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Frohlich J, Liorni N, Mangoni M, Lochmanová G, Pírek P, Kaštánková N, Pata P, Kucera J, Chaldakov GN, Tonchev AB, Pata I, Gorbunova V, Leire E, Zdráhal Z, Mazza T, Vinciguerra M. Epigenetic and transcriptional control of adipocyte function by centenarian-associated SIRT6 N308K/A313S mutant. Clin Epigenetics 2024; 16:96. [PMID: 39033117 PMCID: PMC11265064 DOI: 10.1186/s13148-024-01710-1] [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: 05/14/2024] [Accepted: 07/18/2024] [Indexed: 07/23/2024] Open
Abstract
BACKGROUND Obesity is a major health burden. Preadipocytes proliferate and differentiate in mature adipocytes in the adipogenic process, which could be a potential therapeutic approach for obesity. Deficiency of SIRT6, a stress-responsive protein deacetylase and mono-ADP ribosyltransferase enzyme, blocks adipogenesis. Mutants of SIRT6 (N308K/A313S) were recently linked to the in the long lifespan Ashkenazi Jews. In this study, we aimed to clarify how these new centenarian-associated SIRT6 genetic variants affect adipogenesis at the transcriptional and epigenetic level. METHODS We analyzed the role of SIRT6 wild-type (WT) or SIRT6 centenarian-associated mutant (N308K/A313S) overexpression in adipogenesis, by creating stably transduced preadipocyte cell lines using lentivirus on the 3T3-L1 model. Histone post-translational modifications (PTM: acetylation, methylation) and transcriptomic changes were analyzed by mass spectrometry (LC-MS/MS) and RNA-Seq, respectively, in 3T3-L1 adipocytes. In addition, the adipogenic process and related signaling pathways were investigated by bioinformatics and biochemical approaches. RESULTS Overexpression of centenarian-associated SIRT6 mutant increased adipogenic differentiation to a similar extent compared to the WT form. However, it triggered distinct histone PTM profiles in mature adipocytes, with significantly higher acetylation levels, and activated divergent transcriptional programs, including those dependent on signaling related to the sympathetic innervation and to PI3K pathway. 3T3-L1 mature adipocytes overexpressing SIRT6 N308K/A313S displayed increased insulin sensitivity in a neuropeptide Y (NPY)-dependent manner. CONCLUSIONS SIRT6 N308K/A313S overexpression in mature adipocytes ameliorated glucose sensitivity and impacted sympathetic innervation signaling. These findings highlight the importance of targeting SIRT6 enzymatic activities to regulate the co-morbidities associated with obesity.
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Affiliation(s)
- Jan Frohlich
- International Clinical Research Center, St. Anne's University Hospital and Masaryk University, Brno, Czech Republic
| | - Niccolò Liorni
- IRCCS, Bioinformatics Unit, Casa Sollievo Della Sofferenza, San Giovanni Rotondo, Italy
| | - Manuel Mangoni
- IRCCS, Bioinformatics Unit, Casa Sollievo Della Sofferenza, San Giovanni Rotondo, Italy
| | - Gabriela Lochmanová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Pavlína Pírek
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Nikola Kaštánková
- International Clinical Research Center, St. Anne's University Hospital and Masaryk University, Brno, Czech Republic
| | | | - Jan Kucera
- RECETOX, Faculty of Science, Masaryk University, Brno, Czech Republic
- Department of Physical Activities and Health, Faculty of Sports Studies, Masaryk University, Brno, Czech Republic
| | - George N Chaldakov
- Department of Translational Stem Cell Biology, Research Institute of the Medical University, Varna, Bulgaria
- Department of Anatomy and Cell Biology, Faculty of Medicine, Varna, Bulgaria
| | - Anton B Tonchev
- Department of Translational Stem Cell Biology, Research Institute of the Medical University, Varna, Bulgaria
- Department of Anatomy and Cell Biology, Faculty of Medicine, Varna, Bulgaria
| | | | - Vera Gorbunova
- Departments of Biology and Medicine, University of Rochester, Rochester, NY, USA
| | - Eric Leire
- GenFlow Biosciences Srl, Charleroi, Belgium
- Clinique 135, Brussels, Belgium
| | - Zbyněk Zdráhal
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Tommaso Mazza
- IRCCS, Bioinformatics Unit, Casa Sollievo Della Sofferenza, San Giovanni Rotondo, Italy
| | - Manlio Vinciguerra
- International Clinical Research Center, St. Anne's University Hospital and Masaryk University, Brno, Czech Republic.
- Department of Translational Stem Cell Biology, Research Institute of the Medical University, Varna, Bulgaria.
- Faculty of Science, Liverpool John Moores University (LJMU), Liverpool, UK.
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Franek M, Nešpor Dadejová M, Pírek P, Kryštofová K, Dobisová T, Zdráhal Z, Dvořáčková M, Lochmanová G. Histone Chaperone Deficiency in Arabidopsis Plants Triggers Adaptive Epigenetic Changes in Histone Variants and Modifications. Mol Cell Proteomics 2024; 23:100795. [PMID: 38848995 PMCID: PMC11263794 DOI: 10.1016/j.mcpro.2024.100795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 05/14/2024] [Accepted: 06/04/2024] [Indexed: 06/09/2024] Open
Abstract
At the molecular scale, adaptive advantages during plant growth and development rely on modulation of gene expression, primarily provided by epigenetic machinery. One crucial part of this machinery is histone posttranslational modifications, which form a flexible system, driving transient changes in chromatin, and defining particular epigenetic states. Posttranslational modifications work in concert with replication-independent histone variants further adapted for transcriptional regulation and chromatin repair. However, little is known about how such complex regulatory pathways are orchestrated and interconnected in cells. In this work, we demonstrate the utility of mass spectrometry-based approaches to explore how different epigenetic layers interact in Arabidopsis mutants lacking certain histone chaperones. We show that defects in histone chaperone function (e.g., chromatin assembly factor-1 or nucleosome assembly protein 1 mutations) translate into an altered epigenetic landscape, which aids the plant in mitigating internal instability. We observe changes in both the levels and distribution of H2A.W.7, altogether with partial repurposing of H3.3 and changes in the key repressive (H3K27me1/2) or euchromatic marks (H3K36me1/2). These shifts in the epigenetic profile serve as a compensatory mechanism in response to impaired integration of the H3.1 histone in the fas1 mutants. Altogether, our findings suggest that maintaining genome stability involves a two-tiered approach. The first relies on flexible adjustments in histone marks, while the second level requires the assistance of chaperones for histone variant replacement.
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Affiliation(s)
- Michal Franek
- Mendel Center for Plant Genomics and Proteomics, Central European Institute of Technology, Brno, Czech Republic
| | - Martina Nešpor Dadejová
- Mendel Center for Plant Genomics and Proteomics, Central European Institute of Technology, Brno, Czech Republic
| | - Pavlína Pírek
- Mendel Center for Plant Genomics and Proteomics, Central European Institute of Technology, Brno, Czech Republic
| | - Karolína Kryštofová
- Mendel Center for Plant Genomics and Proteomics, Central European Institute of Technology, Brno, Czech Republic; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | | | - Zbyněk Zdráhal
- Mendel Center for Plant Genomics and Proteomics, Central European Institute of Technology, Brno, Czech Republic; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Martina Dvořáčková
- Mendel Center for Plant Genomics and Proteomics, Central European Institute of Technology, Brno, Czech Republic; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic.
| | - Gabriela Lochmanová
- Mendel Center for Plant Genomics and Proteomics, Central European Institute of Technology, Brno, Czech Republic; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic.
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Pírek P, Kryštofová K, Kováčová I, Kromerová A, Zachová D, Helia O, Panzarová K, Fajkus J, Zdráhal Z, Lochmanová G, Fojtová M. Unraveling Epigenetic Changes in A. thaliana Calli: Impact of HDAC Inhibitors. PLANTS (BASEL, SWITZERLAND) 2023; 12:4177. [PMID: 38140504 PMCID: PMC10747063 DOI: 10.3390/plants12244177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 11/29/2023] [Accepted: 12/12/2023] [Indexed: 12/24/2023]
Abstract
The ability for plant regeneration from dedifferentiated cells opens up the possibility for molecular bioengineering to produce crops with desirable traits. Developmental and environmental signals that control cell totipotency are regulated by gene expression via dynamic chromatin remodeling. Using a mass spectrometry-based approach, we investigated epigenetic changes to the histone proteins during callus formation from roots and shoots of Arabidopsis thaliana seedlings. Increased levels of the histone H3.3 variant were found to be the major and most prominent feature of 20-day calli, associated with chromatin relaxation. The methylation status in root- and shoot-derived calli reached the same level during long-term propagation, whereas differences in acetylation levels provided a long-lasting imprint of root and shoot origin. On the other hand, epigenetic signs of origin completely disappeared during 20 days of calli propagation in the presence of histone deacetylase inhibitors (HDACi), sodium butyrate, and trichostatin A. Each HDACi affected the state of post-translational histone modifications in a specific manner; NaB-treated calli were epigenetically more similar to root-derived calli, and TSA-treated calli resembled shoot-derived calli.
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Affiliation(s)
- Pavlína Pírek
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, 62500 Brno, Czech Republic; (P.P.); (K.K.); (I.K.); (D.Z.); (J.F.); (Z.Z.)
| | - Karolína Kryštofová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, 62500 Brno, Czech Republic; (P.P.); (K.K.); (I.K.); (D.Z.); (J.F.); (Z.Z.)
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic;
| | - Ingrid Kováčová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, 62500 Brno, Czech Republic; (P.P.); (K.K.); (I.K.); (D.Z.); (J.F.); (Z.Z.)
| | - Anna Kromerová
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic;
| | - Dagmar Zachová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, 62500 Brno, Czech Republic; (P.P.); (K.K.); (I.K.); (D.Z.); (J.F.); (Z.Z.)
| | - Ondřej Helia
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, 62500 Brno, Czech Republic; (P.P.); (K.K.); (I.K.); (D.Z.); (J.F.); (Z.Z.)
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic;
| | - Klára Panzarová
- PSI (Photon Systems Instruments), spol. s.r.o., 66424 Drásov, Czech Republic;
| | - Jiří Fajkus
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, 62500 Brno, Czech Republic; (P.P.); (K.K.); (I.K.); (D.Z.); (J.F.); (Z.Z.)
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic;
| | - Zbyněk Zdráhal
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, 62500 Brno, Czech Republic; (P.P.); (K.K.); (I.K.); (D.Z.); (J.F.); (Z.Z.)
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic;
| | - Gabriela Lochmanová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, 62500 Brno, Czech Republic; (P.P.); (K.K.); (I.K.); (D.Z.); (J.F.); (Z.Z.)
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic;
| | - Miloslava Fojtová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, 62500 Brno, Czech Republic; (P.P.); (K.K.); (I.K.); (D.Z.); (J.F.); (Z.Z.)
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic;
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Barbosa H, Ramadan W, Matzenbacher dos Santos J, Benite-Ribeiro SA. Effects of Physical Exercise on Mitochondrial Biogenesis of Skeletal Muscle Modulated by Histones Modifications in Type 2 Diabetes. Open Access Maced J Med Sci 2022. [DOI: 10.3889/oamjms.2022.10095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Epigenetic modification in skeletal muscle induced by environmental factors seems to modulate several metabolic pathways that underlie Type 2 Diabetes Mellitus (T2DM) development. Mitochondrial biogenesis is an important process for maintaining lipid metabolism homeostasis, as well as epigenetic modifications in proteins that regulate this pathway have been observed in the skeletal muscle of T2DM subjects. Moreover, physical exercise affects several metabolic pathways attenuating metabolic deregulation observed in T2DM. The pathways that regulate mitochondrial homeostasis are one of the key components for understanding such physical exercise beneficial effects. Thus, in this study, we investigate the epigenetic mechanisms underlying mitochondrial biogenesis in the skeletal muscle in T2DM, focusing on histone modifications and the possible mechanisms by which physical exercise delay or inhibit T2DM onset. The results indicate that exercise promotes improvements in cellular metabolism through increasing enzymes of the antioxidant system, AMPK and ATP-citrate lyase activity, Acetyl-CoA concentration, and enhancing the acetylation of histones. A key mediator of mitochondrial biogenesis such as peroxisome proliferator-activated receptor γ coactivator-1α (PGC1) seems to be upregulated by exercise in T2DM and such factor positively regulates the skeletal muscle mitochondrial biogenesis, which improves energy metabolism and glucose homeostasis inhibiting or delaying insulin resistance and further T2DM.
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Quantitative Acetylomics Uncover Acetylation-Mediated Pathway Changes Following Histone Deacetylase Inhibition in Anaplastic Large Cell Lymphoma. Cells 2022; 11:cells11152380. [PMID: 35954222 PMCID: PMC9368142 DOI: 10.3390/cells11152380] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 07/28/2022] [Accepted: 07/30/2022] [Indexed: 12/10/2022] Open
Abstract
Histone deacetylases (HDACs) target acetylated lysine residues in histone and non-histone proteins. HDACs are implicated in the regulation of genomic stability, cell cycle, cell death and differentiation and thus critically involved in tumorigenesis. Further, HDACs regulate T-cell development and HDAC inhibitors (HDACis) have been approved for clinical use in some T-cell malignancies. Still, the exact targets and mechanisms of HDAC inhibition in cancer are understudied. We isolated tumor cell lines from a transgenic mouse model of anaplastic large cell lymphoma (ALCL), a rare T-cell lymphoma, and abrogated HDAC activity by treatment with the HDACis Vorinostat and Entinostat or Cre-mediated deletion of Hdac1. Changes in overall protein expression as well as histone and protein acetylation were measured following Hdac1 deletion or pharmacological inhibition using label-free liquid chromatography mass spectrometry (LC-MS/MS). We found changes in overall protein abundance and increased acetylation of histones and non-histone proteins, many of which were newly discovered and associated with major metabolic and DNA damage pathways. For non-histone acetylation, we mapped a total of 1204 acetylated peptides corresponding to 603 proteins, including chromatin modifying proteins and transcription factors. Hyperacetylated proteins were involved in processes such as transcription, RNA metabolism and DNA damage repair (DDR). The DDR pathway was majorly affected by hyperacetylation following HDAC inhibition. This included acetylation of H2AX, PARP1 and previously unrecognized acetylation sites in TP53BP1. Our data provide a comprehensive view of the targets of HDAC inhibition in malignant T cells with general applicability and could have translational impact for the treatment of ALCL with HDACis alone or in combination therapies.
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Vincent SA, Kim JM, Pérez-Salamó I, To TK, Torii C, Ishida J, Tanaka M, Endo TA, Bhat P, Devlin PF, Seki M, Devoto A. Jasmonates and Histone deacetylase 6 activate Arabidopsis genome-wide histone acetylation and methylation during the early acute stress response. BMC Biol 2022; 20:83. [PMID: 35399062 PMCID: PMC8996529 DOI: 10.1186/s12915-022-01273-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 03/07/2022] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND Jasmonates (JAs) mediate trade-off between responses to both biotic and abiotic stress and growth in plants. The Arabidopsis thaliana HISTONE DEACETYLASE 6 is part of the CORONATINE INSENSITIVE1 receptor complex, co-repressing the HDA6/COI1-dependent acetic acid-JA pathway that confers plant drought tolerance. The decrease in HDA6 binding to target DNA mirrors histone H4 acetylation (H4Ac) changes during JA-mediated drought response, and mutations in HDA6 also cause depletion in the constitutive repressive marker H3 lysine 27 trimethylation (H3K27me3). However, the genome-wide effect of HDA6 on H4Ac and much of the impact of JAs on histone modifications and chromatin remodelling remain elusive. RESULTS We performed high-throughput ChIP-Seq on the HDA6 mutant, axe1-5, and wild-type plants with or without methyl jasmonate (MeJA) treatment to assess changes in active H4ac and repressive H3K27me3 histone markers. Transcriptional regulation was investigated in parallel by microarray analysis in the same conditions. MeJA- and HDA6-dependent histone modifications on genes for specialized metabolism; linolenic acid and phenylpropanoid pathways; and abiotic and biotic stress responses were identified. H4ac and H3K27me3 enrichment also differentially affects JAs and HDA6-mediated genome integrity and gene regulatory networks, substantiating the role of HDA6 interacting with specific families of transposable elements in planta and highlighting further specificity of action as well as novel targets of HDA6 in the context of JA signalling for abiotic and biotic stress responses. CONCLUSIONS The findings demonstrate functional overlap for MeJA and HDA6 in tuning plant developmental plasticity and response to stress at the histone modification level. MeJA and HDA6, nonetheless, maintain distinct activities on histone modifications to modulate genetic variability and to allow adaptation to environmental challenges.
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Affiliation(s)
- Stacey A Vincent
- Plant Molecular Science and Centre of Systems and Synthetic Biology, Department of Biological Sciences, Royal Holloway University of London, Egham, Surrey, TW20 0EX, UK
| | - Jong-Myong Kim
- Center for Sustainable Resource Science, RIKEN, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan
- Cluster for Pioneering Research, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
- Present address: Ac-Planta Inc., 2-16-9 Yushima, Bunkyo-ku, Tokyo, 113-0034, Japan
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Imma Pérez-Salamó
- Plant Molecular Science and Centre of Systems and Synthetic Biology, Department of Biological Sciences, Royal Holloway University of London, Egham, Surrey, TW20 0EX, UK
| | - Taiko Kim To
- Center for Sustainable Resource Science, RIKEN, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan
- Cluster for Pioneering Research, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
- Present address: Department of Biological Sciences, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Chieko Torii
- Center for Sustainable Resource Science, RIKEN, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan
- Cluster for Pioneering Research, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Junko Ishida
- Center for Sustainable Resource Science, RIKEN, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan
- Cluster for Pioneering Research, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Maho Tanaka
- Center for Sustainable Resource Science, RIKEN, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan
- Cluster for Pioneering Research, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Takaho A Endo
- Bioinformatics and Systems Engineering Division, RIKEN, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan
- Present address: Center for Integrative Medical Sciences, RIKEN, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan
| | - Prajwal Bhat
- Plant Molecular Science and Centre of Systems and Synthetic Biology, Department of Biological Sciences, Royal Holloway University of London, Egham, Surrey, TW20 0EX, UK
| | - Paul F Devlin
- Plant Molecular Science and Centre of Systems and Synthetic Biology, Department of Biological Sciences, Royal Holloway University of London, Egham, Surrey, TW20 0EX, UK
| | - Motoaki Seki
- Center for Sustainable Resource Science, RIKEN, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan.
- Cluster for Pioneering Research, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.
| | - Alessandra Devoto
- Plant Molecular Science and Centre of Systems and Synthetic Biology, Department of Biological Sciences, Royal Holloway University of London, Egham, Surrey, TW20 0EX, UK.
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Sai CB, Chidambaranathan P, Samantaray S. Role of histone deacetylase inhibitors in androgenic callus induction of Oryza sativa sub indica, in sight into evolution and mode of action of histone deacetylase genes. Mol Biol Rep 2022; 49:2169-2183. [PMID: 34985645 DOI: 10.1007/s11033-021-07036-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 11/29/2021] [Indexed: 11/27/2022]
Abstract
BACKGROUND The potential of paddy breeding has reached its pinnacle, and hybrids have been the principal research outcome. Hence, our hypothesis was based on improvising the callus induction efficiency of recalcitrant Oryza sativa sub. indica hybrids by intervening into their cellular functions like cell division and histone regulation for the production of doubled haploids, a better output compared to hybrids. METHODOLOGY AND RESULTS Insight into the mechanism of cell division is the foremost concern in altering the same and hence studies on evolution, expression and action of histone deacetylase and its 12 genes (9 HDA and 3 HD-tunin genes) were chosen in the hypothesis. Expression of HDA genes at three stages (anther dehiscence, 1st callusing and second callusing stages) with inhibitor (trichostatin-A) interventions indicated 1st callusing stage as the most important in influencing callus induction and also the genes HDA19, 6, 15 and 5 were the most important. TSA alone had a significant impact on the regulation of the genes HDT 702, HDA19, HDA9, and HDA6. Higher expression of HDA19 and HDA6 was involved in maximizing callus induction; HDA15 had an antagonistic expression compared to HDA19/6 and might be involved in chlorophyll regulation during regeneration. Results of evolutionary analysis on histone deacetylases indicated a long and single lineage of origin denoting its importance in the basic cellular functions. The tubulin deacetylation gene HDA5, which was exclusively found in dicotyledons, had a recent evolutionary history only from terrestrial plants, and also had significant conservation in its motifs and NLS region. CONCLUSION By combating the recalcitrant nature of Indica cultivars, molecular editing on a combination of HDA genes will enhance the callus induction and regeneration efficiency of the next generation of doubled haploids, therby improving the total yield.
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Affiliation(s)
- Cayalvizhi B Sai
- Lab No 225, Crop Improvement Division, National Rice Research Institute (ICAR-NRRI), CRRI-Post, Cuttack, Odisha, 753006, India.
| | - Parameswaran Chidambaranathan
- Lab No 225, Crop Improvement Division, National Rice Research Institute (ICAR-NRRI), CRRI-Post, Cuttack, Odisha, 753006, India
| | - Sangamitra Samantaray
- Lab No 225, Crop Improvement Division, National Rice Research Institute (ICAR-NRRI), CRRI-Post, Cuttack, Odisha, 753006, India
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Kuchaříková H, Plšková Z, Zdráhal Z, Fojtová M, Kerchev P, Lochmanová G. Quantitative Analysis of Posttranslational Modifications of Plant Histones. Methods Mol Biol 2022; 2526:241-257. [PMID: 35657525 DOI: 10.1007/978-1-0716-2469-2_18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Reshaping of the chromatin landscape under oxidative stress is of paramount importance for mounting an effective stress response. Unbiased systemic identification and quantification of histone marks is crucial for understanding the epigenetic component of plant responses to adverse environmental conditions. We describe a detailed method for isolation of plant histones and subsequent bottom-up proteomics approach for characterization of acetylation and methylation status. By performing label-free quantitative mass spectrometry analysis, relative abundances of histone marks can be statistically compared between experimental conditions.
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Affiliation(s)
- Hana Kuchaříková
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Zuzana Plšková
- Phytophthora Research Centre, Department of Molecular Biology and Radiobiology, Faculty of AgriSciences, Mendel University in Brno, Brno, Czech Republic
| | - Zbyněk Zdráhal
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Miloslava Fojtová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Pavel Kerchev
- Phytophthora Research Centre, Department of Molecular Biology and Radiobiology, Faculty of AgriSciences, Mendel University in Brno, Brno, Czech Republic
| | - Gabriela Lochmanová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czech Republic.
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Kuchaříková H, Dobrovolná P, Lochmanová G, Zdráhal Z. Trimethylacetic Anhydride-Based Derivatization Facilitates Quantification of Histone Marks at the MS1 Level. Mol Cell Proteomics 2021; 20:100114. [PMID: 34129942 PMCID: PMC8283018 DOI: 10.1016/j.mcpro.2021.100114] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 05/11/2021] [Accepted: 06/08/2021] [Indexed: 12/30/2022] Open
Abstract
Histone post-translational modifications (hPTMs) are epigenetic marks that strongly affect numerous processes, including cell cycling and protein interactions. They have been studied by both antibody- and MS-based methods for years, but the analyses are still challenging, mainly because of the diversity of histones and their modifications arising from high contents of reactive amine groups in their amino acid sequences. Here, we introduce use of trimethylacetic anhydride (TMA) as a new reagent for efficient histone derivatization, which is a requirement for bottom-up proteomic hPTM analysis. TMA can derivatize unmodified amine groups of lysine residues and amine groups generated at peptide N-termini by trypsin digestion. The derivatization is facilitated by microwave irradiation, which also reduces incubation times to minutes. We demonstrate that histone derivatization with TMA reliably provides high yields of fully derivatized peptides and thus is an effective alternative to conventional methods. TMA afforded more than 98% and 99% labeling efficiencies for histones H4 and H3, respectively, thereby enabling accurate quantification of peptide forms. Trimethylacetylation substantially improves chromatographic separation of peptide forms, which is essential for direct quantification based on signals extracted from MS1 data. For this purpose, software widely applied by the proteomics community can be used without additional computational development. Thorough comparison with widely applied propionylation highlights the advantages of TMA-based histone derivatization for monitoring hPTMs in biological samples.
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Affiliation(s)
- Hana Kuchaříková
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic; Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Pavlína Dobrovolná
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Gabriela Lochmanová
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic.
| | - Zbyněk Zdráhal
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic; Faculty of Science, Masaryk University, Brno, Czech Republic.
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10
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10-hydroxy-2E-decenoic acid (10HDA) does not promote caste differentiation in Melipona scutellaris stingless bees. Sci Rep 2021; 11:9882. [PMID: 33972627 PMCID: PMC8110752 DOI: 10.1038/s41598-021-89212-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 04/16/2021] [Indexed: 02/03/2023] Open
Abstract
In bees from genus Melipona, differential feeding is not enough to fully explain female polyphenism. In these bees, there is a hypothesis that in addition to the environmental component (food), a genetic component is also involved in caste differentiation. This mechanism has not yet been fully elucidated and may involve epigenetic and metabolic regulation. Here, we verified that the genes encoding histone deacetylases HDAC1 and HDAC4 and histone acetyltransferase KAT2A were expressed at all stages of Melipona scutellaris, with fluctuations between developmental stages and castes. In larvae, the HDAC genes showed the same profile of Juvenile Hormone titers-previous reported-whereas the HAT gene exhibited the opposite profile. We also investigated the larvae and larval food metabolomes, but we did not identify the putative queen-fate inducing compounds, geraniol and 10-hydroxy-2E-decenoic acid (10HDA). Finally, we demonstrated that the histone deacetylase inhibitor 10HDA-the major lipid component of royal jelly and hence a putative regulator of honeybee caste differentiation-was unable to promote differentiation in queens in Melipona scutellaris. Our results suggest that epigenetic and hormonal regulations may act synergistically to drive caste differentiation in Melipona and that 10HDA is not a caste-differentiation factor in Melipona scutellaris.
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11
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Bie XM, Dong L, Li XH, Wang H, Gao XQ, Li XG. Trichostatin A and sodium butyrate promotes plant regeneration in common wheat. PLANT SIGNALING & BEHAVIOR 2020; 15:1820681. [PMID: 32962515 PMCID: PMC7671042 DOI: 10.1080/15592324.2020.1820681] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Histone acetylation modification plays a vital role in plant cell division and differentiation. However, the function on wheat mature embryo culture has not been reported. Here, we used the mature embryo of wheat genotypes including CB037, Fielder, and Chinese Spring (CS) as materials to analyze the effects of different concentrations of trichostatin A (TSA) and sodium butyrate (SB) on plant regeneration efficiency. The results showed that, compared with the control group, the induction rates of embryogenic callus and green shoot were significantly increased with the addition of 0.5 µM TSA, while they were reduced under treatment of 2.5 µM TSA on wheat mature embryo. With the respective addition of 200 µM and 1000 µM SB, regeneration frequency of three genotypes was enhanced, especially in Fielder, which reached significant difference compared with the control group. Unfortunately, 0.5 µM TSA and 200 µM SB combination had no apparent effect on wheat regeneration frequency. The results indicated that TSA and SB increase plant regeneration in common wheat. In addition, TSA had a common effect and SB had different effect among genotypes on wheat regeneration frequency. The mechanism of action needs further investigation.
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Affiliation(s)
- Xiao Min Bie
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai′an, Shandong, China
- CONTACT Xiao Min Bie
| | - Luhao Dong
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai′an, Shandong, China
| | - Xiao Hui Li
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai′an, Shandong, China
| | - He Wang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai′an, Shandong, China
| | - Xi-Qi Gao
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai′an, Shandong, China
| | - Xing Guo Li
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai′an, Shandong, China
- Xing Guo Li State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai′an, Shandong271018, China
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12
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Lee MH, Lee J, Choi SH, Jie EY, Jeong JC, Kim CY, Kim SW. The Effect of Sodium Butyrate on Adventitious Shoot Formation Varies among the Plant Species and the Explant Types. Int J Mol Sci 2020; 21:E8451. [PMID: 33182800 PMCID: PMC7696800 DOI: 10.3390/ijms21228451] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 11/06/2020] [Accepted: 11/08/2020] [Indexed: 12/24/2022] Open
Abstract
Histone acetylation plays an important role in plant growth and development. Here, we investigated the effect of sodium butyrate (NaB), a histone deacetylase inhibitor, on adventitious shoot formation from protoplast-derived calli and cotyledon explants of tobacco (Nicotiana benthamiana) and tomato (Solanum lycopersicum). The frequency of adventitious shoot formation from protoplast-derived calli was higher in shoot induction medium (SIM) containing NaB than in the control. However, the frequency of adventitious shoot formation from cotyledon explants of tobacco under the 0.1 mM NaB treatment was similar to that in the control, but it decreased with increasing NaB concentration. Unlike in tobacco, NaB decreased adventitious shoot formation in tomato explants in a concentration-dependent manner, but it did not have any effect on adventitious shoot formation in calli. NaB inhibited or delayed the expression of D-type cyclin (CYCD3-1) and shoot-regeneration regulatory gene WUSCHEL (WUS) in cotyledon explants of tobacco and tomato. However, compared to that in control SIM, the expression of WUS was promoted more rapidly in tobacco calli cultured in NaB-containing SIM, but the expression of CYCD3-1 was inhibited. In conclusion, the effect of NaB on adventitious shoot formation and expression of CYCD3-1 and WUS genes depended on the plant species and whether the effects were tested on explants or protoplast-derived calli.
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Affiliation(s)
| | | | | | | | | | | | - Suk Weon Kim
- Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup 56212, Korea; (M.H.L.); (J.L.); (S.H.C.); (E.Y.J.); (J.C.J.); (C.Y.K.)
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Wang L, Qiao H. Chromatin regulation in plant hormone and plant stress responses. CURRENT OPINION IN PLANT BIOLOGY 2020; 57:164-170. [PMID: 33142261 PMCID: PMC8237520 DOI: 10.1016/j.pbi.2020.08.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 08/27/2020] [Accepted: 08/28/2020] [Indexed: 05/05/2023]
Abstract
The gene expression is tightly regulated temporally and spatially to ensure the plant and animal proper development, function, growth, and survival under different environmental conditions. Chromatin regulation plays a central role in the gene expression by providing transcription factors and the transcription machinery with dynamic access to an otherwise tightly packaged genome. In this review, we will summarize recent progress in understanding the roles of chromatin regulation in the gene expression, and their contribution to the plant hormone and stress responses. We highlight the most recent publications within this topic and underline the roles of chromatin regulation in gene expression.
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Affiliation(s)
- Likai Wang
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, USA; Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Hong Qiao
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, USA; Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA.
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14
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Chromatin, Epigenetics and Plant Physiology. Int J Mol Sci 2020; 21:ijms21082763. [PMID: 32316114 PMCID: PMC7215297 DOI: 10.3390/ijms21082763] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 04/14/2020] [Accepted: 04/14/2020] [Indexed: 12/31/2022] Open
Abstract
The ever-increasing interest in epigenetics comes from the fact that in the diverse life situations of organisms, e [...].
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