecht Demedts
- Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, 9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Universiteit Gent, 9052, Gent, Belgium
| | - Manoj Kumar
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, SE-90183, Umeå, Sweden
| | - Lorenz Gerber
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, SE-90183, Umeå, Sweden
| | - András Gorzsás
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, SE-90183, Umeå, Sweden
| | - Geert Goeminne
- Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, 9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Universiteit Gent, 9052, Gent, Belgium
| | | | - Brian Ellis
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Wout Boerjan
- Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, 9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Universiteit Gent, 9052, Gent, Belgium
| | - Björn Sundberg
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, SE-90183, Umeå, Sweden
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Nagels Durand A, Moses T, De Clercq R, Goossens A, Pauwels L. A MultiSite Gateway™ vector set for the functional analysis of genes in the model Saccharomyces cerevisiae. BMC Mol Biol 2012; 13:30. [PMID: 22994806 PMCID: PMC3519679 DOI: 10.1186/1471-2199-13-30] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2012] [Accepted: 09/17/2012] [Indexed: 12/02/2022] Open
Abstract
Background Recombinatorial cloning using the GatewayTM technology has been the method of choice for high-throughput omics projects, resulting in the availability of entire ORFeomes in GatewayTM compatible vectors. The MultiSite GatewayTM system allows combining multiple genetic fragments such as promoter, ORF and epitope tag in one single reaction. To date, this technology has not been accessible in the yeast Saccharomyces cerevisiae, one of the most widely used experimental systems in molecular biology, due to the lack of appropriate destination vectors. Results Here, we present a set of three-fragment MultiSite GatewayTM destination vectors that have been developed for gene expression in S. cerevisiae and that allow the assembly of any promoter, open reading frame, epitope tag arrangement in combination with any of four auxotrophic markers and three distinct replication mechanisms. As an example of its applicability, we used yeast three-hybrid to provide evidence for the assembly of a ternary complex of plant proteins involved in jasmonate signalling and consisting of the JAZ, NINJA and TOPLESS proteins. Conclusion Our vectors make MultiSite GatewayTM cloning accessible in S. cerevisiae and implement a fast and versatile cloning method for the high-throughput functional analysis of (heterologous) proteins in one of the most widely used model organisms for molecular biology research.
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Affiliation(s)
- Astrid Nagels Durand
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052, Gent, Belgium
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Junker A, Mönke G, Rutten T, Keilwagen J, Seifert M, Thi TMN, Renou JP, Balzergue S, Viehöver P, Hähnel U, Ludwig-Müller J, Altschmied L, Conrad U, Weisshaar B, Bäumlein H. Elongation-related functions of LEAFY COTYLEDON1 during the development of Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2012; 71:427-42. [PMID: 22429691 DOI: 10.1111/j.1365-313x.2012.04999.x] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The transcription factor LEAFY COTYLEDON1 (LEC1) controls aspects of early embryogenesis and seed maturation in Arabidopsis thaliana. To identify components of the LEC1 regulon, transgenic plants were derived in which LEC1 expression was inducible by dexamethasone treatment. The cotyledon-like leaves and swollen root tips developed by these plants contained seed-storage compounds and resemble the phenotypes produced by increased auxin levels. In agreement with this, LEC1 was found to mediate up-regulation of the auxin synthesis gene YUCCA10. Auxin accumulated primarily in the elongation zone at the root-hypocotyl junction (collet). This accumulation correlates with hypocotyl growth, which is either inhibited in LEC1-induced embryonic seedlings or stimulated in the LEC1-induced long-hypocotyl phenotype, therefore resembling etiolated seedlings. Chromatin immunoprecipitation analysis revealed a number of phytohormone- and elongation-related genes among the putative LEC1 target genes. LEC1 appears to be an integrator of various regulatory events, involving the transcription factor itself as well as light and hormone signalling, especially during somatic and early zygotic embryogenesis. Furthermore, the data suggest non-embryonic functions for LEC1 during post-germinative etiolation.
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Affiliation(s)
- Astrid Junker
- Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstraße 3, D-06466 Gatersleben, Germany.
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Xing S, Poirier Y. The protein acetylome and the regulation of metabolism. TRENDS IN PLANT SCIENCE 2012; 17:423-30. [PMID: 22503580 DOI: 10.1016/j.tplants.2012.03.008] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2011] [Revised: 03/14/2012] [Accepted: 03/17/2012] [Indexed: 05/23/2023]
Abstract
Acetyl-coenzyme A (CoA) is a central metabolite involved in numerous anabolic and catabolic pathways, as well as in protein acetylation. Beyond histones, a large number of metabolic enzymes are acetylated in both animal and bacteria, and the protein acetylome is now emerging in plants. Protein acetylation is influenced by the cellular level of both acetyl-CoA and NAD(+), and regulates the activity of several enzymes. Acetyl-CoA is thus ideally placed to act as a key molecule linking the energy balance of the cell to the regulation of gene expression and metabolic pathways via the control of protein acetylation. Better knowledge over how to influence acetyl-CoA levels and the acetylation process promises to be an invaluable tool to control metabolic pathways.
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Affiliation(s)
- Shufan Xing
- Department of Plant Molecular Biology, Biophore Building, University of Lausanne, CH-1015 Lausanne, Switzerland
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69
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Mönke G, Seifert M, Keilwagen J, Mohr M, Grosse I, Hähnel U, Junker A, Weisshaar B, Conrad U, Bäumlein H, Altschmied L. Toward the identification and regulation of the Arabidopsis thaliana ABI3 regulon. Nucleic Acids Res 2012; 40:8240-54. [PMID: 22730287 PMCID: PMC3458547 DOI: 10.1093/nar/gks594] [Citation(s) in RCA: 122] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The plant-specific, B3 domain-containing transcription factor ABSCISIC ACID INSENSITIVE3 (ABI3) is an essential component of the regulatory network controlling the development and maturation of the Arabidopsis thaliana seed. Genome-wide chromatin immunoprecipitation (ChIP-chip), transcriptome analysis, quantitative reverse transcriptase–polymerase chain reaction and a transient promoter activation assay have been combined to identify a set of 98 ABI3 target genes. Most of these presumptive ABI3 targets require the presence of abscisic acid for their activation and are specifically expressed during seed maturation. ABI3 target promoters are enriched for G-box-like and RY-like elements. The general occurrence of these cis motifs in non-ABI3 target promoters suggests the existence of as yet unidentified regulatory signals, some of which may be associated with epigenetic control. Several members of the ABI3 regulon are also regulated by other transcription factors, including the seed-specific, B3 domain-containing FUS3 and LEC2. The data strengthen and extend the notion that ABI3 is essential for the protection of embryonic structures from desiccation and raise pertinent questions regarding the specificity of promoter recognition.
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Affiliation(s)
- Gudrun Mönke
- Department of Molecular Genetics, Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK) Corrensstr. 3, D-06466 Gatersleben, Germany
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Li J, Terzaghi W, Deng XW. Genomic basis for light control of plant development. Protein Cell 2012; 3:106-16. [PMID: 22426979 PMCID: PMC4875414 DOI: 10.1007/s13238-012-2016-7] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2012] [Accepted: 02/05/2012] [Indexed: 10/28/2022] Open
Abstract
Light is one of the key environmental signals regulating plant growth and development. Therefore, understanding the mechanisms by which light controls plant development has long been of great interest to plant biologists. Traditional genetic and molecular approaches have successfully identified key regulatory factors in light signaling, but recent genomic studies have revealed massive reprogramming of plant transcriptomes by light, identified binding sites across the entire genome of several pivotal transcription factors in light signaling, and discovered the involvement of epigenetic regulation in light-regulated gene expression. This review summarizes the key genomic work conducted in the last decade which provides new insights into light control of plant development.
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Affiliation(s)
- Jigang Li
- Peking-Yale Joint Center for Plant Molecular Genetics and Agro-biotechnology, State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, 100871 China
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520-8104 USA
| | - William Terzaghi
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520-8104 USA
- Department of Biology, Wilkes University, Wilkes-Barre, PA 18766 USA
| | - Xing Wang Deng
- Peking-Yale Joint Center for Plant Molecular Genetics and Agro-biotechnology, State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, 100871 China
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520-8104 USA
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Mazur MJ, van den Burg HA. Global SUMO Proteome Responses Guide Gene Regulation, mRNA Biogenesis, and Plant Stress Responses. FRONTIERS IN PLANT SCIENCE 2012. [PMID: 23060889 DOI: 10.3389/fpls.2012.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Small Ubiquitin-like MOdifier (SUMO) is a key regulator of abiotic stress, disease resistance, and development in plants. The identification of >350 plant SUMO targets has revealed many processes modulated by SUMO and potential consequences of SUMO on its targets. Importantly, highly related proteins are SUMO-modified in plants, yeast, and metazoans. Overlapping SUMO targets include heat-shock proteins (HSPs), transcription regulators, histones, histone-modifying enzymes, proteins involved in DNA damage repair, but also proteins involved in mRNA biogenesis and nucleo-cytoplasmic transport. Proteomics studies indicate key roles for SUMO in gene repression by controlling histone (de)acetylation activity at genomic loci. The responsible heavily sumoylated transcriptional repressor complexes are recruited by plant transcription factors (TFs) containing an (ERF)-associated Amphiphilic Repression (EAR) motif. These TFs are not necessarily themselves a SUMO target. Conversely, SUMO acetylation (Ac) prevents binding of downstream partners by blocking binding of their SUMO-interaction peptide motifs to Ac-SUMO. In addition, SUMO acetylation has emerged as a mechanism to recruit specifically bromodomains. Bromodomains are generally linked with gene activation. These findings strengthen the idea of a bi-directional sumo-acetylation switch in gene regulation. Quantitative proteomics has highlighted that global sumoylation provides a dynamic response to protein damage involving SUMO chain-mediated protein degradation, but also SUMO E3 ligase-dependent transcription of HSP genes. With these insights in SUMO function and novel technical advancements, we can now study SUMO dynamics in responses to (a)biotic stress in plants.
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Affiliation(s)
- Magdalena J Mazur
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences, University of Amsterdam Amsterdam, Netherlands
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72
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Mazur MJ, van den Burg HA. Global SUMO Proteome Responses Guide Gene Regulation, mRNA Biogenesis, and Plant Stress Responses. FRONTIERS IN PLANT SCIENCE 2012; 3:215. [PMID: 23060889 PMCID: PMC3443746 DOI: 10.3389/fpls.2012.00215] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2012] [Accepted: 08/23/2012] [Indexed: 05/13/2023]
Abstract
Small Ubiquitin-like MOdifier (SUMO) is a key regulator of abiotic stress, disease resistance, and development in plants. The identification of >350 plant SUMO targets has revealed many processes modulated by SUMO and potential consequences of SUMO on its targets. Importantly, highly related proteins are SUMO-modified in plants, yeast, and metazoans. Overlapping SUMO targets include heat-shock proteins (HSPs), transcription regulators, histones, histone-modifying enzymes, proteins involved in DNA damage repair, but also proteins involved in mRNA biogenesis and nucleo-cytoplasmic transport. Proteomics studies indicate key roles for SUMO in gene repression by controlling histone (de)acetylation activity at genomic loci. The responsible heavily sumoylated transcriptional repressor complexes are recruited by plant transcription factors (TFs) containing an (ERF)-associated Amphiphilic Repression (EAR) motif. These TFs are not necessarily themselves a SUMO target. Conversely, SUMO acetylation (Ac) prevents binding of downstream partners by blocking binding of their SUMO-interaction peptide motifs to Ac-SUMO. In addition, SUMO acetylation has emerged as a mechanism to recruit specifically bromodomains. Bromodomains are generally linked with gene activation. These findings strengthen the idea of a bi-directional sumo-acetylation switch in gene regulation. Quantitative proteomics has highlighted that global sumoylation provides a dynamic response to protein damage involving SUMO chain-mediated protein degradation, but also SUMO E3 ligase-dependent transcription of HSP genes. With these insights in SUMO function and novel technical advancements, we can now study SUMO dynamics in responses to (a)biotic stress in plants.
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Affiliation(s)
- Magdalena J. Mazur
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences, University of AmsterdamAmsterdam, Netherlands
| | - Harrold A. van den Burg
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences, University of AmsterdamAmsterdam, Netherlands
- *Correspondence: Harrold A. van den Burg, Molecular Plant Pathology, Swammerdam Institute for Life Sciences, University of Amsterdam, P.O. box 94215, 1090 GE Amsterdam, Netherlands. e-mail:
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73
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Wehner N, Hartmann L, Ehlert A, Böttner S, Oñate-Sánchez L, Dröge-Laser W. High-throughput protoplast transactivation (PTA) system for the analysis of Arabidopsis transcription factor function. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2011; 68:560-9. [PMID: 21749507 DOI: 10.1111/j.1365-313x.2011.04704.x] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Genomic approaches have generated large Arabidopsis open reading frame (ORF) collections. However, molecular tools are required to characterize this ORFeome functionally. A high-throughput microtiter plate-based protoplast transactivation (PTA) system has been established that can be used in a screening approach to define which transcription factor (TF) regulates a given promoter in planta. Using to this procedure, the transactivation properties of 96 TFs can be analyzed rapidly, making use of promoter:Luciferase (LUC)-reporters and luciferase imaging. Applying GATEWAY® technology, we have established a platform to assay more than 700 Arabidopsis TFs. As a proof-of-principle, the ethylene response factor (ERF) family has been studied to evaluate this system. Importantly, distinct subsets of related ERF factors were found to activate specifically the well described target promoters RD29A and PDF1.2 that are under control of DRE or GCC box cis-elements, respectively. Furthermore, several applications of the PTA system have been demonstrated, such as analysis of transcriptional repressors, salt-inducible gene expression or functional interaction of signaling molecules like kinases and TFs. This novel molecular tool will improve functional studies on transcriptional regulation in plants significantly.
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Affiliation(s)
- Nora Wehner
- Julius-von-Sachs-Institut, Pharmazeutische Biologie, Julius-Maximilians-Universität Würzburg, Julius-von-Sachs-Platz 2, D-97082 Würzburg, Germany
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Vlachonasios KE, Kaldis A, Nikoloudi A, Tsementzi D. The role of transcriptional coactivator ADA2b in Arabidopsis abiotic stress responses. PLANT SIGNALING & BEHAVIOR 2011; 6:1475-8. [PMID: 21897124 PMCID: PMC3256374 DOI: 10.4161/psb.6.10.17695] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2011] [Accepted: 08/09/2011] [Indexed: 05/23/2023]
Abstract
Plant growth and crop production can be greatly affected by common environmental stresses such as drought, high salinity and low temperatures. Gene expression is affected by several abiotic stresses. Stress-inducible genes are regulated by transcription factors and epigenetic mechanisms such as histone modifications. In this Mini-Review, we have explored the role of transcriptional adaptor ADA2b in Arabidopsis responses to abiotic stress. ADA2b is required for the expression of genes involved in abiotic stress either by controlling H3 and H4 acetylation in the case of salt stress or affecting nucleosome occupancy in low temperatures response.
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Affiliation(s)
- Konstantinos E Vlachonasios
- Department of Botany, School of Biology, Faculty of Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece.
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Abstract
The structure and compaction of chromatin exerts a major regulatory influence on eukaryotic transcription. Changes in both histone composition and post-translational modifications of individual histone proteins can lead to remodelling of higher order chromatin structure. Chromatin remodelling regulates transcriptional activity through modifying gene accessibility, via DNA/histone interactions and the recruitment of non-histone proteins to DNA. Plant growth and development is regulated by the integration of multiple environmental signals. Of these, light is one of the most important. Chromatin remodelling processes have been identified in plants following a variety of different light treatments. These include the initiation of seedling de-etiolation, changes in photon irradiance and ultraviolet-B radiation exposure. In this review, we will summarize the roles of chromatin remodelling in plant photomorphogenesis and discuss these in the wider context of plant environmental adaptation.
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Affiliation(s)
- Alex J Fisher
- Department of Biology, University of Leicester, Leicester LE1 7RH, UK School of Biological Sciences, University of Bristol, Bristol BS81UG, UK
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Vanneste S, Coppens F, Lee E, Donner TJ, Xie Z, Van Isterdael G, Dhondt S, De Winter F, De Rybel B, Vuylsteke M, De Veylder L, Friml J, Inzé D, Grotewold E, Scarpella E, Sack F, Beemster GTS, Beeckman T. Developmental regulation of CYCA2s contributes to tissue-specific proliferation in Arabidopsis. EMBO J 2011; 30:3430-41. [PMID: 21772250 DOI: 10.1038/emboj.2011.240] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2011] [Accepted: 06/24/2011] [Indexed: 11/09/2022] Open
Abstract
In multicellular organisms, morphogenesis relies on a strict coordination in time and space of cell proliferation and differentiation. In contrast to animals, plant development displays continuous organ formation and adaptive growth responses during their lifespan relying on a tight coordination of cell proliferation. How developmental signals interact with the plant cell-cycle machinery is largely unknown. Here, we characterize plant A2-type cyclins, a small gene family of mitotic cyclins, and show how they contribute to the fine-tuning of local proliferation during plant development. Moreover, the timely repression of CYCA2;3 expression in newly formed guard cells is shown to require the stomatal transcription factors FOUR LIPS/MYB124 and MYB88, providing a direct link between developmental programming and cell-cycle exit in plants. Thus, transcriptional downregulation of CYCA2s represents a critical mechanism to coordinate proliferation during plant development.
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Berr A, Shafiq S, Shen WH. Histone modifications in transcriptional activation during plant development. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2011; 1809:567-76. [PMID: 21777708 DOI: 10.1016/j.bbagrm.2011.07.001] [Citation(s) in RCA: 152] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2011] [Revised: 06/30/2011] [Accepted: 07/06/2011] [Indexed: 12/24/2022]
Abstract
In eukaryotic cell nuclei, chromatin states dictated by different combinations of post-translational modifications of histones, such as acetylation, methylation and monoubiquitination of lysine residues, are part of the multitude of epigenomes involved in the fine-tuning of all genetic functions and in particular transcription. During the past decade, an increasing number of 'writers', 'readers' and 'erasers' of histone modifications have been identified. Characterization of these factors in Arabidopsis has unraveled their pivotal roles in the regulation of essential processes, such as floral transition, cell differentiation, gametogenesis, and plant response/adaptation to environmental stresses. In this review we focus on histone modification marks associated with transcriptional activation to highlight current knowledge on Arabidopsis 'writers', 'readers' and 'erasers' of histone modifications and to discuss recent findings on molecular mechanisms of integration of histone modifications with the RNA polymerase II transcriptional machinery during transcription of the flowering repressor gene FLC.
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Affiliation(s)
- Alexandre Berr
- Institut de Biologie Moléculaire des Plantes du CNRS, Université de Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg CEDEX, France
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Feller A, Machemer K, Braun EL, Grotewold E. Evolutionary and comparative analysis of MYB and bHLH plant transcription factors. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2011; 66:94-116. [PMID: 21443626 DOI: 10.1111/j.1365-313x.2010.04459.x] [Citation(s) in RCA: 696] [Impact Index Per Article: 53.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The expansion of gene families encoding regulatory proteins is typically associated with the increase in complexity characteristic of multi-cellular organisms. The MYB and basic helix-loop-helix (bHLH) families provide excellent examples of how gene duplication and divergence within particular groups of transcription factors are associated with, if not driven by, the morphological and metabolic diversity that characterize the higher plants. These gene families expanded dramatically in higher plants; for example, there are approximately 339 and 162 MYB and bHLH genes, respectively, in Arabidopsis, and approximately 230 and 111, respectively, in rice. In contrast, the Chlamydomonas genome has only 38 MYB genes and eight bHLH genes. In this review, we compare the MYB and bHLH gene families from structural, evolutionary and functional perspectives. The knowledge acquired on the role of many of these factors in Arabidopsis provides an excellent reference to explore sequence-function relationships in crops and other plants. The physical interaction and regulatory synergy between particular sub-classes of MYB and bHLH factors is perhaps one of the best examples of combinatorial plant gene regulation. However, members of the MYB and bHLH families also interact with a number of other regulatory proteins, forming complexes that either activate or repress the expression of sets of target genes that are increasingly being identified through a diversity of high-throughput genomic approaches. The next few years are likely to witness an increasing understanding of the extent to which conserved transcription factors participate at similar positions in gene regulatory networks across plant species.
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Affiliation(s)
- Antje Feller
- Plant Biotechnology Center and Department of Molecular Genetics, Ohio State University, Columbus, OH 43210, USA
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Kaldis A, Tsementzi D, Tanriverdi O, Vlachonasios KE. Arabidopsis thaliana transcriptional co-activators ADA2b and SGF29a are implicated in salt stress responses. PLANTA 2011; 233:749-62. [PMID: 21193996 DOI: 10.1007/s00425-010-1337-0] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2010] [Accepted: 12/13/2010] [Indexed: 05/21/2023]
Abstract
The transcriptional co-activator ADA2b is a component of GCN5-containing complexes in eukaryotes. In Arabidopsis, ada2b mutants result in pleiotropic developmental defects and altered responses to low-temperature stress. SGF29 has recently been identified as another component of GCN5-containing complexes. In the Arabidopsis genome there are two orthologs of yeast SGF29, designated as SGF29a and SGF29b. We hypothesized that, in Arabidopsis, one or both SGF29 proteins may work in concert with ADA2b to regulate genes in response to abiotic stress, and we set out to explore the role of SGF29a and ADA2b in salt stress responses. In root growth and seed germination assays, sgf29a-1 mutants were more resistant to salt stress than their wild-type counterparts, whereas ada2b-1 mutant was hypersensitive. The sgf29a;ada2b double mutant displayed similar phenotypes to ada2b-1 mutant with reduced salt sensitivity. The expression of several abiotic stress-responsive genes was reduced in ada2b-1 mutants after 3 h of salt stress in comparison with sgf29a-1 and wild-type plants. In the sgf29a-1;ada2b-1 double mutant, the salt-induced gene expression was affected similarly to ada2b-1. These results suggest that under salt stress the function of SGF29a was masked by ADA2b and perhaps SGF29a could play an auxiliary role to ADA2b action. In chromatin immunoprecipitation assays, reduced levels of histone H3 and H4 acetylation in the promoter and coding region of COR6.6, RAB18, and RD29b genes were observed in ada2b-1 mutants relative to wild-type plants. In conclusion, ADA2b positively regulates salt-induced gene expression by maintaining the locus-specific acetylation of histones H4 and H3.
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Affiliation(s)
- Athanasios Kaldis
- Department of Botany, School of Biology, Faculty of Sciences, Aristotle University of Thessaloniki, Thessaloniki, 54124, Greece
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Dèrozier S, Samson F, Tamby JP, Guichard C, Brunaud V, Grevet P, Gagnot S, Label P, Leplé JC, Lecharny A, Aubourg S. Exploration of plant genomes in the FLAGdb++ environment. PLANT METHODS 2011; 7:8. [PMID: 21447150 PMCID: PMC3073958 DOI: 10.1186/1746-4811-7-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2010] [Accepted: 03/29/2011] [Indexed: 05/04/2023]
Abstract
BACKGROUND In the contexts of genomics, post-genomics and systems biology approaches, data integration presents a major concern. Databases provide crucial solutions: they store, organize and allow information to be queried, they enhance the visibility of newly produced data by comparing them with previously published results, and facilitate the exploration and development of both existing hypotheses and new ideas. RESULTS The FLAGdb++ information system was developed with the aim of using whole plant genomes as physical references in order to gather and merge available genomic data from in silico or experimental approaches. Available through a JAVA application, original interfaces and tools assist the functional study of plant genes by considering them in their specific context: chromosome, gene family, orthology group, co-expression cluster and functional network. FLAGdb++ is mainly dedicated to the exploration of large gene groups in order to decipher functional connections, to highlight shared or specific structural or functional features, and to facilitate translational tasks between plant species (Arabidopsis thaliana, Oryza sativa, Populus trichocarpa and Vitis vinifera). CONCLUSION Combining original data with the output of experts and graphical displays that differ from classical plant genome browsers, FLAGdb++ presents a powerful complementary tool for exploring plant genomes and exploiting structural and functional resources, without the need for computer programming knowledge. First launched in 2002, a 15th version of FLAGdb++ is now available and comprises four model plant genomes and over eight million genomic features.
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Affiliation(s)
- Sandra Dèrozier
- Unité de Recherche en Génomique Végétale (URGV), UMR INRA 1165 - Université d'Evry Val d'Essonne - ERL CNRS 8196, 2 Rue Gaston Crémieux, CP 5708, F-91057 Evry Cedex, France
- Unité Mathématique Informatique et Génome (MIG), UR INRA 1077, Domaine de Vilvert, F-78352 Jouy-en-Josas Cedex, France
| | - Franck Samson
- Unité de Recherche en Génomique Végétale (URGV), UMR INRA 1165 - Université d'Evry Val d'Essonne - ERL CNRS 8196, 2 Rue Gaston Crémieux, CP 5708, F-91057 Evry Cedex, France
- Unité Mathématique Informatique et Génome (MIG), UR INRA 1077, Domaine de Vilvert, F-78352 Jouy-en-Josas Cedex, France
| | - Jean-Philippe Tamby
- Unité de Recherche en Génomique Végétale (URGV), UMR INRA 1165 - Université d'Evry Val d'Essonne - ERL CNRS 8196, 2 Rue Gaston Crémieux, CP 5708, F-91057 Evry Cedex, France
| | - Cécile Guichard
- Unité de Recherche en Génomique Végétale (URGV), UMR INRA 1165 - Université d'Evry Val d'Essonne - ERL CNRS 8196, 2 Rue Gaston Crémieux, CP 5708, F-91057 Evry Cedex, France
| | - Véronique Brunaud
- Unité de Recherche en Génomique Végétale (URGV), UMR INRA 1165 - Université d'Evry Val d'Essonne - ERL CNRS 8196, 2 Rue Gaston Crémieux, CP 5708, F-91057 Evry Cedex, France
| | - Philippe Grevet
- Unité de Recherche en Génomique Végétale (URGV), UMR INRA 1165 - Université d'Evry Val d'Essonne - ERL CNRS 8196, 2 Rue Gaston Crémieux, CP 5708, F-91057 Evry Cedex, France
| | - Séverine Gagnot
- Unité de Recherche en Génomique Végétale (URGV), UMR INRA 1165 - Université d'Evry Val d'Essonne - ERL CNRS 8196, 2 Rue Gaston Crémieux, CP 5708, F-91057 Evry Cedex, France
- Laboratoire de Chimie Bactérienne (LCB), UPR CNRS 9043 - IFR 88, 31 Chemin Joseph Aiguier, F-13009 Marseille, France
| | - Philippe Label
- Unité Amélioration, Génétique et Physiologie Forestières (UAGPF), UR INRA 588, 2163 avenue de la Pomme de Pin, CS 4001 Ardon, F-45075 Orléans, France
| | - Jean-Charles Leplé
- Unité Amélioration, Génétique et Physiologie Forestières (UAGPF), UR INRA 588, 2163 avenue de la Pomme de Pin, CS 4001 Ardon, F-45075 Orléans, France
| | - Alain Lecharny
- Unité de Recherche en Génomique Végétale (URGV), UMR INRA 1165 - Université d'Evry Val d'Essonne - ERL CNRS 8196, 2 Rue Gaston Crémieux, CP 5708, F-91057 Evry Cedex, France
| | - Sébastien Aubourg
- Unité de Recherche en Génomique Végétale (URGV), UMR INRA 1165 - Université d'Evry Val d'Essonne - ERL CNRS 8196, 2 Rue Gaston Crémieux, CP 5708, F-91057 Evry Cedex, France
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Jang IC, Chung PJ, Hemmes H, Jung C, Chua NH. Rapid and reversible light-mediated chromatin modifications of Arabidopsis phytochrome A locus. THE PLANT CELL 2011; 23:459-70. [PMID: 21317377 PMCID: PMC3077797 DOI: 10.1105/tpc.110.080481] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2010] [Revised: 12/14/2010] [Accepted: 01/28/2011] [Indexed: 05/19/2023]
Abstract
Recent genome-wide surveys showed that acetylation of H3K9 and H3K27 is correlated with gene activation during deetiolation of Arabidopsis thaliana seedlings, but less is known regarding changes in the histone status of repressed genes. Phytochrome A (phyA) is the major photoreceptor of deetiolation, and phyA expression is reversibly repressed by light. We found that in adult Arabidopsis plants, phyA activation in darkness was accompanied by a significant enrichment in the phyA transcription and translation start sites of not only H3K9/14ac and H3K27ac but also H3K4me3, and there was also moderate enrichment of H4K5ac, H4K8ac, H4K12ac, and H4K16ac. Conversely, when phyA expression was repressed by light, H3K27me3 was enriched with a corresponding decline in H3K27ac; moreover, demethylation of H3K4me3 and deacetylation of H3K9/14 were also seen. These histone modifications, which were focused around the phyA transcription/translation start sites, were detected within 1 h of deetiolation. Mutant analysis showed that HDA19/HD1 mediated deacetylation of H3K9/14 and uncovered possible histone crosstalk between H3K9/14ac and H3K4me3. Neither small RNA pathways nor the circadian clock affected H3 modification status of the phyA locus, and DNA methylation was unchanged by light. The presence of activating and repressive histone marks suggests a mechanism for the rapid and reversible regulation of phyA by dark and light.
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82
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Abstract
Epigenetic research is at the forefront of plant biology and molecular genetics. Studies on higher plants underscore the significant role played by epigenetics in both plant development and stress response. Relatively recent advances in analytical methodology have allowed for a significant expansion of what is known about genome-wide mapping of DNA methylation and histone modifications. In this review, we explore the different modification patterns in plant epigenetics, and the key factors involved in the epigenetic process, in order to illustrate various putative mechanisms. Experimental technology to exploit these modifications, and proposed focus areas for future plant epigenetic research, are also presented.
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Affiliation(s)
- Ming Chen
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, China.
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83
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A Novel Aux/IAA28 Signaling Cascade Activates GATA23-Dependent Specification of Lateral Root Founder Cell Identity. Curr Biol 2010; 20:1697-706. [DOI: 10.1016/j.cub.2010.09.007] [Citation(s) in RCA: 354] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2010] [Revised: 08/03/2010] [Accepted: 08/27/2010] [Indexed: 11/22/2022]
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84
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Servet C, Conde e Silva N, Zhou DX. Histone acetyltransferase AtGCN5/HAG1 is a versatile regulator of developmental and inducible gene expression in Arabidopsis. MOLECULAR PLANT 2010; 3:670-7. [PMID: 20457643 DOI: 10.1093/mp/ssq018] [Citation(s) in RCA: 125] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Histone acetylation/deacetylation is a dynamic process and plays an important role in gene regulation. Histone acetylation homeostasis is regulated by antagonist actions of histone acetyltransferases (HAT) and deacetylases (HDAC). Plant genome encodes multiple HATs and HDACs. The Arabidopsis HAT gene AtGCN5/HAG1plays an essential role in many plant development processes, such as meristem function, cell differentiation, leaf and floral organogenesis, and responses to environmental conditions such as light and cold, indicating an important role of this HAT in the regulation of both long-term developmental switches and short-term inducible gene expression. AtGCN5 targets to a large number of promoters and is required for acetylation of several histone H3 lysine residues. Recruitment of AtGCN5 to target promoters is likely to be mediated by direct or indirect interaction with DNA-binding transcription factors and/or by interaction with acetylated histone lysine residues on the targets. Interplay between AtGCN5 and other HAT and HDAC is demonstrated to control specific regulatory pathways. Analysis of the role of AtGCN5 in light-inducible gene expression suggests a function of AtGCN5 in preparing chromatin commitment for priming inducible gene activation in plants.
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Affiliation(s)
- Caroline Servet
- Institut de Biologie des Plantes, Université Paris-sud 11, 91405 Orsay, France
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85
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Putative Arabidopsis transcriptional adaptor protein (PROPORZ1) is required to modulate histone acetylation in response to auxin. Proc Natl Acad Sci U S A 2010; 107:10308-13. [PMID: 20479223 DOI: 10.1073/pnas.0913918107] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Plant development is highly adaptable and controlled by a combination of various regulatory circuits that integrate internal and environmental cues. The phytohormone auxin mediates such growth responses, acting as a dynamic signal in the control of morphogenesis via coordinating the interplay between cell cycle progression and cell differentiation. Mutants in the chromatin-remodeling component PROPORZ1 (PRZ1; also known as AtADA2b) are impaired in auxin effects on morphogenesis, suggestive of an involvement of PRZ1-dependent control of chromatin architecture in the determination of hormone responses. Here we demonstrate that PRZ1 is required for accurate histone acetylation at auxin-controlled loci. Specifically, PRZ1 is involved in the modulation of histone modifications and corresponding adjustments in gene expression of Arabidopsis KIP RELATED PROTEIN (KRP) CDK inhibitor genes in response to auxin. Deregulated KRP expression in KRP silencer lines phenocopies prz1 hyperproliferative growth phenotypes, whereas in a KRP overexpression background some mutant phenotypes are suppressed. Collectively, our findings support a model in which translation of positional signals into developmental cues involves adjustments in chromatin modifications that orchestrate auxin effects on cell proliferation.
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86
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Kaufmann K, Muiño JM, Østerås M, Farinelli L, Krajewski P, Angenent GC. Chromatin immunoprecipitation (ChIP) of plant transcription factors followed by sequencing (ChIP-SEQ) or hybridization to whole genome arrays (ChIP-CHIP). Nat Protoc 2010; 5:457-72. [PMID: 20203663 DOI: 10.1038/nprot.2009.244] [Citation(s) in RCA: 217] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Chromatin immunoprecipitation (ChIP) is a powerful technique to study interactions between transcription factors (TFs) and DNA in vivo. For genome-wide de novo discovery of TF-binding sites, the DNA that is obtained in ChIP experiments needs to be processed for sequence identification. The sequences can be identified by direct sequencing (ChIP-SEQ) or hybridization to microarrays (ChIP-CHIP). Given the small amounts of DNA that are usually obtained in ChIP experiments, successful and reproducible sample processing is challenging. Here we provide a detailed procedure for ChIP of plant TFs, as well as protocols for sample preparation for ChIP-SEQ and for ChIP-CHIP. Our ChIP procedure is optimized for high signal-to-noise ratio starting with tissue fixation, followed by nuclei isolation, immunoprecipitation, DNA amplification and purification. We also provide a guide for primary data analysis of ChIP-SEQ data. The complete protocol for ChIP-SEQ/ChIP-CHIP sample preparation starting from plant harvest takes approximately 7 d.
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Affiliation(s)
- Kerstin Kaufmann
- Laboratory of Molecular Biology, Wageningen University, Wageningen, The Netherlands
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87
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Plant Elongator regulates auxin-related genes during RNA polymerase II transcription elongation. Proc Natl Acad Sci U S A 2010; 107:1678-83. [PMID: 20080602 DOI: 10.1073/pnas.0913559107] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
In eukaryotes, transcription of protein-encoding genes is strongly regulated by posttranslational modifications of histones that affect the accessibility of the DNA by RNA polymerase II (RNAPII). The Elongator complex was originally identified in yeast as a histone acetyltransferase (HAT) complex that activates RNAPII-mediated transcription. In Arabidopsis thaliana, the Elongator mutants elo1, elo2, and elo3 with decreased leaf and primary root growth due to reduced cell proliferation identified homologs of components of the yeast Elongator complex, Elp4, Elp1, and Elp3, respectively. Here we show that the Elongator complex was purified from plant cell cultures as a six-component complex. The role of plant Elongator in transcription elongation was supported by colocalization of the HAT enzyme, ELO3, with euchromatin and the phosphorylated form of RNAPII, and reduced histone H3 lysine 14 acetylation at the coding region of the SHORT HYPOCOTYL 2 auxin repressor and the LAX2 auxin influx carrier gene with reduced expression levels in the elo3 mutant. Additional auxin-related genes were down-regulated in the transcriptome of elo mutants but not targeted by the Elongator HAT activity showing specificity in target gene selection. Biological relevance was apparent by auxin-related phenotypes and marker gene analysis. Ethylene and jasmonic acid signaling and abiotic stress responses were up-regulated in the elo transcriptome and might contribute to the pleiotropic elo phenotype. Thus, although the structure of Elongator and its substrate are conserved, target gene selection has diverged, showing that auxin signaling and influx are under chromatin control.
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88
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Charron JBF, He H, Elling AA, Deng XW. Dynamic landscapes of four histone modifications during deetiolation in Arabidopsis. THE PLANT CELL 2009; 21:3732-48. [PMID: 20008096 PMCID: PMC2814509 DOI: 10.1105/tpc.109.066845] [Citation(s) in RCA: 175] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2009] [Revised: 10/08/2009] [Accepted: 11/18/2009] [Indexed: 05/18/2023]
Abstract
Although landscapes of several histone marks are now available for Arabidopsis thaliana and Oryza sativa, such profiles remain static and do not provide information about dynamic changes of plant epigenomes in response to developmental or environmental cues. Here, we analyzed the effects of light on four histone modifications (acetylation and trimethylation of lysines 9 and 27 on histone H3: H3K9ac, H3K9me3, H3K27ac, and H3K27me3, respectively). Our genome-wide profiling of H3K9ac and H3K27ac revealed that these modifications are nontransposable element gene-specific. By contrast, we found that H3K9me3 and H3K27me3 target nontransposable element genes, but also intergenic regions and transposable elements. Specific light conditions affected the number of modified regions as well as the overall correlation strength between the presence of specific modifications and transcription. Furthermore, we observed that acetylation marks not only ELONGATED HYPOCOTYL5 and HY5-HOMOLOG upon deetiolation, but also their downstream targets. We found that the activation of photosynthetic genes correlates with dynamic acetylation changes in response to light, while H3K27ac and H3K27me3 potentially contribute to light regulation of the gibberellin metabolism. Thus, this work provides a dynamic portrait of the variations in histone modifications in response to the plant's changing light environment and strengthens the concept that histone modifications represent an additional layer of control for light-regulated genes involved in photomorphogenesis.
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Affiliation(s)
- Jean-Benoit F. Charron
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520
| | - Hang He
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520
- Peking-Yale Joint Center of Plant Molecular Genetics and Agrobiotechnology, College of Life Sciences, Peking University, Beijing 100871, People's Republic of China
| | - Axel A. Elling
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520
| | - Xing Wang Deng
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520
- Peking-Yale Joint Center of Plant Molecular Genetics and Agrobiotechnology, College of Life Sciences, Peking University, Beijing 100871, People's Republic of China
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89
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Cohen R, Schocken J, Kaldis A, Vlachonasios KE, Hark AT, McCain ER. The histone acetyltransferase GCN5 affects the inflorescence meristem and stamen development in Arabidopsis. PLANTA 2009; 230:1207-21. [PMID: 19771450 DOI: 10.1007/s00425-009-1012-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2009] [Accepted: 08/23/2009] [Indexed: 05/11/2023]
Abstract
A central question in biology is to understand how gene expression is precisely regulated to give rise to a variety of forms during the process of development. Epigenetic effects such as DNA methylation or histone modification have been increasingly shown to play a critical role in regulation of genome function. GCN5 is a prototypical histone acetyltransferase that participates in regulating developmental gene expression in several metazoan species. In Arabidopsis thaliana, plants with T-DNA insertions in GCN5 (also known as HAG1) display a variety of pleiotropic effects including dwarfism, loss of apical dominance, and floral defects affecting fertility. We sought to determine when during early development floral abnormalities first arise. Using scanning electron microscopy, we demonstrate that gcn5-1/hag1-1 and gcn5-5/hag1-5 mutants display overproliferation of young buds and development of abnormal structures around the inflorescence meristem. gcn5 mutants also display defects in stamen number and arrangement at later stages. This analysis provides temporal and spatial information to aid in the identification of GCN5 target genes in the developing flower. Preliminary studies of putative targets using reverse transcriptase PCR suggest that the floral meristem identity gene LEAFY is among factors upregulated in gcn5-1 mutants.
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Affiliation(s)
- Ross Cohen
- Biology Department, Muhlenberg College, Allentown, PA, 18104, USA
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90
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Zheng Y, Ren N, Wang H, Stromberg AJ, Perry SE. Global identification of targets of the Arabidopsis MADS domain protein AGAMOUS-Like15. THE PLANT CELL 2009; 21:2563-77. [PMID: 19767455 PMCID: PMC2768919 DOI: 10.1105/tpc.109.068890] [Citation(s) in RCA: 164] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2009] [Revised: 08/06/2009] [Accepted: 08/23/2009] [Indexed: 05/18/2023]
Abstract
AGAMOUS-Like15 (AGL15) is a MADS domain transcriptional regulator that promotes somatic embryogenesis by binding DNA and regulating gene expression. Chromatin immunoprecipitation (ChIP) analysis previously identified DNA fragments with which AGL15 associates in vivo, and a low-throughput approach revealed a role for AGL15 in gibberellic acid catabolism that is relevant to embryogenesis. However, higher throughput methods are needed to identify targets of AGL15. Here, we mapped AGL15 in vivo binding sites using a ChIP-chip approach and the Affymetrix tiling arrays for Arabidopsis thaliana and found that approximately 2000 sites represented in three biological replicates of the experiment are annotated to nearby genes. These results were combined with high-throughput measurement of gene expression in response to AGL15 accumulation to discriminate responsive direct targets from those further downstream in the network. LEAFY COTYLEDON2, FUSCA3, and ABA INSENSITIVE3, which encode B3 domain transcription factors that are key regulators of embryogenesis, were identified and verified as direct target genes of AGL15. Genes identified as targets of the B3 genes are also targets of AGL15, and we found that INDOLEACETIC ACID-INDUCED PROTEIN30 is involved in promotion of somatic embryo development. The data presented here and elsewhere suggest that much cross-regulation occurs in gene regulatory networks underpinning embryogenesis.
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Affiliation(s)
- Yumei Zheng
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, Kentucky 40546-0312
| | - Na Ren
- Department of Statistics, University of Kentucky, Lexington, Kentucky 40506-0027
| | - Huai Wang
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, Kentucky 40546-0312
| | - Arnold J. Stromberg
- Department of Statistics, University of Kentucky, Lexington, Kentucky 40506-0027
| | - Sharyn E. Perry
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, Kentucky 40546-0312
- Address correspondence to
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91
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Kim W, Benhamed M, Servet C, Latrasse D, Zhang W, Delarue M, Zhou DX. Histone acetyltransferase GCN5 interferes with the miRNA pathway in Arabidopsis. Cell Res 2009; 19:899-909. [DOI: 10.1038/cr.2009.59] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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92
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Kornet N, Scheres B. Members of the GCN5 histone acetyltransferase complex regulate PLETHORA-mediated root stem cell niche maintenance and transit amplifying cell proliferation in Arabidopsis. THE PLANT CELL 2009; 21:1070-9. [PMID: 19376933 PMCID: PMC2685635 DOI: 10.1105/tpc.108.065300] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2008] [Revised: 03/16/2009] [Accepted: 04/01/2009] [Indexed: 05/18/2023]
Abstract
The PLETHORA (PLT) stem cell transcription factors form a developmentally instructive protein gradient in Arabidopsis thaliana roots. Histone acetylation is known to facilitate gene transcription and plays an important role in developmental processes. Here, we show that histone acetyltransferase GCN5 (for general control nonderepressible 5) attenuates the PLT gradient. Based on genetic evidence, we establish that GCN5 is essential for root stem cell niche maintenance and acts in the PLT pathway. The GCN5-associated factor ADA2b (for alteration/deficiency in activation 2b) is also positioned in the PLT pathway and regulates PLT expression, similar to GCN5. Both GCN5 and ADA2b mediate proliferation of the transit amplifying cells, but ADA2b does not affect stem cell niche maintenance. Overexpression of PLT2 rescues the stem cell niche defect of gcn5 mutants, indicating that GCN5 regulation of PLT expression is essential for maintenance of the root stem cell niche. We conclude that histone acetylation complexes play an important role in shaping a developmentally instructive gradient in the root.
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Affiliation(s)
- Noortje Kornet
- Department of Biology, Faculty of Science, Utrecht University, 3584 CH Utrecht, The Netherlands
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