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Nie Y, Song C, Huang H, Mao S, Ding K, Tang H. Chromatin modifiers in human disease: from functional roles to regulatory mechanisms. MOLECULAR BIOMEDICINE 2024; 5:12. [PMID: 38584203 PMCID: PMC10999406 DOI: 10.1186/s43556-024-00175-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 02/21/2024] [Indexed: 04/09/2024] Open
Abstract
The field of transcriptional regulation has revealed the vital role of chromatin modifiers in human diseases from the beginning of functional exploration to the process of participating in many types of disease regulatory mechanisms. Chromatin modifiers are a class of enzymes that can catalyze the chemical conversion of pyrimidine residues or amino acid residues, including histone modifiers, DNA methyltransferases, and chromatin remodeling complexes. Chromatin modifiers assist in the formation of transcriptional regulatory circuits between transcription factors, enhancers, and promoters by regulating chromatin accessibility and the ability of transcription factors to acquire DNA. This is achieved by recruiting associated proteins and RNA polymerases. They modify the physical contact between cis-regulatory factor elements, transcription factors, and chromatin DNA to influence transcriptional regulatory processes. Then, abnormal chromatin perturbations can impair the homeostasis of organs, tissues, and cells, leading to diseases. The review offers a comprehensive elucidation on the function and regulatory mechanism of chromatin modifiers, thereby highlighting their indispensability in the development of diseases. Furthermore, this underscores the potential of chromatin modifiers as biomarkers, which may enable early disease diagnosis. With the aid of this paper, a deeper understanding of the role of chromatin modifiers in the pathogenesis of diseases can be gained, which could help in devising effective diagnostic and therapeutic interventions.
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Affiliation(s)
- Yali Nie
- Hunan Provincial Key Laboratory of Multi-omics and Artificial Intelligence of Cardiovascular Diseases, University of South China, Hengyang, Hunan, 421001, China
- The First Affiliated Hospital, Department of Cardiology, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
- The First Affiliated Hospital, Institute of Cardiovascular Disease, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
- Clinical Research Center for Myocardial Injury in Hunan Province, Hengyang, Hunan, 421001, China
| | - Chao Song
- Hunan Provincial Key Laboratory of Multi-omics and Artificial Intelligence of Cardiovascular Diseases, University of South China, Hengyang, Hunan, 421001, China
- The First Affiliated Hospital, Department of Cardiology, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
- The First Affiliated Hospital, Institute of Cardiovascular Disease, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
- The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
| | - Hong Huang
- Hunan Provincial Key Laboratory of Multi-omics and Artificial Intelligence of Cardiovascular Diseases, University of South China, Hengyang, Hunan, 421001, China
- The First Affiliated Hospital, Department of Cardiology, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
- The First Affiliated Hospital, Institute of Cardiovascular Disease, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
- Clinical Research Center for Myocardial Injury in Hunan Province, Hengyang, Hunan, 421001, China
- The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
| | - Shuqing Mao
- Hunan Provincial Key Laboratory of Multi-omics and Artificial Intelligence of Cardiovascular Diseases, University of South China, Hengyang, Hunan, 421001, China
- The First Affiliated Hospital, Department of Cardiology, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
- The First Affiliated Hospital, Institute of Cardiovascular Disease, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
- Clinical Research Center for Myocardial Injury in Hunan Province, Hengyang, Hunan, 421001, China
| | - Kai Ding
- The First Affiliated Hospital, Department of Cardiology, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
- The First Affiliated Hospital, Institute of Cardiovascular Disease, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
- Clinical Research Center for Myocardial Injury in Hunan Province, Hengyang, Hunan, 421001, China
| | - Huifang Tang
- Hunan Provincial Key Laboratory of Multi-omics and Artificial Intelligence of Cardiovascular Diseases, University of South China, Hengyang, Hunan, 421001, China.
- The First Affiliated Hospital, Department of Cardiology, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.
- The First Affiliated Hospital, Institute of Cardiovascular Disease, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.
- Clinical Research Center for Myocardial Injury in Hunan Province, Hengyang, Hunan, 421001, China.
- The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.
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Edwards MB, Ballerini ES, Kramer EM. Complex developmental and transcriptional dynamics underlie pollinator-driven evolutionary transitions in nectar spur morphology in Aquilegia (columbine). AMERICAN JOURNAL OF BOTANY 2022; 109:1360-1381. [PMID: 35971626 DOI: 10.1002/ajb2.16046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 07/17/2022] [Accepted: 07/18/2022] [Indexed: 06/15/2023]
Abstract
PREMISE Determining the developmental programs underlying morphological variation is key to elucidating the evolutionary processes that generated the stunning biodiversity of the angiosperms. Here, we characterized the developmental and transcriptional dynamics of the elaborate petal nectar spur of Aquilegia (columbine) in species with contrasting pollination syndromes and spur morphologies. METHODS We collected petal epidermal cell number and length data across four Aquilegia species, two with short, curved nectar spurs of the bee-pollination syndrome and two with long, straight spurs of the hummingbird-pollination syndrome. We also performed RNA-seq on A. brevistyla (bee) and A. canadensis (hummingbird) distal and proximal spur compartments at multiple developmental stages. Finally, we intersected these data sets with a previous QTL mapping study on spur length and shape to identify new candidate loci. RESULTS The differential growth between the proximal and distal surfaces of curved spurs is primarily driven by differential cell division. However, independent transitions to straight spurs in the hummingbird syndrome have evolved by increasing differential cell elongation between spur surfaces. The RNA-seq data reveal these tissues to be transcriptionally distinct and point to auxin signaling as being involved with the differential cell elongation responsible for the evolution of straight spurs. We identify several promising candidate genes for future study. CONCLUSIONS Our study, taken together with previous work in Aquilegia, reveals the complexity of the developmental mechanisms underlying trait variation in this system. The framework we established here will lead to exciting future work examining candidate genes and processes involved in the rapid radiation of the genus.
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Affiliation(s)
- Molly B Edwards
- Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Ave., Cambridge, MA, 02138, USA
| | - Evangeline S Ballerini
- Department of Biological Sciences, California State University Sacramento, 6000 J St., Sacramento, CA, 95819, USA
| | - Elena M Kramer
- Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Ave., Cambridge, MA, 02138, USA
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Xue H, Zhang Q, Wang P, Cao B, Jia C, Cheng B, Shi Y, Guo WF, Wang Z, Liu ZX, Cheng H. qPTMplants: an integrative database of quantitative post-translational modifications in plants. Nucleic Acids Res 2021; 50:D1491-D1499. [PMID: 34718741 PMCID: PMC8728288 DOI: 10.1093/nar/gkab945] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 09/28/2021] [Accepted: 10/06/2021] [Indexed: 12/13/2022] Open
Abstract
As a crucial molecular mechanism, post-translational modifications (PTMs) play critical roles in a wide range of biological processes in plants. Recent advances in mass spectrometry-based proteomic technologies have greatly accelerated the profiling and quantification of plant PTM events. Although several databases have been constructed to store plant PTM data, a resource including more plant species and more PTM types with quantitative dynamics still remains to be developed. In this paper, we present an integrative database of quantitative PTMs in plants named qPTMplants (http://qptmplants.omicsbio.info), which hosts 1 242 365 experimentally identified PTM events for 429 821 nonredundant sites on 123 551 proteins under 583 conditions for 23 PTM types in 43 plant species from 293 published studies, with 620 509 quantification events for 136 700 PTM sites on 55 361 proteins under 354 conditions. Moreover, the experimental details, such as conditions, samples, instruments and methods, were manually curated, while a variety of annotations, including the sequence and structural characteristics, were integrated into qPTMplants. Then, various search and browse functions were implemented to access the qPTMplants data in a user-friendly manner. Overall, we anticipate that the qPTMplants database will be a valuable resource for further research on PTMs in plants.
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Affiliation(s)
- Han Xue
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Qingfeng Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Panqin Wang
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Bijin Cao
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Chongchong Jia
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Ben Cheng
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Yuhua Shi
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Wei-Feng Guo
- School of Electrical Engineering, Zhengzhou University, Zhengzhou 450001, China
| | - Zhenlong Wang
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Ze-Xian Liu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Han Cheng
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
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Lu C, Coradin M, Janssen KA, Sidoli S, Garcia BA. Combinatorial Histone H3 Modifications Are Dynamically Altered in Distinct Cell Cycle Phases. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:1300-1311. [PMID: 33818074 PMCID: PMC8380055 DOI: 10.1021/jasms.0c00451] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The cell cycle is a highly regulated and evolutionary conserved process that results in the duplication of cell content and the equal distribution of the duplicated chromosomes into a pair of daughter cells. Histones are fundamental structural components of chromatin in eukaryotic cells, and their post-translational modifications (PTMs) benchmark DNA readout and chromosome condensation. Aberrant regulation of the cell cycle associated with dysregulation of histone PTMs is the cause of critical diseases such as cancer. Monitoring changes of histone PTMs could pave the way to understanding the molecular mechanisms associated with epigenetic regulation of cell proliferation. Previously, our lab established a novel middle-down workflow using porous graphitic carbon (PGC) as a stationary phase to analyze histone PTMs, which utilizes the same reversed-phase chromatography for gradient separation as canonical proteomics coupled with online mass spectrometry (MS). Here, we applied this novel workflow for high-throughput analysis of histone modifications of H3.1 and H3.2 during the cell cycle. Collectively, we identified 1133 uniquely modified canonical histone H3 N-terminal tails. Consistent with previous findings, histone H3 phosphorylation increased significantly during the mitosis (M) phase. Histone H3 variant-specific and cell-cycle-dependent expressions of PTMs were observed, underlining the need to not combine H3.1 and H3.2 together as H3. We confirmed previously known H3 PTM crosstalk (e.g., K9me-S10ph) and revealed new information in this area as well. These findings imply that the combinatorial PTMs play a role in cell cycle control, and they may serve as markers for proliferation.
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Affiliation(s)
- Congcong Lu
- Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Mariel Coradin
- Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Biochemistry and Molecular Biophysics graduate group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Kevin A. Janssen
- Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Biochemistry and Molecular Biophysics graduate group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Simone Sidoli
- Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Benjamin A. Garcia
- Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- To whom correspondence should be addressed.
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Wang J, Yan X, Chen H, Feng J, Han R. Enhanced UV-B radiation affects AUR1 regulation of mitotic spindle morphology leading to aberrant mitosis. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 159:160-170. [PMID: 33370689 DOI: 10.1016/j.plaphy.2020.12.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 12/16/2020] [Indexed: 06/12/2023]
Abstract
Enhanced UV-B radiation can lead to a variety of stress responses, including effects on cell cycle regulation and mitosis. Aurora kinases are part of the serine/threonine kinase family and play important roles in cell cycle regulation and mitosis. We hypothesize that there may be a connection between these two processes. In this study, the dynamics of chromosomal (H2B-YFP) and AUR1-GFP changes after enhanced UV-B radiation were observed using confocal microscopy, and gene and protein expression patterns under UV-B stress were quantified using RT-qPCR and Western blotting techniques. We analyzed the responses of the AUR1 overexpression to UV-B stress. We measured maximum quantum yield of photosystem Ⅱ as a proxy for UV-B stress. The recovery capacity of AUR1 overexpression strains was analyzed. In our research, we observed that enhanced UV-B radiation affects the subcellular positioning of AUR1, resulting in abnormalities in the positioning and location of the spindle at the poles, which ultimately affects the separation of chromosomes, resulting in "partition-bundle division" and the incorrect direction of division. At the same time, our results also indicated that low-dose UV-B can induce the expression of AUR1, and this overexpression of AUR1 can alleviate the damage caused by UV-B radiation. In summary, the results of our study show that enhanced UV-B radiation can change the activity and expression of AUR1, which is one of the causes of abnormal chromosome segregation. AUR1 participates in the response to UV-B stress, and, to a certain extent, can improve the UV-B tolerance of plants.
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Affiliation(s)
- Jianhua Wang
- College of Life Science, Shanxi Normal University, Linfen, Shanxi, 041004, People's Republic of China; Higher Education Key Laboratory of Plant Molecular and Environmental Stress Response (Shanxi Normal University) in Shanxi Province, Linfen, Shanxi, 041000, People's Republic of China.
| | - Xiaoyan Yan
- College of Life Science, Shanxi Normal University, Linfen, Shanxi, 041004, People's Republic of China; Higher Education Key Laboratory of Plant Molecular and Environmental Stress Response (Shanxi Normal University) in Shanxi Province, Linfen, Shanxi, 041000, People's Republic of China.
| | - Huize Chen
- College of Life Science, Shanxi Normal University, Linfen, Shanxi, 041004, People's Republic of China; Higher Education Key Laboratory of Plant Molecular and Environmental Stress Response (Shanxi Normal University) in Shanxi Province, Linfen, Shanxi, 041000, People's Republic of China.
| | - Jinlin Feng
- College of Life Science, Shanxi Normal University, Linfen, Shanxi, 041004, People's Republic of China; Higher Education Key Laboratory of Plant Molecular and Environmental Stress Response (Shanxi Normal University) in Shanxi Province, Linfen, Shanxi, 041000, People's Republic of China.
| | - Rong Han
- College of Life Science, Shanxi Normal University, Linfen, Shanxi, 041004, People's Republic of China; Higher Education Key Laboratory of Plant Molecular and Environmental Stress Response (Shanxi Normal University) in Shanxi Province, Linfen, Shanxi, 041000, People's Republic of China.
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Dvořák Tomaštíková E, Rutten T, Dvořák P, Tugai A, Ptošková K, Petrovská B, van Damme D, Houben A, Doležel J, Demidov D. Functional Divergence of Microtubule-Associated TPX2 Family Members in Arabidopsis thaliana. Int J Mol Sci 2020; 21:ijms21062183. [PMID: 32235723 PMCID: PMC7139753 DOI: 10.3390/ijms21062183] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 03/18/2020] [Accepted: 03/19/2020] [Indexed: 01/21/2023] Open
Abstract
TPX2 (Targeting Protein for Xklp2) is an evolutionary conserved microtubule-associated protein important for microtubule nucleation and mitotic spindle assembly. The protein was described as an activator of the mitotic kinase Aurora A in humans and the Arabidopsis AURORA1 (AUR1) kinase. In contrast to animal genomes that encode only one TPX2 gene, higher plant genomes encode a family with several TPX2-LIKE gene members (TPXL). TPXL genes of Arabidopsis can be divided into two groups. Group A proteins (TPXL2, 3, 4, and 8) contain Aurora binding and TPX2_importin domains, while group B proteins (TPXL1, 5, 6, and 7) harbor an Xklp2 domain. Canonical TPX2 contains all the above-mentioned domains. We confirmed using in vitro kinase assays that the group A proteins contain a functional Aurora kinase binding domain. Transient expression of Arabidopsis TPX2-like proteins in Nicotiana benthamiana revealed preferential localization to microtubules and nuclei. Co-expression of AUR1 together with TPX2-like proteins changed the localization of AUR1, indicating that these proteins serve as targeting factors for Aurora kinases. Taken together, we visualize the various localizations of the TPX2-LIKE family in Arabidopsis as a proxy to their functional divergence and provide evidence of their role in the targeted regulation of AUR1 kinase activity.
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Affiliation(s)
- Eva Dvořák Tomaštíková
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Hana for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-77900 Olomouc, Czech Republic; (K.P.); (B.P.); (J.D.)
- Correspondence: (E.D.T.); (D.D.); Tel.: +420-585-238-725 (E.D.T.); +49-394825-733 (D.D.)
| | - Twan Rutten
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Corrensstrasse 3, 06466 Seeland, Germany; (T.R.); (A.T.); (A.H.)
| | - Petr Dvořák
- Department of Botany, Faculty of Science, Palacký University Olomouc, Šlechtitelů 27, CZ-78371 Olomouc, Czech Republic;
| | - Alisa Tugai
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Corrensstrasse 3, 06466 Seeland, Germany; (T.R.); (A.T.); (A.H.)
| | - Klara Ptošková
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Hana for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-77900 Olomouc, Czech Republic; (K.P.); (B.P.); (J.D.)
| | - Beáta Petrovská
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Hana for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-77900 Olomouc, Czech Republic; (K.P.); (B.P.); (J.D.)
| | - Daniel van Damme
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium;
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Andreas Houben
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Corrensstrasse 3, 06466 Seeland, Germany; (T.R.); (A.T.); (A.H.)
| | - Jaroslav Doležel
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Hana for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-77900 Olomouc, Czech Republic; (K.P.); (B.P.); (J.D.)
| | - Dmitri Demidov
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Corrensstrasse 3, 06466 Seeland, Germany; (T.R.); (A.T.); (A.H.)
- Correspondence: (E.D.T.); (D.D.); Tel.: +420-585-238-725 (E.D.T.); +49-394825-733 (D.D.)
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Torres-Martínez HH, Rodríguez-Alonso G, Shishkova S, Dubrovsky JG. Lateral Root Primordium Morphogenesis in Angiosperms. FRONTIERS IN PLANT SCIENCE 2019; 10:206. [PMID: 30941149 PMCID: PMC6433717 DOI: 10.3389/fpls.2019.00206] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 02/07/2019] [Indexed: 05/14/2023]
Abstract
Morphogenetic processes are the basis of new organ formation. Lateral roots (LRs) are the building blocks of the root system. After LR initiation and before LR emergence, a new lateral root primordium (LRP) forms. During this period, the organization and functionality of the prospective LR is defined. Thus, proper LRP morphogenesis is a decisive process during root system formation. Most current studies on LRP morphogenesis have been performed in the model species Arabidopsis thaliana; little is known about this process in other angiosperms. To understand LRP morphogenesis from a wider perspective, we review both contemporary and earlier studies. The latter are largely forgotten, and we attempted to integrate them into present-day research. In particular, we consider in detail the participation of parent root tissue in LRP formation, cell proliferation and timing during LRP morphogenesis, and the hormonal and genetic regulation of LRP morphogenesis. Cell type identity acquisition and new stem cell establishement during LRP morphogenesis are also considered. Within each of these facets, unanswered or poorly understood questions are identified to help define future research in the field. Finally, we discuss emerging research avenues and new technologies that could be used to answer the remaining questions in studies of LRP morphogenesis.
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Affiliation(s)
| | | | | | - Joseph G. Dubrovsky
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
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Demidov D, Heckmann S, Weiss O, Rutten T, Dvořák Tomaštíková E, Kuhlmann M, Scholl P, Municio CM, Lermontova I, Houben A. Deregulated Phosphorylation of CENH3 at Ser65 Affects the Development of Floral Meristems in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2019; 10:928. [PMID: 31404279 PMCID: PMC6671561 DOI: 10.3389/fpls.2019.00928] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 07/02/2019] [Indexed: 05/03/2023]
Abstract
Several histone variants are posttranslationally phosphorylated. Little is known about phosphorylation of the centromere-specific histone 3 (CENH3) variant in plants. We show that CENH3 of Arabidopsis thaliana is phosphorylated in vitro by Aurora3, predominantly at serine 65. Interaction of Aurora3 and CENH3 was found by immunoprecipitation (IP) in A. thaliana and by bimolecular fluorescence complementation. Western blotting with an anti-CENH3 pS65 antibody showed that CENH3 pS65 is more abundant in flower buds than elsewhere in the plant. Substitution of serine 65 by either alanine or aspartic acid resulted in a range of phenotypic abnormalities, especially in reproductive tissues. We conclude that Aurora3 phosphorylates CENH3 at S65 and that this post-translational modification is required for the proper development of the floral meristem.
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Affiliation(s)
- Dmitri Demidov
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
- *Correspondence: Dmitri Demidov,
| | - Stefan Heckmann
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Oda Weiss
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Twan Rutten
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Eva Dvořák Tomaštíková
- Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany Academy of Sciences, Olomouc, Czechia
- Department of Plant Biology, Uppsala BioCenter and Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Markus Kuhlmann
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Patrick Scholl
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
- Independent Researcher, Plankstadt, Germany
| | - Celia Maria Municio
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Inna Lermontova
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Andreas Houben
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
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Baerenfaller K, Shu H, Hirsch-Hoffmann M, Fütterer J, Opitz L, Rehrauer H, Hennig L, Gruissem W. Diurnal changes in the histone H3 signature H3K9ac|H3K27ac|H3S28p are associated with diurnal gene expression in Arabidopsis. PLANT, CELL & ENVIRONMENT 2016; 39:2557-2569. [PMID: 27487196 DOI: 10.1111/pce.12811] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Revised: 07/26/2016] [Accepted: 07/27/2016] [Indexed: 05/18/2023]
Abstract
Post-translational chromatin modifications are an important regulatory mechanism in light signalling and circadian clock function. The regulation of diurnal transcript level changes requires fine-tuning of the expression of generally active genes depending on the prevailing environmental conditions. We investigated the association of histone modifications H3K4me3, H3K9ac, H3K9me2, H3S10p, H3K27ac, H3K27me3 and H3S28p with diurnal changes in transcript expression using chromatin immunoprecipitations followed by sequencing (ChIP-Seq) in fully expanded leaves 6 of Arabidopsis thaliana grown in short-day optimal and water-deficit conditions. We identified a differential H3K9ac, H3K27ac and H3S28p signature between end-of-day and end-of-night that is correlated with changes in diurnal transcript levels. Genes with this signature have particular over-represented promoter elements and encode proteins that are significantly enriched for transcription factors, circadian clock and starch catabolic process. Additional activating modifications were prevalent in optimally watered (H3S10p) and in water-deficit (H3K4me3) plants. The data suggest a mechanism for diurnal transcript level regulation in which reduced binding of repressive transcription factors facilitates activating H3K9ac, H3K27ac and H3S28p chromatin modifications. The presence of activating chromatin modification patterns on genes only at times of the day when their expression is required can explain why some genes are differentially inducible during the diurnal cycle.
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Affiliation(s)
| | - Huan Shu
- Department of Biology, ETH Zurich, Zurich, 8092, Switzerland
- Program of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | | | | | - Lennart Opitz
- Functional Genomics Center Zurich, ETH Zurich/University of Zurich, Zurich, 8057, Switzerland
| | - Hubert Rehrauer
- Functional Genomics Center Zurich, ETH Zurich/University of Zurich, Zurich, 8057, Switzerland
| | - Lars Hennig
- Department of Plant Biology, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, SE-75007, Sweden
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Accurate Chromosome Segregation at First Meiotic Division Requires AGO4, a Protein Involved in RNA-Dependent DNA Methylation in Arabidopsis thaliana. Genetics 2016; 204:543-553. [PMID: 27466226 DOI: 10.1534/genetics.116.189217] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 07/25/2016] [Indexed: 11/18/2022] Open
Abstract
The RNA-directed DNA methylation (RdDM) pathway is important for the transcriptional repression of transposable elements and for heterochromatin formation. Small RNAs are key players in this process by regulating both DNA and histone methylation. Taking into account that methylation underlies gene silencing and that there are genes with meiosis-specific expression profiles, we have wondered whether genes involved in RdDM could play a role during this specialized cell division. To address this issue, we have characterized meiosis progression in pollen mother cells from Arabidopsis thaliana mutant plants defective for several proteins related to RdDM. The most relevant results were obtained for ago4-1 In this mutant, meiocytes display a slight reduction in chiasma frequency, alterations in chromatin conformation around centromeric regions, lagging chromosomes at anaphase I, and defects in spindle organization. These abnormalities lead to the formation of polyads instead of tetrads at the end of meiosis, and might be responsible for the fertility defects observed in this mutant. Findings reported here highlight an involvement of AGO4 during meiosis by ensuring accurate chromosome segregation at anaphase I.
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11
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Lin S, Yuan ZF, Han Y, Marchione DM, Garcia BA. Preferential Phosphorylation on Old Histones during Early Mitosis in Human Cells. J Biol Chem 2016; 291:15342-57. [PMID: 27226594 DOI: 10.1074/jbc.m116.726067] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Indexed: 12/25/2022] Open
Abstract
How histone post-translational modifications (PTMs) are inherited through the cell cycle remains poorly understood. Canonical histones are made in the S phase of the cell cycle. Combining mass spectrometry-based technologies and stable isotope labeling by amino acids in cell culture, we question the distribution of multiple histone PTMs on old versus new histones in synchronized human cells. We show that histone PTMs can be grouped into three categories according to their distributions. Most lysine mono-methylation and acetylation PTMs are either symmetrically distributed on old and new histones or are enriched on new histones. In contrast, most di- and tri-methylation PTMs are enriched on old histones, suggesting that the inheritance of different PTMs is regulated distinctly. Intriguingly, old and new histones are distinct in their phosphorylation status during early mitosis in the following three human cell types: HeLa, 293T, and human foreskin fibroblast cells. The mitotic hallmark H3S10ph is predominantly associated with old H3 at early mitosis and becomes symmetric with the progression of mitosis. This same distribution was observed with other mitotic phosphorylation marks, including H3T3/T6ph, H3.1/2S28ph, and H1.4S26ph but not S28/S31ph on the H3 variant H3.3. Although H3S10ph often associates with the neighboring Lys-9 di- or tri-methylations, they are not required for the asymmetric distribution of Ser-10 phosphorylation on the same H3 tail. Inhibition of the kinase Aurora B does not change the distribution despite significant reduction of H3S10ph levels. However, K9me2 abundance on the new H3 is significantly reduced after Aurora B inhibition, suggesting a cross-talk between H3S10ph and H3K9me2.
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Affiliation(s)
- Shu Lin
- From the Epigenetics Program, Department of Biochemistry and Biophysics, and
| | - Zuo-Fei Yuan
- From the Epigenetics Program, Department of Biochemistry and Biophysics, and
| | - Yumiao Han
- From the Epigenetics Program, Department of Biochemistry and Biophysics, and
| | - Dylan M Marchione
- the Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Benjamin A Garcia
- From the Epigenetics Program, Department of Biochemistry and Biophysics, and
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12
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Neumann P, Schubert V, Fuková I, Manning JE, Houben A, Macas J. Epigenetic Histone Marks of Extended Meta-Polycentric Centromeres of Lathyrus and Pisum Chromosomes. FRONTIERS IN PLANT SCIENCE 2016; 7:234. [PMID: 26973677 PMCID: PMC4771749 DOI: 10.3389/fpls.2016.00234] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 02/11/2016] [Indexed: 05/19/2023]
Abstract
Species of the legume genera Lathyrus and Pisum possess chromosomes that exhibit a unique structure of their centromeric regions, which is clearly apparent during metaphase by the formation of extended primary constrictions which span up to a third of the length of the chromosome. In addition, these species express two different variants of the CenH3 protein which are co-localized in multiple domains along the poleward surface of the primary constrictions. Here, we show that the constrictions represent a distinct type of chromatin differing from the chromosome arms. In metaphase, histone phosphorylation patterns including H3S10ph, H3S28ph, and H3T3ph were observed along the entire constriction, in a way similar to holocentric chromosomes. On the other hand, distribution of phosphorylated H2AT120 was different from that previously reported from either, holocentric and monocentric chromosomes, occurring at chromatin surrounding but not overlapping CenH3 domains. Since some of these phosphorylations play a role in chromatid cohesion, it can be assumed that they facilitate correct chromosome segregation by ensuring that multiple separate CenH3 domains present on the same chromatid are oriented toward the same pole. The constrictions also displayed distinct patterns of histone methylation marks, being enriched in H3K9me2 and depleted in H3K4me3 and H3K27me2 compared to the chromosome arms. Super-resolution fluorescence microscopy revealed that although both CenH3 protein variants are present in all CenH3 domains detected on metaphase chromosomes, they are only partially co-localized while there are chromatin subdomains which are mostly made of only one CenH3 variant. Taken together, these data revealed specific features of extended primary constrictions of Lathyrus and Pisum and support the idea that they may represent an intermediate stage between monocentric and holocentric chromosomes.
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Affiliation(s)
- Pavel Neumann
- Laboratory of Molecular Cytogenetics, Biology Centre of the Czech Academy of Sciences, Institute of Plant Molecular BiologyČeské Budějovice, Czech Republic
| | - Veit Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Gatersleben, Germany
| | - Iva Fuková
- Laboratory of Molecular Cytogenetics, Biology Centre of the Czech Academy of Sciences, Institute of Plant Molecular BiologyČeské Budějovice, Czech Republic
| | - Jasper E. Manning
- Laboratory of Molecular Cytogenetics, Biology Centre of the Czech Academy of Sciences, Institute of Plant Molecular BiologyČeské Budějovice, Czech Republic
| | - Andreas Houben
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Gatersleben, Germany
| | - Jiří Macas
- Laboratory of Molecular Cytogenetics, Biology Centre of the Czech Academy of Sciences, Institute of Plant Molecular BiologyČeské Budějovice, Czech Republic
- *Correspondence: Jiří Macas
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13
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Weimer AK, Demidov D, Lermontova I, Beeckman T, Van Damme D. Aurora Kinases Throughout Plant Development. TRENDS IN PLANT SCIENCE 2016; 21:69-79. [PMID: 26616196 DOI: 10.1016/j.tplants.2015.10.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Revised: 09/10/2015] [Accepted: 10/02/2015] [Indexed: 06/05/2023]
Abstract
Aurora kinases are evolutionarily conserved key mitotic determinants in all eukaryotes. Yeasts contain a single Aurora kinase, whereas multicellular eukaryotes have at least two functionally diverged members. The involvement of Aurora kinases in human cancers has provided an in-depth mechanistic understanding of their roles throughout cell division in animal and yeast models. By contrast, understanding Aurora kinase function in plants is only starting to emerge. Nevertheless, genetic, cell biological, and biochemical approaches have revealed functional diversification between the plant Aurora kinases and suggest a role in formative (asymmetric) divisions, chromatin modification, and genome stability. This review provides an overview of the accumulated knowledge on the function of plant Aurora kinases as well as some major challenges for the future.
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Affiliation(s)
- Annika K Weimer
- Department of Plant Systems Biology, Flanders Institute for Biotechnology (VIB), 9052 Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Dmitri Demidov
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Stadt Seeland, 06466 Germany
| | - Inna Lermontova
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Stadt Seeland, 06466 Germany
| | - Tom Beeckman
- Department of Plant Systems Biology, Flanders Institute for Biotechnology (VIB), 9052 Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Daniël Van Damme
- Department of Plant Systems Biology, Flanders Institute for Biotechnology (VIB), 9052 Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium.
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14
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Takatani S, Otani K, Kanazawa M, Takahashi T, Motose H. Structure, function, and evolution of plant NIMA-related kinases: implication for phosphorylation-dependent microtubule regulation. JOURNAL OF PLANT RESEARCH 2015; 128:875-91. [PMID: 26354760 DOI: 10.1007/s10265-015-0751-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 08/20/2015] [Indexed: 05/25/2023]
Abstract
Microtubules are highly dynamic structures that control the spatiotemporal pattern of cell growth and division. Microtubule dynamics are regulated by reversible protein phosphorylation involving both protein kinases and phosphatases. Never in mitosis A (NIMA)-related kinases (NEKs) are a family of serine/threonine kinases that regulate microtubule-related mitotic events in fungi and animal cells (e.g. centrosome separation and spindle formation). Although plants contain multiple members of the NEK family, their functions remain elusive. Recent studies revealed that NEK6 of Arabidopsis thaliana regulates cell expansion and morphogenesis through β-tubulin phosphorylation and microtubule destabilization. In addition, plant NEK members participate in organ development and stress responses. The present phylogenetic analysis indicates that plant NEK genes are diverged from a single NEK6-like gene, which may share a common ancestor with other kinases involved in the control of microtubule organization. On the contrary, another mitotic kinase, polo-like kinase, might have been lost during the evolution of land plants. We propose that plant NEK members have acquired novel functions to regulate cell growth, microtubule organization, and stress responses.
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Affiliation(s)
- Shogo Takatani
- Division of Bioscience, Graduate School of Natural Science and Technology, Okayama University, Tsushimanaka 3-1-1, Okayama, 700-8530, Japan
| | - Kento Otani
- Division of Bioscience, Graduate School of Natural Science and Technology, Okayama University, Tsushimanaka 3-1-1, Okayama, 700-8530, Japan
| | - Mai Kanazawa
- Department of Biology, Faculty of Science, Okayama University, Tsushimanaka 3-1-1, Okayama, 700-8530, Japan
| | - Taku Takahashi
- Division of Bioscience, Graduate School of Natural Science and Technology, Okayama University, Tsushimanaka 3-1-1, Okayama, 700-8530, Japan
- Department of Biology, Faculty of Science, Okayama University, Tsushimanaka 3-1-1, Okayama, 700-8530, Japan
| | - Hiroyasu Motose
- Division of Bioscience, Graduate School of Natural Science and Technology, Okayama University, Tsushimanaka 3-1-1, Okayama, 700-8530, Japan.
- Department of Biology, Faculty of Science, Okayama University, Tsushimanaka 3-1-1, Okayama, 700-8530, Japan.
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15
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Abstract
Plant kinases are one of the largest protein families in Arabidopsis. There are almost 600 membrane-located receptor kinases and almost 400 soluble kinases with distinct functions in signal transduction. In this minireview we discuss phylogeny and functional context of prominent members from major protein kinase subfamilies in plants.
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Affiliation(s)
- Monika Zulawski
- Max Planck Institute of molecular Plant Physiology, 14470, Potsdam, Germany
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16
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Demidov D, Lermontova I, Weiss O, Fuchs J, Rutten T, Kumke K, Sharbel TF, Van Damme D, De Storme N, Geelen D, Houben A. Altered expression of Aurora kinases in Arabidopsis results in aneu- and polyploidization. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 80:449-61. [PMID: 25146886 DOI: 10.1111/tpj.12647] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Revised: 08/11/2014] [Accepted: 08/14/2014] [Indexed: 05/20/2023]
Abstract
Aurora is an evolutionary conserved protein kinase family involved in monitoring of chromosome segregation via phosphorylation of different substrates. In plants, however, the involvement of Aurora proteins in meiosis and in sensing microtubule attachment remains to be proven, although the downstream components leading to the targeting of spindle assembly checkpoint signals to anaphase-promoting complex have been described. To analyze the three members of Aurora family (AtAurora1, -2, and -3) of Arabidopsis we employed different combinations of T-DNA insertion mutants and/or RNAi transformants. Meiotic defects and the formation of unreduced pollen were revealed including plants with an increased ploidy level. The effect of reduced expression of Aurora was mimicked by application of the ATP-competitive Aurora inhibitor II. In addition, strong overexpression of any member of the AtAurora family is not possible. Only tagged or truncated forms of Aurora kinases can be overexpressed. Expression of truncated AtAurora1 resulted in a high number of aneuploids in Arabidopsis, while expression of AtAurora1-TAPi construct in tobacco resulted in 4C (possible tetraploid) progeny. In conclusion, our data demonstrate an essential role of Aurora kinases in the monitoring of meiosis in plants.
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Affiliation(s)
- Dmitri Demidov
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, 06466, Gatersleben, Germany
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17
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Rybaczek D. Ultrastructural changes associated with the induction of premature chromosome condensation in Vicia faba root meristem cells. PLANT CELL REPORTS 2014; 33:1547-1564. [PMID: 24898011 PMCID: PMC4133037 DOI: 10.1007/s00299-014-1637-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2014] [Revised: 05/15/2014] [Accepted: 05/19/2014] [Indexed: 06/03/2023]
Abstract
PCC induction is regulated by several signaling pathways, and all observed effects associated with PCC induction are strongly dependent on the mechanism of action of each PCC inducer used. Electron microscopic observations of cells with symptoms of premature chromosome condensation (PCC) showed that the interphase chromatin and mitotic chromosomes differed with respect to a chemical compound inducing PCC. Induction of this process under the influence of hydroxyurea and caffeine as well as hydroxyurea and sodium metavanadate led to a slight decrease in interphase chromatin condensation and the formation of chromosomes with a considerably loosened structure in comparison with the control. Incubation in the mixture of hydroxyurea and 2-aminopurine brought about clear chromatin dispersion in interphase and very strong mitotic chromosome condensation. Electron microscopic examinations also revealed the characteristic features of the structural organization of cytoplasm of Vicia faba root meristems, which seemed to be dependent on the type of the PCC inducer used. The presence of the following was observed: (i) large plastids filled with starch grains (caffeine), (ii) mitochondria and plastids of electron dense matrix with dilated invaginations of their internal membranes (2-aminopurine), and (iii) large mitochondria of electron clear matrix and plastids containing protein crystals in their interior (sodium metavanadate). Moreover, since caffeine causes either the most effective loosening of chromatin fibrils (within the prematurely condensed chromosomes) or induction of starch formation (in the plastids surrounding the nuclei), this may be a proof that demonstrates the existence of a link between physical accessibility to chromatin and the effectiveness of cellular signaling (e.g., phosphothreonine-connected).
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Affiliation(s)
- Dorota Rybaczek
- Department of Cytophysiology, Institute of Experimental Biology, Faculty of Biology and Environmental Protection, University of Łódź, Pomorska 141/143, 90-236, Lodz, Poland,
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18
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Bigeard J, Rayapuram N, Pflieger D, Hirt H. Phosphorylation-dependent regulation of plant chromatin and chromatin-associated proteins. Proteomics 2014; 14:2127-40. [PMID: 24889195 DOI: 10.1002/pmic.201400073] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Revised: 04/28/2014] [Accepted: 05/26/2014] [Indexed: 12/25/2022]
Abstract
In eukaryotes, most of the DNA is located in the nucleus where it is organized with histone proteins in a higher order structure as chromatin. Chromatin and chromatin-associated proteins contribute to DNA-related processes such as replication and transcription as well as epigenetic regulation. Protein functions are often regulated by PTMs among which phosphorylation is one of the most abundant PTM. Phosphorylation of proteins affects important properties, such as enzyme activity, protein stability, or subcellular localization. We here describe the main specificities of protein phosphorylation in plants and review the current knowledge on phosphorylation-dependent regulation of plant chromatin and chromatin-associated proteins. We also outline some future challenges to further elucidate protein phosphorylation and chromatin regulation.
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Affiliation(s)
- Jean Bigeard
- Unité de Recherche en Génomique Végétale (URGV), UMR INRA/CNRS/Université d'Evry Val d'Essonne/Saclay Plant Sciences, Evry, France
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19
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Zhang B, Dong Q, Su H, Birchler JA, Han F. Histone phosphorylation: its role during cell cycle and centromere identity in plants. Cytogenet Genome Res 2014; 143:144-9. [PMID: 24713809 DOI: 10.1159/000360435] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
As the main protein components of chromatin, histones can alter the structural/functional capabilities of chromatin by undergoing extensive post-translational modifications (PTMs) such as phosphorylation, methylation, acetylation, ubiquitination, sumoylation, and so on. These PTMs are thought to transmit signals from the chromatin to the cell machinery to regulate various processes. Histone phosphorylation is associated with chromosome condensation/segregation, activation of transcription, and DNA damage repair. In this review, we focus on how different histone phosphorylations mark for chromatin change during the cell cycle, the relationship between histone phosphorylation and functional centromeres, and the candidate kinases that trigger and the phosphatase or kinase inhibitors that alter histone phosphorylation. Finally, we review the crosstalk between different PTMs.
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Affiliation(s)
- B Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
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20
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Desvoyes B, Fernández-Marcos M, Sequeira-Mendes J, Otero S, Vergara Z, Gutierrez C. Looking at plant cell cycle from the chromatin window. FRONTIERS IN PLANT SCIENCE 2014; 5:369. [PMID: 25120553 PMCID: PMC4110626 DOI: 10.3389/fpls.2014.00369] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Accepted: 07/11/2014] [Indexed: 05/03/2023]
Abstract
The cell cycle is defined by a series of complex events, finely coordinated through hormonal, developmental and environmental signals, which occur in a unidirectional manner and end up in producing two daughter cells. Accumulating evidence reveals that chromatin is not a static entity throughout the cell cycle. In fact, there are many changes that include nucleosome remodeling, histone modifications, deposition and exchange, among others. Interestingly, it is possible to correlate the occurrence of several of these chromatin-related events with specific processes necessary for cell cycle progression, e.g., licensing of DNA replication origins, the E2F-dependent transcriptional wave in G1, the activation of replication origins in S-phase, the G2-specific transcription of genes required for mitosis or the chromatin packaging occurring in mitosis. Therefore, an emerging view is that chromatin dynamics must be considered as an intrinsic part of cell cycle regulation. In this article, we review the main features of several key chromatin events that occur at defined times throughout the cell cycle and discuss whether they are actually controlling the transit through specific cell cycle stages.
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Affiliation(s)
| | | | | | | | | | - Crisanto Gutierrez
- *Correspondence: Crisanto Gutierrez, Centro de Biologia Molecular Severo Ochoa, Consejo Superior de Investigaciones Cientificas, Universidad Autónoma de Madrid, Nicolas Cabrera 1, Cantoblanco, Madrid 28049, Spain e-mail:
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21
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McMichael CM, Bednarek SY. Cytoskeletal and membrane dynamics during higher plant cytokinesis. THE NEW PHYTOLOGIST 2013; 197:1039-1057. [PMID: 23343343 DOI: 10.1111/nph.12122] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2012] [Accepted: 12/02/2012] [Indexed: 05/08/2023]
Abstract
Following mitosis, cytoplasm, organelles and genetic material are partitioned into daughter cells through the process of cytokinesis. In somatic cells of higher plants, two cytoskeletal arrays, the preprophase band and the phragmoplast, facilitate the positioning and de novo assembly of the plant-specific cytokinetic organelle, the cell plate, which develops across the division plane and fuses with the parental plasma membrane to yield distinct new cells. The coordination of cytoskeletal and membrane dynamics required to initiate, assemble and shape the cell plate as it grows toward the mother cell cortex is dependent upon a large array of proteins, including molecular motors, membrane tethering, fusion and restructuring factors and biosynthetic, structural and regulatory elements. This review focuses on the temporal and molecular requirements of cytokinesis in somatic cells of higher plants gleaned from recent studies using cell biology, genetics, pharmacology and biochemistry.
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Affiliation(s)
- Colleen M McMichael
- Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Dr, Madison, WI, 53713, USA
| | - Sebastian Y Bednarek
- Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Dr, Madison, WI, 53713, USA
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22
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Kurihara D, Hamamura Y, Higashiyama T. Live-cell analysis of plant reproduction: Live-cell imaging, optical manipulation, and advanced microscopy technologies. Dev Growth Differ 2013; 55:462-73. [DOI: 10.1111/dgd.12040] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Revised: 12/29/2012] [Accepted: 01/04/2013] [Indexed: 02/05/2023]
Affiliation(s)
| | - Yuki Hamamura
- Division of Biological Science; Graduate School of Science; Furo-cho, Chikusa-ku; Nagoya; Aichi; 464-8602; Japan
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23
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Bräutigam K, Vining KJ, Lafon-Placette C, Fossdal CG, Mirouze M, Marcos JG, Fluch S, Fraga MF, Guevara MÁ, Abarca D, Johnsen Ø, Maury S, Strauss SH, Campbell MM, Rohde A, Díaz-Sala C, Cervera MT. Epigenetic regulation of adaptive responses of forest tree species to the environment. Ecol Evol 2013; 3:399-415. [PMID: 23467802 PMCID: PMC3586649 DOI: 10.1002/ece3.461] [Citation(s) in RCA: 222] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Revised: 11/19/2012] [Accepted: 11/27/2012] [Indexed: 12/25/2022] Open
Abstract
Epigenetic variation is likely to contribute to the phenotypic plasticity and adaptative capacity of plant species, and may be especially important for long-lived organisms with complex life cycles, including forest trees. Diverse environmental stresses and hybridization/polyploidization events can create reversible heritable epigenetic marks that can be transmitted to subsequent generations as a form of molecular "memory". Epigenetic changes might also contribute to the ability of plants to colonize or persist in variable environments. In this review, we provide an overview of recent data on epigenetic mechanisms involved in developmental processes and responses to environmental cues in plant, with a focus on forest tree species. We consider the possible role of forest tree epigenetics as a new source of adaptive traits in plant breeding, biotechnology, and ecosystem conservation under rapid climate change.
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Affiliation(s)
- Katharina Bräutigam
- Centre for the Analysis of Genome Evolution and Function, Department of Cell & Systems Biology, University of TorontoToronto, ON, M5S 3B2, Canada
| | - Kelly J Vining
- Department of Forest Ecosystems and Society, Oregon State UniversityCorvallis, OR, 97331-5752, USA
| | - Clément Lafon-Placette
- UFR-Faculté des Sciences, UPRES EA 1207 ‘Laboratoire de Biologie des Ligneux et des Grandes Cultures’ (LBLGC), INRA, USC1328 ‘Arbres et Réponses aux Contraintes Hydrique et Environnementales’ (ARCHE), University of OrléansRue de Chartres, BP 6759, F-45067, Orléans, France
| | - Carl G Fossdal
- Department of Biology and Environment, Norwegian Forest and Landscape InstitutePO Box 115, N-1431, Aas, Norway
| | - Marie Mirouze
- Epigenetic Regulations and Seed Development, Institut de Recherche pour le Développement, UMR232 ERL5300 CNRS-IRD911 Av. Agropolis, 34394, Montpellier, France
| | - José Gutiérrez Marcos
- School of Life Sciences, University of WarwickWellesbourne, Warkwick, CV35 9EF, United Kingdom
| | - Silvia Fluch
- Platform for Integrated Clone Management (PICME), Health & Environment Department, AIT Austrian Institute of Technology GmbHKonrad-Lorenz-Straße 24, 3430, Tulln, Austria
| | - Mario Fernández Fraga
- Cancer Epigenetics Laboratory, Institute of Oncology of Asturias (IUOPA–HUCA), University of OviedoSpain
| | - M Ángeles Guevara
- Dpt. of Forest Ecology and Genetics, Forest Genomics and Ecophysiology group, Forest Research Centre (CIFOR). INIACrta. La Coruña km 7,5, 28040, Madrid, Spain
- Mixed Unit of Forest Genomics and Ecophysiology, INIA/UPMMadrid, Spain
| | - Dolores Abarca
- Department of Life Sciences, University of AlcaláCtra. Madrid-Barcelona Km. 33,600, 28871, Alcalá de Henares, Madrid, Spain
| | - Øystein Johnsen
- Department of Plant and Environmental Sciences, Norwegian University of Life SciencesPO Box 5003, N-1432, Ås, Norway
| | - Stéphane Maury
- UFR-Faculté des Sciences, UPRES EA 1207 ‘Laboratoire de Biologie des Ligneux et des Grandes Cultures’ (LBLGC), INRA, USC1328 ‘Arbres et Réponses aux Contraintes Hydrique et Environnementales’ (ARCHE), University of OrléansRue de Chartres, BP 6759, F-45067, Orléans, France
| | - Steven H Strauss
- Department of Forest Ecosystems and Society, Oregon State UniversityCorvallis, OR, 97331-5752, USA
| | - Malcolm M Campbell
- Centre for the Analysis of Genome Evolution and Function, Department of Cell & Systems Biology, University of TorontoToronto, ON, M5S 3B2, Canada
- Department of Biological Sciences, University of Toronto Scarborough, University of Toronto1265 Military Trail, Toronto, ON, M1C 1A4, Canada
| | - Antje Rohde
- Department Plant Growth & Development, Institute of Agriculture and Fisheries ResearchCaritasstraat 21, 9090, Melle, Belgium
| | - Carmen Díaz-Sala
- Department of Life Sciences, University of AlcaláCtra. Madrid-Barcelona Km. 33,600, 28871, Alcalá de Henares, Madrid, Spain
| | - María-Teresa Cervera
- Dpt. of Forest Ecology and Genetics, Forest Genomics and Ecophysiology group, Forest Research Centre (CIFOR). INIACrta. La Coruña km 7,5, 28040, Madrid, Spain
- Mixed Unit of Forest Genomics and Ecophysiology, INIA/UPMMadrid, Spain
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25
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Matsunaga S, Katagiri Y, Nagashima Y, Sugiyama T, Hasegawa J, Hayashi K, Sakamoto T. New insights into the dynamics of plant cell nuclei and chromosomes. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2013; 305:253-301. [PMID: 23890384 DOI: 10.1016/b978-0-12-407695-2.00006-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The plant lamin-like protein NMCP/AtLINC and orthologues of the SUN-KASH complex across the nuclear envelope (NE) show the universality of nuclear structure in eukaryotes. However, depletion of components in the connection complex of the NE in plants does not induce severe defects, unlike in animals. Appearance of the Rabl configuration is not dependent on genome size in plant species. Topoisomerase II and condensin II are not essential for plant chromosome condensation. Plant endoreduplication shares several common characteristics with animals, including involvement of cyclin-dependent kinases and E2F transcription factors. Recent finding regarding endomitosis regulator GIG1 shed light on the suppression mechanism of endomitosis in plants. The robustness of plants, compared with animals, is reflected in their genome redundancy. Spatiotemporal functional analyses using chromophore-assisted light inactivation, super-resolution microscopy, and 4D (3D plus time) imaging will reveal new insights into plant nuclear and chromosomal dynamics.
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Affiliation(s)
- Sachihiro Matsunaga
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Noda, Chiba, Japan.
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Petrovská B, Cenklová V, Pochylová Ž, Kourová H, Doskočilová A, Plíhal O, Binarová L, Binarová P. Plant Aurora kinases play a role in maintenance of primary meristems and control of endoreduplication. THE NEW PHYTOLOGIST 2012; 193:590-604. [PMID: 22150830 DOI: 10.1111/j.1469-8137.2011.03989.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
• The conserved family of Aurora kinases has multiple functions during mitosis. The roles of plant Aurora kinases have been characterized using inhibitor treatments. • We down-regulated Aurora kinases in Arabidopsis thaliana using RNA interference (RNAi). We carried out a detailed phenotypic analysis of Aurora RNAi plants, biochemical and microscopic studies of AtAurora1 kinase together with AtTPX2 (targeting protein for Xklp2) and γ-tubulin. • Cell division defects were observed in plants with reduced expression of Aurora kinases. Furthermore, the maintenance of primary meristems was compromised and RNAi seedlings entered endoreduplication prematurely. AtAurora1, its activator AtTPX2, and γ-tubulin were associated with microtubules in vitro; they were attached to regrowing kinetochore microtubules and colocalized on spindle microtubules and with a subset of early phragmoplast microtubules. Only the AtAurora1 kinase was translocated to the area of the cell plate. • RNAi silencing of Aurora kinases showed that, in addition to their function in regulating mitosis, the kinases are required for maintaining meristematic activity and controlling the switch from meristematic cell proliferation to differentiation and endoreduplication. The colocalization and co-fractionation of AtAurora1 with AtTPX2, and γ-tubulin on microtubules in a cell cycle-specific manner suggests that AtAurora1 kinase may function to phosphorylate substrates that are critical to the spatiotemporal regulation of acentrosomal microtubule formation and organization.
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Affiliation(s)
- Beáta Petrovská
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany AS CR, v.v.i., Sokolovská 6, Olomouc 772 00, Czech Republic
| | - Věra Cenklová
- Institute of Experimental Botany, AS CR, v.v.i., Sokolovská 6, 772 00, Olomouc, Czech Republic
| | - Žaneta Pochylová
- Institute of Experimental Botany, AS CR, v.v.i., Sokolovská 6, 772 00, Olomouc, Czech Republic
| | - Hana Kourová
- Institute of Microbiology, AS CR, v.v.i., Vídeňská 1083, 142 20 Prague 4, Czech Republic
| | - Anna Doskočilová
- Institute of Microbiology, AS CR, v.v.i., Vídeňská 1083, 142 20 Prague 4, Czech Republic
| | - Ondřej Plíhal
- Institute of Microbiology, AS CR, v.v.i., Vídeňská 1083, 142 20 Prague 4, Czech Republic
| | - Lenka Binarová
- Institute of Experimental Botany, AS CR, v.v.i., Sokolovská 6, 772 00, Olomouc, Czech Republic
| | - Pavla Binarová
- Institute of Microbiology, AS CR, v.v.i., Vídeňská 1083, 142 20 Prague 4, Czech Republic
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Healy S, Khan P, He S, Davie JR. Histone H3 phosphorylation, immediate-early gene expression, and the nucleosomal response: a historical perspective1This article is part of Special Issue entitled Asilomar Chromatin and has undergone the Journal’s usual peer review process. Biochem Cell Biol 2012; 90:39-54. [DOI: 10.1139/o11-092] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Histone H3 is modified at serines 10 and 28 in interphase cells following activation of the RAS-MAPK or p38-MAPK pathways by growth factors or stress. These modifications are involved in the regulation of immediate-early genes, including Jun and Fos, whose increased expression is a trademark of various cancers. This review outlines the series of discoveries that led to the characterization of these modifications, the kinase, MSK1/2, which is activated by both MAPK pathways and directs phosphorylation of H3, and the mechanistic function of these modifications in transcriptional activation. Research examining the effect of deregulated MSK1/2 in human disorders, namely cancer, is evaluated. Recently, a number of reports proposed novel, intervening pathways leading to enrichment of phosphorylated serine 10 and 28 and the activation of MSK1/2. These novel pathways predict an even more complicated signalling mechanism for cell growth, apoptosis, and the immune response, suggesting that MSK1/2 is intrinsically responsible for an even greater number of biological processes. This review proposes that MSK1/2 is an optimal target for cancer therapy, based on its fundamental role in transmitting external signals into varied responses involved in cancer development.
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Affiliation(s)
- Shannon Healy
- MB Institute of Cell Biology, University of Manitoba, 675 McDermot Ave., Winnipeg, MB R3E 0V9, Canada
| | - Protiti Khan
- MB Institute of Cell Biology, University of Manitoba, 675 McDermot Ave., Winnipeg, MB R3E 0V9, Canada
| | - Shihua He
- MB Institute of Cell Biology, University of Manitoba, 675 McDermot Ave., Winnipeg, MB R3E 0V9, Canada
| | - James R. Davie
- MB Institute of Cell Biology, University of Manitoba, 675 McDermot Ave., Winnipeg, MB R3E 0V9, Canada
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28
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Raut VV, Sainis JK. 60Co-γ radiation induces differential acetylation and phosphorylation of histones H3 and H4 in wheat. PLANT BIOLOGY (STUTTGART, GERMANY) 2012; 14:110-117. [PMID: 21973290 DOI: 10.1111/j.1438-8677.2011.00463.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Histone modifications occur during DNA damage and repair in eukaryotes. These modifications were analysed in wheat seedlings exposed to (60) Co-γ radiation. Seedling height was not significantly affected in the first 2 days after irradiation up to 150 Gy. Subsequently, in the next 2 weeks, there was 30-40% reduction in seedling height, indicating that there were late effects of irradiation. The histones isolated from irradiated seedlings were analysed in the initial stages for modifications of H3 and H4 using antibodies. Global acetylation of H3 decreased and H4 increased in a dose-dependent manner till 100 Gy. The time course of individual modifications showed that for H3K4 and H3K9, acetylation decreased, whereas for H3S10 phosphorylation increased. There were fluctuations in acetylation of H4K5, H4K12 and H4K16, whereas H4K8 showed hyper-acetylation. The results indicate that γ radiation induced DNA damage and repair in wheat seedlings and initiated differential acetylation of H3 and H4. This is the first report in plants on site-specific H3 and H4 modifications in response to exposure to ionizing radiation.
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Affiliation(s)
- V V Raut
- Molecular Biology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, India
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Van Damme D, De Rybel B, Gudesblat G, Demidov D, Grunewald W, De Smet I, Houben A, Beeckman T, Russinova E. Arabidopsis α Aurora kinases function in formative cell division plane orientation. THE PLANT CELL 2011; 23:4013-24. [PMID: 22045917 PMCID: PMC3246319 DOI: 10.1105/tpc.111.089565] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2011] [Revised: 10/05/2011] [Accepted: 10/12/2011] [Indexed: 05/19/2023]
Abstract
To establish three-dimensional structures/organs, plant cells continuously have to adapt the orientation of their division plane in a highly regulated manner. However, mechanisms underlying switches in division plane orientation remain elusive. Here, we characterize a viable double knockdown mutant in Arabidopsis thaliana group α Aurora (AUR) kinases, AUR1 and AUR2, (aur1-2 aur2-2), with a primary defect in lateral root formation and outgrowth. Mutant analysis revealed that aur1-2 aur2-2 lateral root primordia are built from randomly oriented cell divisions instead of distinct cell layers. This phenotype could be traced back to cytokinesis defects and misoriented cell plates during the initial anticlinal pericycle cell divisions that give rise to lateral root primordia. Complementation assays showed that the Arabidopsis α group Aurora kinases are functionally divergent from the single β group member AUR3 and that AUR1 functions in division plane orientation prior to cytokinesis. In addition to defective lateral root patterning, aur1-2 aur2-2 plants also show defects in orienting formative divisions during embryogenesis, divisions surrounding the main root stem cell niche, and divisions surrounding stomata formation. Taken together, our results put forward a central role for α Aurora kinases in regulating formative division plane orientation throughout development.
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Affiliation(s)
- Daniël Van Damme
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium.
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30
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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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Kurihara D, Matsunaga S, Omura T, Higashiyama T, Fukui K. Identification and characterization of plant Haspin kinase as a histone H3 threonine kinase. BMC PLANT BIOLOGY 2011; 11:73. [PMID: 21527018 PMCID: PMC3113928 DOI: 10.1186/1471-2229-11-73] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2011] [Accepted: 04/28/2011] [Indexed: 05/08/2023]
Abstract
BACKGROUND Haspin kinases are mitotic kinases that are well-conserved from yeast to human. Human Haspin is a histone H3 Thr3 kinase that has important roles in chromosome cohesion during mitosis. Moreover, phosphorylation of histone H3 at Thr3 by Haspin in fission yeast, Xenopus, and human is required for accumulation of Aurora B on the centromere, and the subsequent activation of Aurora B kinase activity for accurate chromosome alignment and segregation. Although extensive analyses of Haspin have been carried out in yeast and animals, the function of Haspin in organogenesis remains unclear. RESULTS Here, we identified a Haspin kinase, designated AtHaspin, in Arabidopsis thaliana. The purified AtHaspin phosphorylated histone H3 at both Thr3 and Thr11 in vitro. Live imaging of AtHaspin-tdTomato and GFP-α-tubulin in BY-2 cells showed that AtHaspin-tdTomato localized on chromosomes during prometaphase and metaphase, and around the cell plate during cytokinesis. This localization of AtHaspin overlapped with that of phosphorylated Thr3 and Thr11 of histone H3 in BY-2 cells. AtHaspin-GFP driven by the native promoter was expressed in root meristems, shoot meristems, floral meristems, and throughout the whole embryo at stages of high cell division. Overexpression of a kinase domain mutant of AtHaspin decreased the size of the root meristem, which delayed root growth. CONCLUSIONS Our results indicated that the Haspin kinase is a histone H3 threonine kinase in A. thaliana. AtHaspin phosphorylated histone H3 at both Thr3 and Thr11 in vitro. The expression and dominant-negative analysis showed that AtHaspin may have a role in mitotic cell division during plant growth. Further analysis of coordinated mechanisms involving Haspin and Aurora kinases will shed new light on the regulation of chromosome segregation in cell division during plant growth and development.
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Affiliation(s)
- Daisuke Kurihara
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan
- JST ERATO Higashiyama Live-Holonics Project, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan
| | - Sachihiro Matsunaga
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Tomohiro Omura
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Tetsuya Higashiyama
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan
- JST ERATO Higashiyama Live-Holonics Project, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan
| | - Kiichi Fukui
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
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Veiseth SV, Rahman MA, Yap KL, Fischer A, Egge-Jacobsen W, Reuter G, Zhou MM, Aalen RB, Thorstensen T. The SUVR4 histone lysine methyltransferase binds ubiquitin and converts H3K9me1 to H3K9me3 on transposon chromatin in Arabidopsis. PLoS Genet 2011; 7:e1001325. [PMID: 21423664 PMCID: PMC3053343 DOI: 10.1371/journal.pgen.1001325] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2010] [Accepted: 02/03/2011] [Indexed: 12/11/2022] Open
Abstract
Chromatin structure and gene expression are regulated by posttranslational modifications (PTMs) on the N-terminal tails of histones. Mono-, di-, or trimethylation of lysine residues by histone lysine methyltransferases (HKMTases) can have activating or repressive functions depending on the position and context of the modified lysine. In Arabidopsis, trimethylation of lysine 9 on histone H3 (H3K9me3) is mainly associated with euchromatin and transcribed genes, although low levels of this mark are also detected at transposons and repeat sequences. Besides the evolutionarily conserved SET domain which is responsible for enzyme activity, most HKMTases also contain additional domains which enable them to respond to other PTMs or cellular signals. Here we show that the N-terminal WIYLD domain of the Arabidopsis SUVR4 HKMTase binds ubiquitin and that the SUVR4 product specificity shifts from di- to trimethylation in the presence of free ubiquitin, enabling conversion of H3K9me1 to H3K9me3 in vitro. Chromatin immunoprecipitation and immunocytological analysis showed that SUVR4 in vivo specifically converts H3K9me1 to H3K9me3 at transposons and pseudogenes and has a locus-specific repressive effect on the expression of such elements. Bisulfite sequencing indicates that this repression involves both DNA methylation–dependent and –independent mechanisms. Transcribed genes with high endogenous levels of H3K4me3, H3K9me3, and H2Bub1, but low H3K9me1, are generally unaffected by SUVR4 activity. Our results imply that SUVR4 is involved in the epigenetic defense mechanism by trimethylating H3K9 to suppress potentially harmful transposon activity. The characteristics of the diverse cell types in multicellular organisms result from differential gene expression that is dependent on the level of DNA packaging. Genes that are essential for the function of the cell are expressed; while unessential genes, and DNA elements (transposons or “jumping genes”) that can move from one position to another within a genome and potentially cause deleterious mutations, are repressed. The mechanisms evolved in eukaryotes to avoid unwanted gene expression and transposon movement include DNA methylation and specific combinations of post translational modifications (PTMs) of the histones that package DNA. Here we show that the SUVR4 enzyme binds the signaling protein ubiquitin and that ubiquitin enables the enzyme to trimethylate lysine 9 (H3K9me3) of histone H3. In contrast to other reports demonstrating an activating role on expressed genes, we show that H3K9me3 has a locus-specific repressive effect on the expression of transposons. The specificity is maintained by the communication with other PTMs on transposons and euchromatic genes, which has a stimulating or repressing effect on enzyme activity, respectively. Our results demonstrate how repression of transcription can be restricted to specific targets and demonstrate that this repression involves a context-dependent read-out of different PTMs.
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Affiliation(s)
- Silje V. Veiseth
- Department of Molecular Biosciences, University of Oslo, Oslo, Norway
| | | | - Kyoko L. Yap
- Department of Structural and Chemical Biology, Mount Sinai School of Medicine, New York, New York, United States of America
| | - Andreas Fischer
- Institute of Biology, Developmental Genetics, Martin Luther University Halle, Halle, Germany
| | - Wolfgang Egge-Jacobsen
- Department of Molecular Biosciences, University of Oslo, Oslo, Norway
- Glyconor Mass Spectrometry, Department of Molecular Biosciences, University of Oslo, Oslo, Norway
| | - Gunter Reuter
- Institute of Biology, Developmental Genetics, Martin Luther University Halle, Halle, Germany
| | - Ming-Ming Zhou
- Department of Structural and Chemical Biology, Mount Sinai School of Medicine, New York, New York, United States of America
| | - Reidunn B. Aalen
- Department of Molecular Biosciences, University of Oslo, Oslo, Norway
| | - Tage Thorstensen
- Department of Molecular Biosciences, University of Oslo, Oslo, Norway
- * E-mail:
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Breeze E, Harrison E, McHattie S, Hughes L, Hickman R, Hill C, Kiddle S, Kim YS, Penfold CA, Jenkins D, Zhang C, Morris K, Jenner C, Jackson S, Thomas B, Tabrett A, Legaie R, Moore JD, Wild DL, Ott S, Rand D, Beynon J, Denby K, Mead A, Buchanan-Wollaston V. High-resolution temporal profiling of transcripts during Arabidopsis leaf senescence reveals a distinct chronology of processes and regulation. THE PLANT CELL 2011; 23:873-94. [PMID: 21447789 PMCID: PMC3082270 DOI: 10.1105/tpc.111.083345] [Citation(s) in RCA: 566] [Impact Index Per Article: 43.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2011] [Revised: 01/21/2011] [Accepted: 02/28/2011] [Indexed: 05/17/2023]
Abstract
Leaf senescence is an essential developmental process that impacts dramatically on crop yields and involves altered regulation of thousands of genes and many metabolic and signaling pathways, resulting in major changes in the leaf. The regulation of senescence is complex, and although senescence regulatory genes have been characterized, there is little information on how these function in the global control of the process. We used microarray analysis to obtain a high-resolution time-course profile of gene expression during development of a single leaf over a 3-week period to senescence. A complex experimental design approach and a combination of methods were used to extract high-quality replicated data and to identify differentially expressed genes. The multiple time points enable the use of highly informative clustering to reveal distinct time points at which signaling and metabolic pathways change. Analysis of motif enrichment, as well as comparison of transcription factor (TF) families showing altered expression over the time course, identify clear groups of TFs active at different stages of leaf development and senescence. These data enable connection of metabolic processes, signaling pathways, and specific TF activity, which will underpin the development of network models to elucidate the process of senescence.
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Affiliation(s)
- Emily Breeze
- School of Life Sciences, University of Warwick, Wellesbourne, Warwick CV35 9EF, United Kingdom
| | - Elizabeth Harrison
- School of Life Sciences, University of Warwick, Wellesbourne, Warwick CV35 9EF, United Kingdom
| | - Stuart McHattie
- School of Life Sciences, University of Warwick, Wellesbourne, Warwick CV35 9EF, United Kingdom
- Warwick Systems Biology, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Linda Hughes
- School of Life Sciences, University of Warwick, Wellesbourne, Warwick CV35 9EF, United Kingdom
| | - Richard Hickman
- School of Life Sciences, University of Warwick, Wellesbourne, Warwick CV35 9EF, United Kingdom
- Warwick Systems Biology, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Claire Hill
- School of Life Sciences, University of Warwick, Wellesbourne, Warwick CV35 9EF, United Kingdom
| | - Steven Kiddle
- School of Life Sciences, University of Warwick, Wellesbourne, Warwick CV35 9EF, United Kingdom
- Warwick Systems Biology, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Youn-sung Kim
- School of Life Sciences, University of Warwick, Wellesbourne, Warwick CV35 9EF, United Kingdom
| | | | - Dafyd Jenkins
- Warwick Systems Biology, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Cunjin Zhang
- School of Life Sciences, University of Warwick, Wellesbourne, Warwick CV35 9EF, United Kingdom
| | - Karl Morris
- School of Life Sciences, University of Warwick, Wellesbourne, Warwick CV35 9EF, United Kingdom
| | - Carol Jenner
- School of Life Sciences, University of Warwick, Wellesbourne, Warwick CV35 9EF, United Kingdom
| | - Stephen Jackson
- School of Life Sciences, University of Warwick, Wellesbourne, Warwick CV35 9EF, United Kingdom
| | - Brian Thomas
- School of Life Sciences, University of Warwick, Wellesbourne, Warwick CV35 9EF, United Kingdom
| | - Alexandra Tabrett
- School of Life Sciences, University of Warwick, Wellesbourne, Warwick CV35 9EF, United Kingdom
| | - Roxane Legaie
- Warwick Systems Biology, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Jonathan D. Moore
- Warwick Systems Biology, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - David L. Wild
- Warwick Systems Biology, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Sascha Ott
- Warwick Systems Biology, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - David Rand
- Warwick Systems Biology, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Jim Beynon
- School of Life Sciences, University of Warwick, Wellesbourne, Warwick CV35 9EF, United Kingdom
- Warwick Systems Biology, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Katherine Denby
- School of Life Sciences, University of Warwick, Wellesbourne, Warwick CV35 9EF, United Kingdom
- Warwick Systems Biology, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Andrew Mead
- School of Life Sciences, University of Warwick, Wellesbourne, Warwick CV35 9EF, United Kingdom
| | - Vicky Buchanan-Wollaston
- School of Life Sciences, University of Warwick, Wellesbourne, Warwick CV35 9EF, United Kingdom
- Warwick Systems Biology, University of Warwick, Coventry CV4 7AL, United Kingdom
- Address correspondence to
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