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Shang JY, Lu YJ, Cai XW, Su YN, Feng C, Li L, Chen S, He XJ. COMPASS functions as a module of the INO80 chromatin remodeling complex to mediate histone H3K4 methylation in Arabidopsis. THE PLANT CELL 2021; 33:3250-3271. [PMID: 34270751 PMCID: PMC8505878 DOI: 10.1093/plcell/koab187] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 07/11/2021] [Indexed: 05/26/2023]
Abstract
In the INO80 chromatin remodeling complex, all of the accessory subunits are assembled on the following three domains of INO80: N-terminal domain (NTD), HSA domain, and ATPase domain. Although the ATPase and HSA domains and their interacting accessory subunits are known to be responsible for chromatin remodeling, it is largely unknown how the accessory subunits that interact with the INO80 NTD regulate chromatin status. Here, we identify both conserved and nonconserved accessory subunits that interact with the three domains in the INO80 complex in Arabidopsis thaliana. While the accessory subunits that interact with all the three INO80 domains can mediate transcriptional repression, the INO80 NTD and the accessory subunits interact with it can contribute to transcriptional activation even when the ATPase domain is absent, suggesting that INO80 has an ATPase-independent role. A subclass of the COMPASS histone H3K4 methyltransferase complexes interact with the INO80 NTD in the INO80 complex and function together with the other accessory subunits that interact with the INO80 NTD, thereby facilitating H3K4 trimethylation and transcriptional activation. This study suggests that the opposite effects of the INO80 complex on transcription are required for the balance between vegetative growth and flowering under diverse environmental conditions.
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Affiliation(s)
| | | | - Xue-Wei Cai
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Yin-Na Su
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Chao Feng
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Lin Li
- National Institute of Biological Sciences, Beijing, 102206, China
| | - She Chen
- National Institute of Biological Sciences, Beijing, 102206, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, 100084, China
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Rona GB, Almeida NP, Santos GC, Fidalgo TKS, Almeida FCL, Eleutherio ECA, Pinheiro AS. 1
H NMR metabolomics reveals increased glutaminolysis upon overexpression of NSD3s or Pdp3 in
Saccharomyces cerevisiae. J Cell Biochem 2018; 120:5377-5385. [DOI: 10.1002/jcb.27816] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 09/12/2018] [Indexed: 12/16/2022]
Affiliation(s)
- Germana B Rona
- Department of Biochemistry Institute of Chemistry, Federal University of Rio de Janeiro Rio de Janeiro Brazil
| | - Natalia P Almeida
- Department of Biochemistry Institute of Chemistry, Federal University of Rio de Janeiro Rio de Janeiro Brazil
| | - Gilson C Santos
- National Center for Nuclear Magnetic Resonance Jiri Jonas (CNRMN), Structural Biology Program, Medical Biochemistry Institute and Center for Structural Biology and Bioimaging I (CENABIO I), Federal University of Rio de Janeiro Rio de Janeiro Brazil
| | - Tatiana KS Fidalgo
- Department of Preventive and Community Dentistry, School of Dentistry, State University of Rio de Janeiro Rio de Janeiro Brazil
| | - Fabio CL Almeida
- National Center for Nuclear Magnetic Resonance Jiri Jonas (CNRMN), Structural Biology Program, Medical Biochemistry Institute and Center for Structural Biology and Bioimaging I (CENABIO I), Federal University of Rio de Janeiro Rio de Janeiro Brazil
| | - Elis CA Eleutherio
- Department of Biochemistry Institute of Chemistry, Federal University of Rio de Janeiro Rio de Janeiro Brazil
| | - Anderson S Pinheiro
- Department of Biochemistry Institute of Chemistry, Federal University of Rio de Janeiro Rio de Janeiro Brazil
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Tan LM, Zhang CJ, Hou XM, Shao CR, Lu YJ, Zhou JX, Li YQ, Li L, Chen S, He XJ. The PEAT protein complexes are required for histone deacetylation and heterochromatin silencing. EMBO J 2018; 37:embj.201798770. [PMID: 30104406 DOI: 10.15252/embj.201798770] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 06/27/2018] [Accepted: 06/28/2018] [Indexed: 01/26/2023] Open
Abstract
In eukaryotes, heterochromatin regions are typically subjected to transcriptional silencing. DNA methylation has an important role in such silencing and has been studied extensively. However, little is known about how methylated heterochromatin regions are subjected to silencing. We conducted a genetic screen and identified an epcr (enhancer of polycomb-related) mutant that releases heterochromatin silencing in Arabidopsis thaliana We demonstrated that EPCR1 functions redundantly with its paralog EPCR2 and interacts with PWWP domain-containing proteins (PWWPs), AT-rich interaction domain-containing proteins (ARIDs), and telomere repeat binding proteins (TRBs), thus forming multiple functionally redundant protein complexes named PEAT (PWWPs-EPCRs-ARIDs-TRBs). The PEAT complexes mediate histone deacetylation and heterochromatin condensation and thereby facilitate heterochromatin silencing. In heterochromatin regions, the production of small interfering RNAs (siRNAs) and DNA methylation is repressed by the PEAT complexes. The study reveals how histone deacetylation, heterochromatin condensation, siRNA production, and DNA methylation interplay with each other and thereby maintain heterochromatin silencing.
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Affiliation(s)
- Lian-Mei Tan
- National Institute of Biological Sciences, Beijing, China.,Graduate School of Peking Union Medical College, Beijing, China
| | - Cui-Jun Zhang
- National Institute of Biological Sciences, Beijing, China
| | - Xiao-Mei Hou
- National Institute of Biological Sciences, Beijing, China
| | | | - Yu-Jia Lu
- National Institute of Biological Sciences, Beijing, China
| | - Jin-Xing Zhou
- National Institute of Biological Sciences, Beijing, China
| | - Yong-Qiang Li
- National Institute of Biological Sciences, Beijing, China
| | - Lin Li
- National Institute of Biological Sciences, Beijing, China
| | - She Chen
- National Institute of Biological Sciences, Beijing, China
| | - Xin-Jian He
- National Institute of Biological Sciences, Beijing, China .,Graduate School of Peking Union Medical College, Beijing, China
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Hohenstatt ML, Mikulski P, Komarynets O, Klose C, Kycia I, Jeltsch A, Farrona S, Schubert D. PWWP-DOMAIN INTERACTOR OF POLYCOMBS1 Interacts with Polycomb-Group Proteins and Histones and Regulates Arabidopsis Flowering and Development. THE PLANT CELL 2018; 30:117-133. [PMID: 29330200 PMCID: PMC5810566 DOI: 10.1105/tpc.17.00117] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Revised: 11/28/2017] [Accepted: 01/09/2018] [Indexed: 05/10/2023]
Abstract
Polycomb-group (PcG) proteins mediate epigenetic gene regulation by setting H3K27me3 via Polycomb Repressive Complex 2 (PRC2). In plants, it is largely unclear how PcG proteins are recruited to their target genes. Here, we identified the PWWP-DOMAIN INTERACTOR OF POLYCOMBS1 (PWO1) protein, which interacts with all three Arabidopsis thaliana PRC2 histone methyltransferases and is required for maintaining full H3 occupancy at several Arabidopsis genes. PWO1 localizes and recruits CURLY LEAF to nuclear speckles in Nicotiana benthamiana nuclei, suggesting a role in spatial organization of PcG regulation. PWO1 belongs to a gene family with three members having overlapping activities: pwo1 pwo2 pwo3 triple mutants are seedling lethal and show shoot and root meristem arrest, while pwo1 single mutants are early flowering. Interestingly, the PWWP domain of PWO1 confers binding to histones, which is reduced by a point mutation in a highly conserved residue of this domain and blocked by phosphorylation of H3S28. PWO1 carrying this mutation is not able to fully complement the pwo1 pwo2 pwo3 triple mutant, indicating the requirement of this domain for PWO1 in vivo activity. Thus, the PWO family may present a novel class of histone readers that are involved in recruiting PcG proteins to subnuclear domains and in promoting Arabidopsis development.
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Affiliation(s)
| | - Pawel Mikulski
- Institute for Genetics, Heinrich-Heine-University, 40225 Duesseldorf, Germany
- Institute of Biology, Freie Universität, 14195 Berlin, Germany
| | - Olga Komarynets
- Institute for Genetics, Heinrich-Heine-University, 40225 Duesseldorf, Germany
- Université de Genève, 1205 Geneva, Switzerland
| | - Constanze Klose
- Institute for Genetics, Heinrich-Heine-University, 40225 Duesseldorf, Germany
| | - Ina Kycia
- Institute for Biochemistry, University of Stuttgart, 70174 Stuttgart, Germany
| | - Albert Jeltsch
- Institute for Biochemistry, University of Stuttgart, 70174 Stuttgart, Germany
| | - Sara Farrona
- Institute for Genetics, Heinrich-Heine-University, 40225 Duesseldorf, Germany
- Plant and AgriBiosciences Centre, National University Ireland, Galway H91 TK33, Ireland
| | - Daniel Schubert
- Institute for Genetics, Heinrich-Heine-University, 40225 Duesseldorf, Germany
- Institute of Biology, Freie Universität, 14195 Berlin, Germany
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5
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Sadiq I, Keren I, Citovsky V. Plant homologs of mammalian MBT-domain protein-regulated KDM1 histone lysine demethylases do not interact with plant Tudor/PWWP/MBT-domain proteins. Biochem Biophys Res Commun 2016; 470:913-6. [PMID: 26826387 DOI: 10.1016/j.bbrc.2016.01.151] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Accepted: 01/23/2016] [Indexed: 11/17/2022]
Abstract
Histone lysine demethylases of the LSD1/KDM1 family play important roles in epigenetic regulation of eukaryotic chromatin, and they are conserved between plants and animals. Mammalian LSD1 is thought to be targeted to its substrates, i.e., methylated histones, by an MBT-domain protein SFMBT1 that represents a component of the LSD1-based repressor complex and binds methylated histones. Because MBT-domain proteins are conserved between different organisms, from animals to plants, we examined whether the KDM1-type histone lysine demethylases KDM1C and FLD of Arabidopsis interact with the Arabidopsis Tudor/PWWP/MBT-domain SFMBT1-like proteins SL1, SL2, SL3, and SL4. No such interaction was detected using the bimolecular fluorescence complementation assay in living plant cells. Thus, plants most likely direct their KDM1 chromatin-modifying enzymes to methylated histones of the target chromatin by a mechanism different from that employed by the mammalian cells.
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Affiliation(s)
- Irfan Sadiq
- Department of Biochemistry and Cell Biology, State University of New York, Stony Brook, NY, 11794-5215, USA; Department of Biosciences, COMSATS Institute of Information Technology Islamabad, Park Road, Islamabad, 44000, Pakistan.
| | - Ido Keren
- Department of Biochemistry and Cell Biology, State University of New York, Stony Brook, NY, 11794-5215, USA.
| | - Vitaly Citovsky
- Department of Biochemistry and Cell Biology, State University of New York, Stony Brook, NY, 11794-5215, USA.
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6
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Kenzior A, Folk WR. Arabidopsis thaliana MSI4/FVE associates with members of a novel family of plant specific PWWP/RRM domain proteins. PLANT MOLECULAR BIOLOGY 2015; 87:329-339. [PMID: 25600937 DOI: 10.1007/s11103-014-0280-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Accepted: 12/30/2014] [Indexed: 06/04/2023]
Abstract
AtMSI4/FVE/ACG1, one of five Arabidopsis thaliana genes encoding MSI1-like proteins, helps determine plant growth and development (including control of flowering), as well as responses to certain biotic and abiotic stresses. We reasoned that the product of this gene, AtMSI4, acts through protein partners, which we have co-immunopurified with AtMSI4 from A. thaliana suspension culture cells and identified by liquid chromatography-mass spectrometry (LC-MS). Many of the proteins associated with AtMSI4 have distinct RNA recognition motif (RRM) domains, which we determined to be responsible for association with AtMSI4; and most of the associated RRM domain proteins also contain PWWP domains that are specific to plants. We propose these novel ATMSI4-associated proteins help form nucleoprotein complexes that determine pleiotropic functional properties of AtMSI4/FVE/ACG1 involving plant development and responses to stress.
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Affiliation(s)
- Alexander Kenzior
- Department of Biochemistry, University of Missouri, 117 Schweitzer Hall, Columbia, MO, 65211, USA,
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Fromm M, Avramova Z. ATX1/AtCOMPASS and the H3K4me3 marks: how do they activate Arabidopsis genes? CURRENT OPINION IN PLANT BIOLOGY 2014; 21:75-82. [PMID: 25047977 DOI: 10.1016/j.pbi.2014.07.004] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Revised: 06/26/2014] [Accepted: 07/02/2014] [Indexed: 06/03/2023]
Abstract
Despite the proven correlation between gene transcriptional activity and the levels of tri-methyl marks on histone 3 lysine4 (H3K4me3) of their nucleosomes, whether H3K4me3 contributes to, or 'registers', activated transcription is still controversial. Other questions of broad relevance are whether histone-modifying proteins are involved in the recruitment of Pol II and the general transcription machinery and whether they have roles other than their enzyme activities. We address these questions as well as the roles of the ARABIDOPSIS HOMOLOG OF TRITHORAX1 (ATX1), of the COMPASS-related (AtCOMPASS) protein complex, and of their product, H3K4me3, at ATX1-dependent genes. We suggest that the ambiguity about the role of H3K4me3 as an activating mark is due to the unknown duality of the ATX1/AtCOMPASS to facilitate PIC assembly and to generate H3K4me3, which is essential for activating transcriptional elongation.
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Affiliation(s)
- Michael Fromm
- Department of Agronomy and Plant Science Innovation, UNL, Lincoln, NE 68588-6008, USA
| | - Zoya Avramova
- School of Biological Science, UNL, Lincoln, NE 68588-6008, USA.
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Jali SS, Rosloski SM, Janakirama P, Steffen JG, Zhurov V, Berleth T, Clark RM, Grbic V. A plant-specific HUA2-LIKE (HULK) gene family in Arabidopsis thaliana is essential for development. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 80:242-54. [PMID: 25070081 PMCID: PMC4283595 DOI: 10.1111/tpj.12629] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Revised: 07/11/2014] [Accepted: 07/21/2014] [Indexed: 05/23/2023]
Abstract
In Arabidopsis thaliana, the HUA2 gene is required for proper expression of FLOWERING LOCUS C (FLC) and AGAMOUS, key regulators of flowering time and reproductive development, respectively. Although HUA2 is broadly expressed, plants lacking HUA2 function have only moderately reduced plant stature, leaf initiation rate and flowering time. To better understand HUA2 activity, and to test whether redundancy with similar genes underlies the absence of strong phenotypes in HUA2 mutant plants, we identified and subsequently characterized three additional HUA2-LIKE (HULK) genes in Arabidopsis. These genes form two clades (HUA2/HULK1 and HULK2/HULK3), with members broadly conserved in both vascular and non-vascular plants, but not present outside the plant kingdom. Plants with progressively reduced HULK activity had increasingly severe developmental defects, and plants homozygous for loss-of-function mutations in all four HULK genes were not recovered. Multiple mutants displayed reproductive, embryonic and post-embryonic abnormalities, and provide detailed insights into the overlapping and unique functions of individual HULK genes. With regard to flowering time, opposing influences were apparent: hua2 hulk1 plants were early-flowering, while hulk2 hulk3 mutants were late-flowering, and hua2 acted epistatically to cause early flowering in all combinations. Genome-wide expression profiling of mutant combinations using RNA-Seq revealed complex transcriptional changes in seedlings, with FLC, a known target of HUA2, among the most affected. Our studies, which include characterization of HULK expression patterns and subcellular localization, suggest that the HULK genes encode conserved nuclear factors with partially redundant but essential functions associated with diverse genetic pathways in plants.
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Affiliation(s)
- Sathya S Jali
- Department of Biology, Western UniversityLondon, ON, N6A 5B7, Canada
| | - Sarah M Rosloski
- Department of Biology, Western UniversityLondon, ON, N6A 5B7, Canada
| | | | - Joshua G Steffen
- Department of Biology, University of UtahSalt Lake City, UT, 84112, USA
- Center for Cell and Genome Science, University of UtahSalt Lake City, UT, 84112, USA
| | - Vladimir Zhurov
- Department of Biology, Western UniversityLondon, ON, N6A 5B7, Canada
| | - Thomas Berleth
- Department of Cell and Systems Biology, University of TorontoToronto, ON, M5S 3B2, Canada
| | - Richard M Clark
- Department of Biology, University of UtahSalt Lake City, UT, 84112, USA
- Center for Cell and Genome Science, University of UtahSalt Lake City, UT, 84112, USA
| | - Vojislava Grbic
- Department of Biology, Western UniversityLondon, ON, N6A 5B7, Canada
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9
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Chen X, Chan WL, Zhu FY, Lo C. Phosphoproteomic analysis of the non-seed vascular plant model Selaginella moellendorffii. Proteome Sci 2014; 12:16. [PMID: 24628833 PMCID: PMC4022089 DOI: 10.1186/1477-5956-12-16] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2013] [Accepted: 03/06/2014] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Selaginella (Selaginella moellendorffii) is a lycophyte which diverged from other vascular plants approximately 410 million years ago. As the first reported non-seed vascular plant genome, Selaginella genome data allow comparative analysis of genetic changes that may be associated with land plant evolution. Proteomics investigations on this lycophyte model have not been extensively reported. Phosphorylation represents the most common post-translational modifications and it is a ubiquitous regulatory mechanism controlling the functional expression of proteins inside living organisms. RESULTS In this study, polyethylene glycol fractionation and immobilized metal ion affinity chromatography were employed to isolate phosphopeptides from wild-growing Selaginella. Using liquid chromatography-tandem mass spectrometry analysis, 1593 unique phosphopeptides spanning 1104 non-redundant phosphosites with confirmed localization on 716 phosphoproteins were identified. Analysis of the Selaginella dataset revealed features that are consistent with other plant phosphoproteomes, such as the relative proportions of phosphorylated Ser, Thr, and Tyr residues, the highest occurrence of phosphosites in the C-terminal regions of proteins, and the localization of phosphorylation events outside protein domains. In addition, a total of 97 highly conserved phosphosites in evolutionary conserved proteins were identified, indicating the conservation of phosphorylation-dependent regulatory mechanisms in phylogenetically distinct plant species. On the other hand, close examination of proteins involved in photosynthesis revealed phosphorylation events which may be unique to Selaginella evolution. Furthermore, phosphorylation motif analyses identified Pro-directed, acidic, and basic signatures which are recognized by typical protein kinases in plants. A group of Selaginella-specific phosphoproteins were found to be enriched in the Pro-directed motif class. CONCLUSIONS Our work provides the first large-scale atlas of phosphoproteins in Selaginella which occupies a unique position in the evolution of terrestrial plants. Future research into the functional roles of Selaginella-specific phosphorylation events in photosynthesis and other processes may offer insight into the molecular mechanisms leading to the distinct evolution of lycophytes.
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Affiliation(s)
- Xi Chen
- School of Biological Sciences, The University of Hong Kong, Pokfulam Hong Kong, China.,Wuhan Institute of Biotechnology, Wuhan, Hubei, China
| | - Wai Lung Chan
- School of Biological Sciences, The University of Hong Kong, Pokfulam Hong Kong, China
| | - Fu-Yuan Zhu
- School of Biological Sciences, The University of Hong Kong, Pokfulam Hong Kong, China
| | - Clive Lo
- School of Biological Sciences, The University of Hong Kong, Pokfulam Hong Kong, China
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Abstract
The nematode Caenorhabditis elegans (C. elegans) has four Sir2 paralogs, sir-2.1, sir-2.2, sir-2.3, and sir-2.4. Thus far, most of the research tools to study worm sirtuins have been developed for sir-2.1, due to its homology to yeast SIR2 and human SIRT1. Here, we have compiled a listing of the currently available strains (including both loss-of-function alleles and transgenics), antibodies, and RNAi constructs relevant to studies on all C. elegans sirtuin family members. We also describe the methods used in the analysis of C. elegans sirtuin function, including life span analysis, various stress-resistance assays, and fat content analysis and provide an overview of all phenotypic data relevant to C. elegans sir-2.1.
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Affiliation(s)
- Mohan Viswanathan
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
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