1
|
Khadka J, Trishla VS, Sannidhi S, Singiri JR, Grandhi R, Pesok A, Novoplansky N, Adler-Agmon Z, Grafi G. Revealing cis- and trans-regulatory elements underlying nuclear distribution and function of the Arabidopsis histone H2B.8 variant. BMC PLANT BIOLOGY 2024; 24:811. [PMID: 39198770 PMCID: PMC11351261 DOI: 10.1186/s12870-024-05532-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Accepted: 08/21/2024] [Indexed: 09/01/2024]
Abstract
The H2B.8 variant has been diverged from other variants by its extended N-terminal region that possesses a conserved domain. We generated transgenic Arabidopsis plants expressing H2B.9 (class I), H2B.5 (class II) and H2B.8 (class III) fused to GFP under the 35 S promoter and studied their nuclear distribution and function. H2B.8-GFP showed peculiar nuclear localization at chromocenters in all cell types examined, while H2B.5-GFP and H2B.9-GFP displayed various patterns often dependent on cell types. H2B variants faithfully assembled onto nucleosomes showing no effect on nuclear organization; H2B.8-GFP appeared as three distinct isoforms in which one isoform appeared to be SUMOylated. Interestingly, transient expression in protoplasts revealed H2B.8 nuclear localization distinct from transgenic plants as it was restricted to the nuclear periphery generating a distinctive ring-like appearance accompanied by nuclear size reduction. This unique appearance was abolished by deletion of the N-terminal conserved domain or when H2B.8-GFP is transiently expressed in ddm1 protoplasts. GFP-TRAP-coupled proteome analysis uncovered H2B.8-partner proteins including H2A.W.12, which characterizes heterochromatin. Thus, our data highlight H2B.8 as a unique variant evolved in angiosperms to control chromatin compaction/aggregation and uncover cis- and trans-regulatory elements underlying its nuclear distribution and function.
Collapse
Affiliation(s)
- Janardan Khadka
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben Gurion, 84990, Israel
- Central Department of Biotechnology, Tribhuvan University, Kirtipur, Nepal
| | - Vikas S Trishla
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben Gurion, 84990, Israel
| | - Sasank Sannidhi
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben Gurion, 84990, Israel
| | - Jeevan R Singiri
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben Gurion, 84990, Israel
| | - Rohith Grandhi
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben Gurion, 84990, Israel
- Department of Chemistry, Biochemistry and Physics, Université du Québec à Trois-Rivières, Trois-Rivières, Québec, G9A 5H9, Canada
| | - Anat Pesok
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben Gurion, 84990, Israel
| | - Nurit Novoplansky
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben Gurion, 84990, Israel
| | - Zachor Adler-Agmon
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben Gurion, 84990, Israel
- Morris Kahn Marine Research Station, University of Haifa, Haifa, 3498838, Israel
| | - Gideon Grafi
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben Gurion, 84990, Israel.
| |
Collapse
|
2
|
Lee SC, Adams DW, Ipsaro JJ, Cahn J, Lynn J, Kim HS, Berube B, Major V, Calarco JP, LeBlanc C, Bhattacharjee S, Ramu U, Grimanelli D, Jacob Y, Voigt P, Joshua-Tor L, Martienssen RA. Chromatin remodeling of histone H3 variants by DDM1 underlies epigenetic inheritance of DNA methylation. Cell 2023; 186:4100-4116.e15. [PMID: 37643610 PMCID: PMC10529913 DOI: 10.1016/j.cell.2023.08.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 05/19/2023] [Accepted: 08/01/2023] [Indexed: 08/31/2023]
Abstract
Nucleosomes block access to DNA methyltransferase, unless they are remodeled by DECREASE in DNA METHYLATION 1 (DDM1LSH/HELLS), a Snf2-like master regulator of epigenetic inheritance. We show that DDM1 promotes replacement of histone variant H3.3 by H3.1. In ddm1 mutants, DNA methylation is partly restored by loss of the H3.3 chaperone HIRA, while the H3.1 chaperone CAF-1 becomes essential. The single-particle cryo-EM structure at 3.2 Å of DDM1 with a variant nucleosome reveals engagement with histone H3.3 near residues required for assembly and with the unmodified H4 tail. An N-terminal autoinhibitory domain inhibits activity, while a disulfide bond in the helicase domain supports activity. DDM1 co-localizes with H3.1 and H3.3 during the cell cycle, and with the DNA methyltransferase MET1Dnmt1, but is blocked by H4K16 acetylation. The male germline H3.3 variant MGH3/HTR10 is resistant to remodeling by DDM1 and acts as a placeholder nucleosome in sperm cells for epigenetic inheritance.
Collapse
Affiliation(s)
- Seung Cho Lee
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - Dexter W Adams
- W. M. Keck Structural Biology Laboratory, Howard Hughes Medical Institute, Cold Spring Harbor, NY 11724, USA; Graduate Program in Genetics, Stony Brook University, Stony Brook, NY 11794, USA
| | - Jonathan J Ipsaro
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA; W. M. Keck Structural Biology Laboratory, Howard Hughes Medical Institute, Cold Spring Harbor, NY 11724, USA
| | - Jonathan Cahn
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - Jason Lynn
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - Hyun-Soo Kim
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - Benjamin Berube
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA; Cold Spring Harbor Laboratory School of Biological Sciences, 1 Bungtown Rd, Cold Spring Harbor, NY 11724, USA
| | - Viktoria Major
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Joseph P Calarco
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA; Cold Spring Harbor Laboratory School of Biological Sciences, 1 Bungtown Rd, Cold Spring Harbor, NY 11724, USA
| | - Chantal LeBlanc
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - Sonali Bhattacharjee
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - Umamaheswari Ramu
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - Daniel Grimanelli
- Institut de Recherche pour le Développement, 911Avenue Agropolis, 34394 Montpelier, France
| | - Yannick Jacob
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - Philipp Voigt
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Leemor Joshua-Tor
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA; W. M. Keck Structural Biology Laboratory, Howard Hughes Medical Institute, Cold Spring Harbor, NY 11724, USA.
| | - Robert A Martienssen
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA.
| |
Collapse
|
3
|
Lee SC, Adams DW, Ipsaro JJ, Cahn J, Lynn J, Kim HS, Berube B, Major V, Calarco JP, LeBlanc C, Bhattacharjee S, Ramu U, Grimanelli D, Jacob Y, Voigt P, Joshua-Tor L, Martienssen RA. Chromatin remodeling of histone H3 variants underlies epigenetic inheritance of DNA methylation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.11.548598. [PMID: 37503143 PMCID: PMC10369972 DOI: 10.1101/2023.07.11.548598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Epigenetic inheritance refers to the faithful replication of DNA methylation and histone modification independent of DNA sequence. Nucleosomes block access to DNA methyltransferases, unless they are remodeled by DECREASE IN DNA METHYLATION1 (DDM1 Lsh/HELLS ), a Snf2-like master regulator of epigenetic inheritance. We show that DDM1 activity results in replacement of the transcriptional histone variant H3.3 for the replicative variant H3.1 during the cell cycle. In ddm1 mutants, DNA methylation can be restored by loss of the H3.3 chaperone HIRA, while the H3.1 chaperone CAF-1 becomes essential. The single-particle cryo-EM structure at 3.2 Å of DDM1 with a variant nucleosome reveals direct engagement at SHL2 with histone H3.3 at or near variant residues required for assembly, as well as with the deacetylated H4 tail. An N-terminal autoinhibitory domain binds H2A variants to allow remodeling, while a disulfide bond in the helicase domain is essential for activity in vivo and in vitro . We show that differential remodeling of H3 and H2A variants in vitro reflects preferential deposition in vivo . DDM1 co-localizes with H3.1 and H3.3 during the cell cycle, and with the DNA methyltransferase MET1 Dnmt1 . DDM1 localization to the chromosome is blocked by H4K16 acetylation, which accumulates at DDM1 targets in ddm1 mutants, as does the sperm cell specific H3.3 variant MGH3 in pollen, which acts as a placeholder nucleosome in the germline and contributes to epigenetic inheritance.
Collapse
Affiliation(s)
- Seung Cho Lee
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory; 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - Dexter W. Adams
- W. M. Keck Structural Biology Laboratory, Howard Hughes Medical Institute; Cold Spring Harbor, NY 11724, USA
- Graduate Program in Genetics, Stony Brook University; Stony Brook, NY 11794, USA
| | - Jonathan J. Ipsaro
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory; 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
- W. M. Keck Structural Biology Laboratory, Howard Hughes Medical Institute; Cold Spring Harbor, NY 11724, USA
| | - Jonathan Cahn
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory; 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - Jason Lynn
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory; 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - Hyun-Soo Kim
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory; 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - Benjamin Berube
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory; 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
- Cold Spring Harbor Laboratory School of Biological Sciences; 1 Bungtown Rd, Cold Spring Harbor, NY 11724, USA
| | - Viktoria Major
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh; Edinburgh EH9 3BF, United Kingdom
| | - Joseph P. Calarco
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory; 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
- Cold Spring Harbor Laboratory School of Biological Sciences; 1 Bungtown Rd, Cold Spring Harbor, NY 11724, USA
| | - Chantal LeBlanc
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory; 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
- Present address: Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences, Yale University; 260 Whitney Ave., New Haven, CT, 06511, USA
| | - Sonali Bhattacharjee
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory; 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - Umamaheswari Ramu
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory; 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - Daniel Grimanelli
- Institut de Recherche pour le Développement; 911 Avenue Agropolis, 34394 Montpellier, France
| | - Yannick Jacob
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory; 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
- Present address: Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences, Yale University; 260 Whitney Ave., New Haven, CT, 06511, USA
| | - Philipp Voigt
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh; Edinburgh EH9 3BF, United Kingdom
- Present address: Epigenetics Programme, Babraham Institute; Cambridge CB22 3AT, United Kingdom
| | - Leemor Joshua-Tor
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory; 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
- W. M. Keck Structural Biology Laboratory, Howard Hughes Medical Institute; Cold Spring Harbor, NY 11724, USA
| | - Robert A. Martienssen
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory; 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
| |
Collapse
|
4
|
Coordinated histone modifications and chromatin reorganization in a single cell revealed by FRET biosensors. Proc Natl Acad Sci U S A 2018; 115:E11681-E11690. [PMID: 30478057 DOI: 10.1073/pnas.1811818115] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The dramatic reorganization of chromatin during mitosis is perhaps one of the most fundamental of all cell processes. It remains unclear how epigenetic histone modifications, despite their crucial roles in regulating chromatin architectures, are dynamically coordinated with chromatin reorganization in controlling this process. We have developed and characterized biosensors with high sensitivity and specificity based on fluorescence resonance energy transfer (FRET). These biosensors were incorporated into nucleosomes to visualize histone H3 Lys-9 trimethylation (H3K9me3) and histone H3 Ser-10 phosphorylation (H3S10p) simultaneously in the same live cell. We observed an anticorrelated coupling in time between H3K9me3 and H3S10p in a single live cell during mitosis. A transient increase of H3S10p during mitosis is accompanied by a decrease of H3K9me3 that recovers before the restoration of H3S10p upon mitotic exit. We further showed that H3S10p is causatively critical for the decrease of H3K9me3 and the consequent reduction of heterochromatin structure, leading to the subsequent global chromatin reorganization and nuclear envelope dissolution as a cell enters mitosis. These results suggest a tight coupling of H3S10p and H3K9me3 dynamics in the regulation of heterochromatin dissolution before a global chromatin reorganization during mitosis.
Collapse
|
5
|
Khan A, Garbelli A, Grossi S, Florentin A, Batelli G, Acuna T, Zolla G, Kaye Y, Paul LK, Zhu JK, Maga G, Grafi G, Barak S. The Arabidopsis STRESS RESPONSE SUPPRESSOR DEAD-box RNA helicases are nucleolar- and chromocenter-localized proteins that undergo stress-mediated relocalization and are involved in epigenetic gene silencing. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 79:28-43. [PMID: 24724701 DOI: 10.1111/tpj.12533] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2014] [Revised: 04/03/2014] [Accepted: 04/08/2014] [Indexed: 05/03/2023]
Abstract
DEAD-box RNA helicases are involved in many aspects of RNA metabolism and in diverse biological processes in plants. Arabidopsis thaliana mutants of two DEAD-box RNA helicases, STRESS RESPONSE SUPPRESSOR1 (STRS1) and STRS2 were previously shown to exhibit tolerance to abiotic stresses and up-regulated stress-responsive gene expression. Here, we show that Arabidopsis STRS-overexpressing lines displayed a less tolerant phenotype and reduced expression of stress-induced genes confirming the STRSs as attenuators of Arabidopsis stress responses. GFP-STRS fusion proteins exhibited localization to the nucleolus, nucleoplasm and chromocenters and exhibited relocalization in response to abscisic acid (ABA) treatment and various stresses. This relocalization was reversed when stress treatments were removed. The STRS proteins displayed mis-localization in specific gene-silencing mutants and exhibited RNA-dependent ATPase and RNA-unwinding activities. In particular, STRS2 showed mis-localization in three out of four mutants of the RNA-directed DNA methylation (RdDM) pathway while STRS1 was mis-localized in the hd2c mutant that is defective in histone deacetylase activity. Furthermore, heterochromatic RdDM target loci displayed reduced DNA methylation and increased expression in the strs mutants. Taken together, our findings suggest that the STRS proteins are involved in epigenetic silencing of gene expression to bring about suppression of the Arabidopsis stress response.
Collapse
Affiliation(s)
- Asif Khan
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, 84990, Israel
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
6
|
Nishigaki M, Kawada Y, Misaki T, Murata K, Goshima T, Hirokawa T, Yamada C, Shimada M, Nakanishi M. Mitotic phosphorylation of MPP8 by cyclin-dependent kinases regulates chromatin dissociation. Biochem Biophys Res Commun 2013; 432:654-9. [DOI: 10.1016/j.bbrc.2013.02.027] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Accepted: 02/04/2013] [Indexed: 11/26/2022]
|
7
|
Wozny M, Schattat MH, Mathur N, Barton K, Mathur J. Color recovery after photoconversion of H2B::mEosFP allows detection of increased nuclear DNA content in developing plant cells. PLANT PHYSIOLOGY 2012; 158:95-106. [PMID: 22108524 PMCID: PMC3252088 DOI: 10.1104/pp.111.187062] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2011] [Accepted: 11/21/2011] [Indexed: 05/10/2023]
Abstract
Many higher plants are polysomatic whereby different cells possess variable amounts of nuclear DNA. The conditional triggering of endocycles results in higher nuclear DNA content (C value) that in some cases has been correlated to increased cell size. While numerous multicolored fluorescent protein (FP) probes have revealed the general behavior of the nucleus and intranuclear components, direct visualization and estimation of changes in nuclear-DNA content in live cells during their development has not been possible. Recently, monomeric Eos fluorescent protein (mEosFP) has emerged as a useful photoconvertible protein whose color changes irreversibly from a green to a red fluorescent form upon exposure to violet-blue light. The stability and irreversibility of red fluorescent mEosFP suggests that detection of green color recovery would be possible as fresh mEosFP is produced after photoconversion. Thus a ratiometric evaluation of the red and green forms of mEosFP following photoconversion could be used to estimate production of a core histone such as H2B during its concomitant synthesis with DNA in the synthesis phase of the cell cycle. Here we present proof of concept observations on transgenic tobacco (Nicotiana tabacum) Bright Yellow 2 cells and Arabidopsis (Arabidopsis thaliana) plants stably expressing H2B::mEosFP. In Arabidopsis seedlings an increase in green fluorescence is observed specifically in cells known to undergo endoreduplication. The detection of changes in nuclear DNA content by correlating color recovery of H2B::mEosFP after photoconversion is a novel approach involving a single FP. The method has potential for facilitating detailed investigations on conditions that favor increased cell size and the development of polysomaty in plants.
Collapse
Affiliation(s)
| | | | | | | | - Jaideep Mathur
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada N1G2W1
| |
Collapse
|
8
|
|
9
|
Lampl N, Budai-Hadrian O, Davydov O, Joss TV, Harrop SJ, Curmi PMG, Roberts TH, Fluhr R. Arabidopsis AtSerpin1, crystal structure and in vivo interaction with its target protease RESPONSIVE TO DESICCATION-21 (RD21). J Biol Chem 2010; 285:13550-60. [PMID: 20181955 DOI: 10.1074/jbc.m109.095075] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
In animals, protease inhibitors of the serpin family are associated with many physiological processes, including blood coagulation and innate immunity. Serpins feature a reactive center loop (RCL), which displays a protease target sequence as a bait. RCL cleavage results in an irreversible, covalent serpin-protease complex. AtSerpin1 is an Arabidopsis protease inhibitor that is expressed ubiquitously throughout the plant. The x-ray crystal structure of recombinant AtSerpin1 in its native stressed conformation was determined at 2.2 A. The electrostatic surface potential below the RCL was found to be highly positive, whereas the breach region critical for RCL insertion is an unusually open structure. AtSerpin1 accumulates in plants as a full-length and a cleaved form. Fractionation of seedling extracts by nonreducing SDS-PAGE revealed the presence of an additional slower migrating complex that was absent when leaves were treated with the specific cysteine protease inhibitor L-trans-epoxysuccinyl-L-leucylamido (4-guanidino)butane. Significantly, RESPONSIVE TO DESICCATION-21 (RD21) was the major protease labeled with the L-trans-epoxysuccinyl-L-leucylamido (4-guanidino)butane derivative DCG-04 in wild type extracts but not in extracts of mutant plants constitutively overexpressing AtSerpin1, indicating competition. Fractionation by nonreducing SDS-PAGE followed by immunoblotting with RD21-specific antibody revealed that the protease accumulated both as a free enzyme and in a complex with AtSerpin1. Importantly, both RD21 and AtSerpin1 knock-out mutants lacked the serpin-protease complex. The results establish that the major Arabidopsis plant serpin interacts with RD21. This is the first report of the structure and in vivo interaction of a plant serpin with its target protease.
Collapse
Affiliation(s)
- Nardy Lampl
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | | | | | | | | | | | | | | |
Collapse
|
10
|
Granot G, Sikron-Persi N, Gaspan O, Florentin A, Talwara S, Paul LK, Morgenstern Y, Granot Y, Grafi G. Histone modifications associated with drought tolerance in the desert plant Zygophyllum dumosum Boiss. PLANTA 2009; 231:27-34. [PMID: 19809832 DOI: 10.1007/s00425-009-1026-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2009] [Accepted: 09/21/2009] [Indexed: 05/02/2023]
Abstract
Zygophyllum dumosum Boiss. is a perennial Saharo-Arabian phytogeographical element and a dominant shrub on the rocky limestone southeast-facing slopes of the Negev desert. The plant is highly active during the winter, and semideciduous during the dry summer, i.e., it sheds its leaflets, while leaving the thick, fleshy petiole green and rather active during the dry season. Being resistant to extreme perennial drought, Z. dumosum appears to provide an intriguing model plant for studying epigenetic mechanisms associated with drought tolerance in natural habitats. The transition from the wet to the dry season was accompanied by a significant decrease in nuclear size and with posttranslational modifications of histone H3 N-terminal tail. Dimethylation of H3 at lysine 4 (H3K4)--a modification associated with active gene expression--was found to be high during the wet season but gradually diminished on progression to the dry season. Unexpectedly, H3K9 di- and trimethylation as well as H3K27 di- and trimethylation could not be detected in Z. dumosum; H3K9 monomethylation appears to be prominent in Z. dumosum during the wet but not during the dry season. Contrary to Z. dumosum, H3K9 dimethylation was detected in other desert plants, including Artemisia sieberi, Anabasis articulata and Haloxylon scoparium. Taken together, our results demonstrate dynamic genome organization and unique pattern of histone H3 methylation displayed by Z. dumosum, which could have an adaptive value in variable environments of the Negev desert.
Collapse
Affiliation(s)
- Gila Granot
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, 84990, Midreshet Ben-Gurion, Israel
| | | | | | | | | | | | | | | | | |
Collapse
|
11
|
Demidov D, Hesse S, Tewes A, Rutten T, Fuchs J, Ashtiyani RK, Lein S, Fischer A, Reuter G, Houben A. Aurora1 phosphorylation activity on histone H3 and its cross-talk with other post-translational histone modifications in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2009; 59:221-30. [PMID: 19582900 DOI: 10.1111/j.1365-313x.2009.03861.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
The enzymological properties of AtAurora1, a kinase responsible for the cell cycle-dependent phosphorylation of histone H3 at S10, and its cross-talk with other post-translational histone modifications, were determined. In vitro phosphorylation of H3S10 by AtAurora1 is strongly increased by K9 acetylation, and decreased by K14 acetylation and T11 phosphorylation. However, S10 phosphorylation activity is unaltered by mono-, di- or trimethylation of K9. An interference of H3K9 dimethylation by SUVR4 occurs by a pre-existing phosphorylation at S10. Hence, cross-talk in plants exists between phosphorylation of H3S10 and methylation, acetylation or phosphorylation of neighbouring amino acid residues. AtAurora1 undergoes autophosphorylation in vivo regardless of the presence of substrate, and forms dimers in planta. Of the three ATP-competitive Aurora inhibitors tested, Hesperadin was most effective in reducing the in vivo kinase activity of AtAurora1. Hesperadin consistently inhibited histone H3S10 phosphorylation during mitosis in Arabidopsis cells, but did not affect other H3 post-translational modifications, suggesting a specific inhibition of AtAurora in vivo. Inactivation of AtAurora also caused lagging chromosomes in a number of anaphase cells, but, unlike the situation in mammalian cells, Hesperadin did not influence the microtubule dynamics in dividing cells.
Collapse
Affiliation(s)
- Dmitri Demidov
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466 Gatersleben, Germany
| | | | | | | | | | | | | | | | | | | |
Collapse
|
12
|
Granot G, Sikron-Persi N, Li Y, Grafi G. Phosphorylated H3S10 occurs in distinct regions of the nucleolus in differentiated leaf cells. BIOCHIMICA ET BIOPHYSICA ACTA 2009; 1789:220-4. [PMID: 19135559 DOI: 10.1016/j.bbagrm.2008.12.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2008] [Revised: 12/08/2008] [Accepted: 12/09/2008] [Indexed: 01/05/2023]
Abstract
Serine 10 phosphorylation of histone H3 (H3S10ph) has long been considered a mitotic marker, which is often associated with chromosome condensation both in plants and animals. Yet, in animal cells, H3S10ph was found associated with transcriptional activation of genes. Here we extend this view to plant cells showing that H3S10ph not only occurs in dividing cells during mitosis, but also in differentiated mesophyll cells. In these cells H3S10ph displayed a peculiar localization within the nucleolus where it was restricted to specific domains reminiscent of fibrillar centers. Chromatin immunoprecipitation analysis showed that H3S10ph is associated with ribosomal DNAs. Thus, in plants H3S10ph appears to be associated with two structurally differing nuclear sites engaged in gene silencing (mitotic centromeres) and in gene transcription (nucleolus).
Collapse
Affiliation(s)
- Gila Granot
- French Associates Institute for Dryland Agriculture and Biotechnology, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben Gurion 84990, Israel
| | | | | | | |
Collapse
|
13
|
Vunsh R, Li J, Hanania U, Edelman M, Flaishman M, Perl A, Wisniewski JP, Freyssinet G. High expression of transgene protein in Spirodela. PLANT CELL REPORTS 2007; 26:1511-9. [PMID: 17492286 DOI: 10.1007/s00299-007-0361-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2006] [Revised: 04/01/2007] [Accepted: 04/06/2007] [Indexed: 05/15/2023]
Abstract
The monocot family Lemnaceae (duckweed) is composed of small, edible, aquatic plants. Spirodela oligorrhiza SP is a duckweed with a biomass doubling time of about 2 days under controlled, axenic conditions. Stably transformed Spirodela plants were obtained following co-cultivation of regenerative calli with Agrobacterium tumefaciens. GFP activity was successfully monitored in different subcellular compartments of the plant and correlated with different targeting sequences. Transgenic lines were followed for a period of at least 18 months and more than 180 vegetative doublings (generations). The lines are stable in morphology, growth rate, transgene expression, and activity as measured by DNA-DNA and immunoblot hybridizations, fluorescence activity measurements, and antibiotic resistance. The level of transgene expression is a function of leader sequences rather than transgene copy number. A stable, transgenic, GFP expression level >25% of total soluble protein is demonstrated for the S. oligorrhiza system, making it among the higher expressing systems for nuclear transformation in a higher plant.
Collapse
Affiliation(s)
- Ron Vunsh
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot, Israel
| | | | | | | | | | | | | | | |
Collapse
|
14
|
Bergmüller E, Gehrig PM, Gruissem W. Characterization of post-translational modifications of histone H2B-variants isolated from Arabidopsis thaliana. J Proteome Res 2007; 6:3655-68. [PMID: 17691833 DOI: 10.1021/pr0702159] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Eukaryotic DNA is structurally packed into chromatin by the basic histone proteins H2A, H2B, H3, and H4. There is increasing evidence that incorporation and post-translational modifications of histone variants have a fundamental role in gene regulation. While modifications of H3 and H4 histones are now well-established, considerably less is known about H2B modifications. Here, we present the first detailed characterization of H2B-variants isolated from the model plant Arabidopsis thaliana. We combined reversed-phase chromatography with tandem mass spectrometry to identify post-translational modifications of the H2B-variants HTB1, HTB2, HTB4, HTB9, and HTB11, isolated from total chromatin and euchromatin-enriched fractions. The HTB9-variant has acetylation sites at lysines 6, 11, 27, 32, 38, and 39, while Lys-145 can be ubiquitinated. Analogous modifications and an additional methylation of Lys-3 were identified for HTB11. HTB2 shows similar acetylation and ubiquitination sites and an additional methylation at Lys-11. Furthermore, the N-terminal alanine residues of HTB9 and HTB11 were found to be mono-, di-, or trimethylated or unmodified. No methylation of arginine residues was detected. The data suggest that most of these modification sites are only partially occupied. Our study significantly expands the map of covalent Arabidopsis histone modifications and is the first step to unraveling the histone code in higher plants.
Collapse
Affiliation(s)
- Eveline Bergmüller
- Institute of Plant Sciences, ETH Zurich, Universitätstrasse 2, 8092 Zurich, Switzerland
| | | | | |
Collapse
|
15
|
Terada Y. Aurora-B/AIM-1 regulates the dynamic behavior of HP1alpha at the G2-M transition. Mol Biol Cell 2006; 17:3232-41. [PMID: 16687578 PMCID: PMC1483052 DOI: 10.1091/mbc.e05-09-0906] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Heterochromatin protein 1 (HP1) plays an important role in heterochromatin formation and undergoes large-scale, progressive dissociation from heterochromatin in prophase cells. However, the mechanisms regulating the dynamic behavior of HP1 are poorly understood. In this study, the role of Aurora-B was investigated with respect to the dynamic behavior of HP1alpha. Mammalian Aurora-B, AIM-1, colocalizes with HP1alpha to the heterochromatin in G2. Depletion of Aurora-B/AIM-1 inhibited dissociation of HP1alpha from the chromosome arms at the G2-M transition. In addition, depletion of INCENP led to aberrant cellular localization of Aurora-B/AIM-1, but it did not affect heterochromatin targeting of HP1alpha. It was proposed in the binary switch hypothesis that phosphorylation of histone H3 at Ser-10 negatively regulates the binding of HP1alpha to the adjacent methylated Lys-9. However, Aurora-B/AIM-1-mediated phosphorylation of H3 induced dissociation of the HP1alpha chromodomain but not of the intact protein in vitro, indicating that the center and/or C-terminal domain of HP1alpha interferes with the effect of H3 phosphorylation on HP1alpha dissociation. Interestingly, Lys-9 methyltransferase SUV39H1 is abnormally localized together along the metaphase chromosome arms in Aurora-B/AIM-1-depleted cells. In conclusion, these results showed that Aurora-B/AIM-1 is necessary for regulated histone modifications involved in binding of HP1alpha by the N terminus of histone H3 during mitosis.
Collapse
Affiliation(s)
- Yasuhiko Terada
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA.
| |
Collapse
|
16
|
Yancheva SD, Shlizerman LA, Golubowicz S, Yabloviz Z, Perl A, Hanania U, Flaishman MA. The use of green fluorescent protein (GFP) improves Agrobacterium-mediated transformation of 'Spadona' pear (Pyrus communis L.). PLANT CELL REPORTS 2006; 25:183-9. [PMID: 16328389 DOI: 10.1007/s00299-005-0025-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2004] [Revised: 03/01/2005] [Accepted: 04/12/2005] [Indexed: 05/05/2023]
Abstract
An efficient and reproducible system for Agrobacterium-mediated transformation of the pear (Pyrus communis L.) cultivar Spadona was developed. Leaf explants of in vitro propagated plants were cocultivated with the disarmed Agrobacterium strain EHA105 harboring the plasmid pME504, carrying the uidA-intron and nptII genes. Under selective conditions, 5% of the plantlets regenerated and were positively stained for GUS. However, most of the GUS-positive plants re-callused and subsequently died, leaving only 0.3-0.8% of these plantlets to reach maturity. In order to identify transformed shoots at early stages of regeneration, we introduced the green fluorescent protein (GFP) into the pear cultivar Spadona using the plasmid PZP carrying the nuclear-targeted GFP and nptII genes. High expression levels of GFP were detected in transgenic cells as early as 7 days after transformation. GFP marked-callii and transformed plants were observed after 14 and 24 days, respectively. Fluorescence microscopy screening of transformed plant material, under the selection of kanamycin, increased the transformation frequency to 3.0-4.0%. We conclude that the introduction of GFP improves the selection of transformed plants of Spadona pear.
Collapse
Affiliation(s)
- S D Yancheva
- Plant Biotechnology Laboratory, Agricultural University, 12 Mendeleev Street, 4000 Plovdiv, Bulgaria
| | | | | | | | | | | | | |
Collapse
|
17
|
Zemach A, Li Y, Ben-Meir H, Oliva M, Mosquna A, Kiss V, Avivi Y, Ohad N, Grafi G. Different domains control the localization and mobility of LIKE HETEROCHROMATIN PROTEIN1 in Arabidopsis nuclei. THE PLANT CELL 2006; 18:133-45. [PMID: 16361394 PMCID: PMC1323489 DOI: 10.1105/tpc.105.036855] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Plants possess a single gene for the structurally related HETEROCHROMATIN PROTEIN1 (HP1), termed LIKE-HP1 (LHP1). We investigated the subnuclear localization, binding properties, and dynamics of LHP1 proteins in Arabidopsis thaliana cells. Transient expression assays showed that tomato (Solanum lycopersicum) LHP1 fused to green fluorescent protein (GFP; Sl LHP1-GFP) and Arabidopsis LHP1 (At LHP1-GFP) localized to heterochromatic chromocenters and showed punctuated distribution within the nucleus; tomato but not Arabidopsis LHP1 was also localized within the nucleolus. Mutations of aromatic cage residues that recognize methyl K9 of histone H3 abolished their punctuated distribution and localization to chromocenters. Sl LHP1-GFP plants displayed cell type-dependent subnuclear localization. The diverse localization pattern of tomato LHP1 did not require the chromo shadow domain (CSD), whereas the chromodomain alone was insufficient for localization to chromocenters; a nucleolar localization signal was identified within the hinge region. Fluorescence recovery after photobleaching showed that Sl LHP1 is a highly mobile protein whose localization and retention are controlled by distinct domains; retention at the nucleolus and chromocenters is conferred by the CSD. Our results imply that LHP1 recruitment to chromatin is mediated, at least in part, through interaction with methyl K9 and that LHP1 controls different nuclear processes via transient binding to its nuclear sites.
Collapse
Affiliation(s)
- Assaf Zemach
- Department of Plant Sciences, Weizman Institute of Science, Rehovot, Israel
| | | | | | | | | | | | | | | | | |
Collapse
|
18
|
Libault M, Tessadori F, Germann S, Snijder B, Fransz P, Gaudin V. The Arabidopsis LHP1 protein is a component of euchromatin. PLANTA 2005; 222:910-25. [PMID: 16244868 DOI: 10.1007/s00425-005-0129-4] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2005] [Accepted: 08/29/2005] [Indexed: 05/05/2023]
Abstract
The HP1 family proteins are involved in several aspects of chromatin function and regulation in Drosophila, mammals and the fission yeast. Here we investigate the localization of LHP1, the unique Arabidopsis thaliana HP1 homolog known at present time, to approach its function. A functional LHP1-GFP fusion protein, able to restore the wild-type phenotype in the lhp1 mutant, was used to analyze the subnuclear distribution of LHP1 in both A. thaliana and Nicotiana tabacum. In A. thaliana interphase nuclei, LHP1 was predominantly located outside the heterochromatic chromocenters. No major aberrations were observed in heterochromatin content or chromocenter organization in lhp1 plants. These data indicate that LHP1 is mainly involved in euchromatin organization in A. thaliana. In tobacco BY-2 cells, the LHP1 distribution, although in foci, slightly differed suggesting that LHP1 localization is determined by the underlying genome organization of plant species. Truncated LHP1 proteins expressed in vivo allowed us to determine the function of the different segments in the localization. The in foci distribution is dependent on the presence of the two chromo domains, whereas the hinge region has some nucleolus-targeting properties. Furthermore, like the animal HP1beta and HP1gamma subtypes, LHP1 dissociates from chromosomes during mitosis. In transgenic plants expressing the LHP1-GFP fusion protein, two major localization patterns were observed according to cell types suggesting that localization evolves with age or differentiation states. Our results show conversed characteristics of the A. thaliana HP1 homolog with the mammal HP1gamma isoform, besides specific plant properties.
Collapse
Affiliation(s)
- Marc Libault
- Laboratoire de Biologie Cellulaire, IJPB, INRA, route de St Cyr, 78026, Versailles Cedex, France
| | | | | | | | | | | |
Collapse
|
19
|
Nakahigashi K, Jasencakova Z, Schubert I, Goto K. The Arabidopsis heterochromatin protein1 homolog (TERMINAL FLOWER2) silences genes within the euchromatic region but not genes positioned in heterochromatin. PLANT & CELL PHYSIOLOGY 2005; 46:1747-56. [PMID: 16131496 DOI: 10.1093/pcp/pci195] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
TERMINAL FLOWER2 (TFL2) is the only homolog of heterochromatin protein1 (HP1) in the Arabidopsis genome. Because proteins of the HP1 family in fission yeast and animals act as key components of gene silencing in heterochromatin by binding to histone H3 methylated on lysine 9 (K9), here we examined whether TFL2 has a similar role in Arabidopsis. Unexpectedly, genes positioned in heterochromatin were not activated in tfl2 mutants. Moreover, the TFL2 protein localized preferentially to euchromatic regions and not to heterochromatic chromocenters, where K9-methylated histone H3 is clustered. Instead, TFL2 acts as a repressor of genes related to plant development, i.e. flowering, floral organ identity, meiosis and seed maturation. Up-regulation of the floral homeotic genes PISTILLATA, APETALA3, AGAMOUS and SEPALLATA3 in tfl2 mutants was independent of LEAFY or APETALA3, known activators of the above genes. In addition, transduced APETALA3 promoter fragments as short as 500 bp were sufficient for TFL2-mediated gene repression. Taken together, TFL2 silences specific genes within euchromatin but not genes positioned in heterochromatin of Arabidopsis.
Collapse
|
20
|
Zemach A, Li Y, Wayburn B, Ben-Meir H, Kiss V, Avivi Y, Kalchenko V, Jacobsen SE, Grafi G. DDM1 binds Arabidopsis methyl-CpG binding domain proteins and affects their subnuclear localization. THE PLANT CELL 2005; 17:1549-58. [PMID: 15805479 PMCID: PMC1091773 DOI: 10.1105/tpc.105.031567] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2005] [Accepted: 03/14/2005] [Indexed: 05/21/2023]
Abstract
Methyl-CpG binding domain (MBD) proteins in Arabidopsis thaliana bind in vitro methylated CpG sites. Here, we aimed to characterize the binding properties of AtMBDs to chromatin in Arabidopsis nuclei. By expressing in wild-type cells AtMBDs fused to green fluorescent protein (GFP), we showed that AtMBD7 was evenly distributed at all chromocenters, whereas AtMBD5 and 6 showed preference for two perinucleolar chromocenters adjacent to nucleolar organizing regions. AtMBD2, previously shown to be incapable of binding in vitro-methylated CpG, was dispersed within the nucleus, excluding chromocenters and the nucleolus. Recruitment of AtMBD5, 6, and 7 to chromocenters was disrupted in ddm1 and met1 mutant cells, where a significant reduction in cytosine methylation occurs. In these mutant cells, however, AtMBD2 accumulated at chromocenters. No effect on localization was observed in the chromomethylase3 mutant showing reduced CpNpG methylation or in kyp-2 displaying a reduction in Lys 9 histone H3 methylation. Transient expression of DDM1 fused to GFP showed that DDM1 shares common sites with AtMBD proteins. Glutathione S-transferase pull-down assays demonstrated that AtMBDs bind DDM1; the MBD motif was sufficient for this interaction. Our results suggest that the subnuclear localization of AtMBD is not solely dependent on CpG methylation; DDM1 may facilitate localization of AtMBDs at specific nuclear domains.
Collapse
Affiliation(s)
- Assaf Zemach
- Department of Plant Sciences, Weizman Institute of Science, Rehovot 76100, Israel
| | | | | | | | | | | | | | | | | |
Collapse
|
21
|
Demidov D, Van Damme D, Geelen D, Blattner FR, Houben A. Identification and dynamics of two classes of aurora-like kinases in Arabidopsis and other plants. THE PLANT CELL 2005; 17:836-48. [PMID: 15722465 PMCID: PMC1069702 DOI: 10.1105/tpc.104.029710] [Citation(s) in RCA: 110] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Aurora-like kinases play key roles in chromosome segregation and cytokinesis in yeast, plant, and animal systems. Here, we characterize three Arabidopsis thaliana protein kinases, designated AtAurora1, AtAurora2, and AtAurora3, which share high amino acid identities with the Ser/Thr kinase domain of yeast Ipl1 and animal Auroras. Structure and expression of AtAurora1 and AtAurora2 suggest that these genes arose by a recent gene duplication, whereas the diversification of plant alpha and beta Aurora kinases predates the origin of land plants. The transcripts and proteins of all three kinases are most abundant in tissues containing dividing cells. Intracellular localization of green fluorescent protein-tagged AtAuroras revealed an AtAurora-type specific association mainly with dynamic mitotic structures, such as microtubule spindles and centromeres, and with the emerging cell plate of dividing tobacco (Nicotiana tabacum) BY-2 cells. Immunolabeling using AtAurora antibodies yielded specific signals at the centromeres that are coincident with histone H3 that is phosphorylated at Ser position10 during mitosis. An in vitro kinase assay demonstrated that AtAurora1 preferentially phosphorylates histone H3 at Ser 10 but not at Ser 28 or Thr 3, 11, and 32. The phylogenetic analysis of available Aurora sequences from different eukaryotic origins suggests that, although a plant Aurora gene has been duplicated early in the evolution of plants, the paralogs nevertheless maintained a role in cell cycle-related signal transduction pathways.
Collapse
Affiliation(s)
- Dmitri Demidov
- Institute of Plant Genetics and Crop Plant Research, D-06466 Gatersleben, Germany
| | | | | | | | | |
Collapse
|
22
|
Li Y, Butenko Y, Grafi G. Histone deacetylation is required for progression through mitosis in tobacco cells. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2005; 41:346-52. [PMID: 15659094 DOI: 10.1111/j.1365-313x.2004.02301.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Post-translational modifications of core histone proteins play a key role in chromatin structure and function. Here, we study histone post-translational modifications during reentry of protoplasts derived from tobacco mesophyll cells into the cell cycle and evaluate their significance for progression through mitosis. Methylation of histone H3 at lysine residues 4 and 9 persisted in chromosomes during all phases of the cell cycle. However, acetylation of H4 and H3 was dramatically reduced during mitosis in a stage-specific manner; while deacetylation of histone H4 commenced at prophase and persisted up to telophase, histone H3 remained acetylated up to metaphase but was deacetylated at anaphase and telophase. Phosphorylation of histone H3 at serine 10 was initiated at prophase, concomitantly with deacetylation of histone H4, and persisted up to telophase. Preventing histone deacetylation by the histone deacetylase inhibitor trichostatin A (TSA) led to accumulation of protoplasts at metaphase-anaphase, and reduced S10 phosphorylation during anaphase and telophase; in cultured tobacco cells, TSA significantly reduced the frequency of mitotic figures. Our results indicate that deacetylation of histone H4 and H3 in tobacco protoplasts occurs during mitosis in a phase-specific manner, and is important for progression through mitosis.
Collapse
Affiliation(s)
- Yan Li
- Department of Plant Sciences, The Weizmann Institute of Science, Rehovot 76100, Israel
| | | | | |
Collapse
|
23
|
Mateescu B, England P, Halgand F, Yaniv M, Muchardt C. Tethering of HP1 proteins to chromatin is relieved by phosphoacetylation of histone H3. EMBO Rep 2004; 5:490-6. [PMID: 15105826 PMCID: PMC1299051 DOI: 10.1038/sj.embor.7400139] [Citation(s) in RCA: 118] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2003] [Revised: 03/01/2004] [Accepted: 03/02/2004] [Indexed: 11/08/2022] Open
Abstract
Histone H3 lysine 9 methylation is associated with long-term transcriptional repression through recruitment of heterochromatin protein 1 (HP1) proteins. These proteins are believed to promote the formation of dense chromatin structures interfering with DNA accessibility. During the G2 phase of the cell cycle, HP1 proteins are delocalized from foci of pericentromeric heterochromatin, while a wave of H3 serine 10 phosphorylation is initiated within these regions. Here, we show that in vivo phosphorylation of serine 10 in G2 can occur on histone tails methylated on lysine 9. Unexpectedly, this modification favours rather than prevents HP1 binding to chromatin. Dissociation of HP1 from the methylated histone H3 tails is observed only after a third modification by acetylation of lysine 14, which occurs in prophase. We propose that phosphoacetylation of histone H3 could be a general mechanism allowing the cell to overcome HP1-mediated transcriptional repression.
Collapse
Affiliation(s)
- Bogdan Mateescu
- Expression Génétique et Maladies, URA1644 du CNRS, Département de Biologie du Développement, Institut Pasteur, Bât. Fernbach, 25, Rue du Docteur Roux, 7S724, Paris Cedex 15, France
| | - Patrick England
- Plate-Forme de Biophysique des Protéines et de leurs Interactions, Département de Biologie Structurale et Chimie, Institut Pasteur, 28 Rue du Docteur Roux, 7S724, Paris Cedex 15, France
| | - Frederic Halgand
- Laboratoire de Spectrométrie de Masse, Institut de Chimie des Substances Naturelles, CNRS, 1 Avenue de la Terrasse, 91198 Gifsur-Yvette, France
| | - Moshe Yaniv
- Expression Génétique et Maladies, URA1644 du CNRS, Département de Biologie du Développement, Institut Pasteur, Bât. Fernbach, 25, Rue du Docteur Roux, 7S724, Paris Cedex 15, France
| | - Christian Muchardt
- Expression Génétique et Maladies, URA1644 du CNRS, Département de Biologie du Développement, Institut Pasteur, Bât. Fernbach, 25, Rue du Docteur Roux, 7S724, Paris Cedex 15, France
- Tel: +33 1 45 68 85 13/+33 1 45 68 85 25; Fax: +33 1 40 61 30 33; E-mail:
| |
Collapse
|
24
|
Williams L, Zhao J, Morozova N, Li Y, Avivi Y, Grafi G. Chromatin reorganization accompanying cellular dedifferentiation is associated with modifications of histone H3, redistribution of HP1, and activation of E2F-target genes. Dev Dyn 2003; 228:113-20. [PMID: 12950085 DOI: 10.1002/dvdy.10348] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The remarkable regeneration capacity of plant cells is based on their capability to dedifferentiate. We recently reported that cellular dedifferentiation proceeds through two distinct phases, each accompanied by chromatin decondensation: acquisition of competence for fate switch followed by a signal-dependent reentry into S phase. The purpose of this study was to (1) characterize changes in chromatin factors associated with chromatin decondensation, and (2) study the relationship between chromatin decondensation and transcriptional activation of pRb/E2F-regulated genes. We show that plant cells competent for fate switch display a disruption of nucleolar domain appearance associated with condensation of 18S ribosomal DNA, as well as modifications of histone H3 and redistribution of heterochromatin protein 1 (HP1). We further show that the pRb/E2F-target genes RNR2 and PCNA are condensed and silent in differentiated leaf cells but become decondensed, although not yet activated, as cells acquire competence for fate switch; transcriptional activation becomes evident during progression into S phase, concomitantly with pRb phosphorylation. We propose that chromatin reorganization is central for reversion of the differentiation process leading to resetting of the gene expression program and activation of silent genes.
Collapse
Affiliation(s)
- Leor Williams
- Department of Plant Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | | | | | | | | | | |
Collapse
|