1
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Gazzarrini S, Song L. LAFL Factors in Seed Development and Phase Transitions. ANNUAL REVIEW OF PLANT BIOLOGY 2024; 75:459-488. [PMID: 38657282 DOI: 10.1146/annurev-arplant-070623-111458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Development is a chain reaction in which one event leads to another until the completion of a life cycle. Phase transitions are milestone events in the cycle of life. LEAFY COTYLEDON1 (LEC1), ABA INSENSITIVE3 (ABI3), FUSCA3 (FUS3), and LEC2 proteins, collectively known as LAFL, are master transcription factors (TFs) regulating seed and other developmental processes. Since the initial characterization of the LAFL genes, more than three decades of active research has generated tremendous amounts of knowledge about these TFs, whose roles in seed development and germination have been comprehensively reviewed. Recent advances in cell biology with genetic and genomic tools have allowed the characterization of the LAFL regulatory networks in previously challenging tissues at a higher throughput and resolution in reference species and crops. In this review, we provide a holistic perspective by integrating advances at the epigenetic, transcriptional, posttranscriptional, and protein levels to exemplify the spatiotemporal regulation of the LAFL networks in Arabidopsis seed development and phase transitions, and we briefly discuss the evolution of these TF networks.
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Affiliation(s)
- Sonia Gazzarrini
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, Ontario, Canada;
| | - Liang Song
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada;
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2
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Oberkofler V, Bäurle I. Plant Epigenetic Editing to Analyze the Function of Histone Modifications in Gene-Specific Regulation. Methods Mol Biol 2024; 2842:193-207. [PMID: 39012597 DOI: 10.1007/978-1-0716-4051-7_10] [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] [Indexed: 07/17/2024]
Abstract
Epigenetic editing enables the locus-specific manipulation of chromatin modifications. It allows the functional analysis of interactions between chromatin modifications and epigenetically stable gene expression states, thus establishing causal relationships, where previously correlations were suspected. Here, we describe the procedures for gene-specific epigenetic editing in plants that are based on targeting a histone modifier using an inactive dCas9 fusion protein that is recruited by a set of three distinct single guide RNAs (sgRNAs) that all target a region within the promoter of the target gene. We outline design principles and emphasize the need for suitable control constructs. In summary, the protocol will be widely useful for plant scientists looking to manipulate chromatin modifications in a locus-specific manner.
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Affiliation(s)
- Vicky Oberkofler
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Isabel Bäurle
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany.
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3
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Pons C, Casals J, Brower M, Sacco A, Riccini A, Hendrickx P, Figás MDR, Fisher J, Grandillo S, Mazzucato A, Soler S, Zamir D, Causse M, Díez MJ, Finkers R, Prohens J, Monforte AJ, Granell A. Diversity and genetic architecture of agro-morphological traits in a core collection of European traditional tomato. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:5896-5916. [PMID: 37527560 PMCID: PMC10540738 DOI: 10.1093/jxb/erad306] [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: 03/07/2023] [Accepted: 07/28/2023] [Indexed: 08/03/2023]
Abstract
European traditional tomato varieties have been selected by farmers given their consistent performance and adaptation to local growing conditions. Here we developed a multipurpose core collection, comprising 226 accessions representative of the genotypic, phenotypic, and geographical diversity present in European traditional tomatoes, to investigate the basis of their phenotypic variation, gene×environment interactions, and stability for 33 agro-morphological traits. Comparison of the traditional varieties with a modern reference panel revealed that some traditional varieties displayed excellent agronomic performance and high trait stability, as good as or better than that of their modern counterparts. We conducted genome-wide association and genome-wide environment interaction studies and detected 141 quantitative trait loci (QTLs). Out of those, 47 QTLs were associated with the phenotype mean (meanQTLs), 41 with stability (stbQTLs), and 53 QTL-by-environment interactions (QTIs). Most QTLs displayed additive gene actions, with the exception of stbQTLs, which were mostly recessive and overdominant QTLs. Both common and specific loci controlled the phenotype mean and stability variation in traditional tomato; however, a larger proportion of specific QTLs was observed, indicating that the stability gene regulatory model is the predominant one. Developmental genes tended to map close to meanQTLs, while genes involved in stress response, hormone metabolism, and signalling were found within regions affecting stability. A total of 137 marker-trait associations for phenotypic means and stability were novel, and therefore our study enhances the understanding of the genetic basis of valuable agronomic traits and opens up a new avenue for an exploitation of the allelic diversity available within European traditional tomato germplasm.
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Affiliation(s)
- Clara Pons
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana (COMAV), Universitat Politècnica de València, València, Spain
- Instituto de Biología Molecular y Celular de Plantas (IBMCP). Consejo Superior de Investigaciones Científicas (CSIC), Universitat Politècnica de València, València, Spain
| | - Joan Casals
- Department of Agri-Food Engineering and Biotechnology/Miquel Agustí Foundation, Universitat Politècnica de Catalunya, Campus Baix Llobregat, Esteve Terrades 8, 08860 Castelldefels, Spain
| | - Matthijs Brower
- Wageningen University & Research, Plant Breeding, POB 386, NL-6700 AJ Wageningen, The Netherlands
| | - Adriana Sacco
- Institute of Biosciences and BioResources (IBBR), National Research Council of Italy (CNR), Via Università 133, 80055 Portici, Italy
| | - Alessandro Riccini
- Department of Agriculture and Forest Sciences (DAFNE), Università degli Studi della Tuscia, Viterbo, Italy
| | - Patrick Hendrickx
- Wageningen University & Research, Plant Breeding, POB 386, NL-6700 AJ Wageningen, The Netherlands
| | - Maria del Rosario Figás
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana (COMAV), Universitat Politècnica de València, València, Spain
| | - Josef Fisher
- Hebrew University of Jerusalem, Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Rehovot, Israel
| | - Silvana Grandillo
- Institute of Biosciences and BioResources (IBBR), National Research Council of Italy (CNR), Via Università 133, 80055 Portici, Italy
| | - Andrea Mazzucato
- Department of Agriculture and Forest Sciences (DAFNE), Università degli Studi della Tuscia, Viterbo, Italy
| | - Salvador Soler
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana (COMAV), Universitat Politècnica de València, València, Spain
| | - Dani Zamir
- Hebrew University of Jerusalem, Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Rehovot, Israel
| | - Mathilde Causse
- INRAE, UR1052, Génétique et Amélioration des Fruits et Légumes 67 Allée des Chênes, Domaine Saint Maurice, CS60094, Montfavet, 84143, France
| | - Maria José Díez
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana (COMAV), Universitat Politècnica de València, València, Spain
| | - Richard Finkers
- Wageningen University & Research, Plant Breeding, POB 386, NL-6700 AJ Wageningen, The Netherlands
| | - Jaime Prohens
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana (COMAV), Universitat Politècnica de València, València, Spain
| | - Antonio Jose Monforte
- Instituto de Biología Molecular y Celular de Plantas (IBMCP). Consejo Superior de Investigaciones Científicas (CSIC), Universitat Politècnica de València, València, Spain
| | - Antonio Granell
- Instituto de Biología Molecular y Celular de Plantas (IBMCP). Consejo Superior de Investigaciones Científicas (CSIC), Universitat Politècnica de València, València, Spain
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4
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Kappel C, Friedrich T, Oberkofler V, Jiang L, Crawford T, Lenhard M, Bäurle I. Genomic and epigenomic determinants of heat stress-induced transcriptional memory in Arabidopsis. Genome Biol 2023; 24:129. [PMID: 37254211 DOI: 10.1186/s13059-023-02970-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 05/11/2023] [Indexed: 06/01/2023] Open
Abstract
BACKGROUND Transcriptional regulation is a key aspect of environmental stress responses. Heat stress induces transcriptional memory, i.e., sustained induction or enhanced re-induction of transcription, that allows plants to respond more efficiently to a recurrent HS. In light of more frequent temperature extremes due to climate change, improving heat tolerance in crop plants is an important breeding goal. However, not all heat stress-inducible genes show transcriptional memory, and it is unclear what distinguishes memory from non-memory genes. To address this issue and understand the genome and epigenome architecture of transcriptional memory after heat stress, we identify the global target genes of two key memory heat shock transcription factors, HSFA2 and HSFA3, using time course ChIP-seq. RESULTS HSFA2 and HSFA3 show near identical binding patterns. In vitro and in vivo binding strength is highly correlated, indicating the importance of DNA sequence elements. In particular, genes with transcriptional memory are strongly enriched for a tripartite heat shock element, and are hallmarked by several features: low expression levels in the absence of heat stress, accessible chromatin environment, and heat stress-induced enrichment of H3K4 trimethylation. These results are confirmed by an orthogonal transcriptomic data set using both de novo clustering and an established definition of memory genes. CONCLUSIONS Our findings provide an integrated view of HSF-dependent transcriptional memory and shed light on its sequence and chromatin determinants, enabling the prediction and engineering of genes with transcriptional memory behavior.
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Affiliation(s)
- Christian Kappel
- Institute for Biochemistry and Biology, University of Potsdam, 14476, Potsdam, Germany
| | - Thomas Friedrich
- Institute for Biochemistry and Biology, University of Potsdam, 14476, Potsdam, Germany
| | - Vicky Oberkofler
- Institute for Biochemistry and Biology, University of Potsdam, 14476, Potsdam, Germany
| | - Li Jiang
- Institute for Biochemistry and Biology, University of Potsdam, 14476, Potsdam, Germany
| | - Tim Crawford
- Institute for Biochemistry and Biology, University of Potsdam, 14476, Potsdam, Germany
| | - Michael Lenhard
- Institute for Biochemistry and Biology, University of Potsdam, 14476, Potsdam, Germany
| | - Isabel Bäurle
- Institute for Biochemistry and Biology, University of Potsdam, 14476, Potsdam, Germany.
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5
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Yang C, Zhu T, Zhou N, Huang S, Zeng Y, Jiang W, Xie Y, Shen WH, Li L. PIF7-mediated epigenetic reprogramming promotes the transcriptional response to shade in Arabidopsis. EMBO J 2023; 42:e111472. [PMID: 36912149 PMCID: PMC10106985 DOI: 10.15252/embj.2022111472] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 01/28/2023] [Accepted: 02/01/2023] [Indexed: 03/14/2023] Open
Abstract
For shade-intolerant plants, changes in light quality through competition from neighbors trigger shade avoidance syndrome (SAS): a series of morphological and physiological adaptations that are ultimately detrimental to plant health and crop yield. Phytochrome-interacting factor 7 (PIF7) is a major transcriptional regulator of SAS in Arabidopsis; however, how it regulates gene expression is not fully understood. Here, we show that PIF7 directly interacts with the histone chaperone anti-silencing factor 1 (ASF1). The ASF1-deprived asf1ab mutant showed defective shade-induced hypocotyl elongation. Histone regulator homolog A (HIRA), which mediates deposition of the H3.3 variant into chromatin, is also involved in SAS. RNA/ChIP-sequencing analyses identified the role of ASF1 in the direct regulation of a subset of PIF7 target genes. Furthermore, shade-elicited gene activation is accompanied by H3.3 enrichment, which is mediated by the PIF7-ASF1-HIRA regulatory module. Collectively, our data reveal that PIF7 recruits ASF1-HIRA to increase H3.3 incorporation into chromatin to promote gene transcription, thus enabling plants to effectively respond to environmental shade.
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Affiliation(s)
- Chuanwei Yang
- State Key Laboratory of Genetic Engineering, Institute of Plants Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Tongdan Zhu
- State Key Laboratory of Genetic Engineering, Institute of Plants Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Nana Zhou
- State Key Laboratory of Genetic Engineering, Department of Biochemistry, Institute of Plants Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Sha Huang
- State Key Laboratory of Genetic Engineering, Institute of Plants Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Yue Zeng
- State Key Laboratory of Genetic Engineering, Institute of Plants Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Wen Jiang
- State Key Laboratory of Genetic Engineering, Department of Biochemistry, Institute of Plants Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Yu Xie
- State Key Laboratory of Genetic Engineering, Institute of Plants Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Wen-Hui Shen
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Lin Li
- State Key Laboratory of Genetic Engineering, Institute of Plants Biology, School of Life Sciences, Fudan University, Shanghai, China
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6
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Yang J, Yang S, Liao Y, Deng Y, Jiao Y. Histone deacetylase inhibitor butyrate inhibits the cellular immunity and increases the serum immunity of pearl oyster Pinctada fucata martensii. FISH & SHELLFISH IMMUNOLOGY 2023; 133:108529. [PMID: 36632915 DOI: 10.1016/j.fsi.2023.108529] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 12/21/2022] [Accepted: 01/07/2023] [Indexed: 06/17/2023]
Abstract
Histone acetylation is a dynamic epigenetic modification and sensitive to the changes in extracellular environment. Butyrate, a histone deacetylase inhibitor, can inhibit the deacetylation process of histones. In this study, we found that the acetylation level of H3 was enhanced at 12 h after lipopolysaccharide (LPS) stimulation and increased at 6 h after combining treatment with LPS and butyrate in pearl oyster Pinctada fucata martensii. Transcriptome analysis indicated that butyrate counter-regulated 29.95%-36.35% of the genes repressed by LPS, and these genes were mainly enriched in the "cell proliferation" and "Notch signaling pathway". Meanwhile, butyrate inhibited the up-regulation of 31.54%-54.96% of the genes induced by LPS, and these genes were mainly enriched in "Notch signaling pathway", "cell proliferation", "NF-kappa B signaling pathway", "TNF signaling pathway", "apoptosis", "NOD-like receptor signaling pathway", "RIG-I-like receptor signaling pathway" and "cytosolic DNA-sensing pathway". Gene expression analysis showed that butyrate downregulated most of cell proliferation, immune-related genes effected by LPS. The activities of LAP, LYS, ACP, ALP, and GSH-Px were up-regulated at 6 h after combining treatment with LPS and butyrate, suggesting that butyrate could activate serum immune-related enzymes in pearl oyster. These results can improve our understanding of the function of histone deacetylase in the immune response of pearl oyster and provide references for an in-depth study of the functions of histone deacetylase in mollusks.
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Affiliation(s)
- Jingmiao Yang
- Fishery College, Guangdong Ocean University, Zhanjiang, 524025, China
| | - Shuai Yang
- Fishery College, Guangdong Ocean University, Zhanjiang, 524025, China
| | - Yongshan Liao
- Fishery College, Guangdong Ocean University, Zhanjiang, 524025, China
| | - Yuewen Deng
- Fishery College, Guangdong Ocean University, Zhanjiang, 524025, China; Pearl Breeding and Processing Engineering Technology Research Centre of Guangdong Province, Zhanjiang, 524088, China; Guangdong Science and Innovation Center for Pearl Culture, Zhanjiang, 524088, China; Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, Zhanjiang, 524088, China; Guangdong Provincial Laboratory of Marine Ecological Early Warning and Monitoring, Zhanjiang, 524088, China
| | - Yu Jiao
- Fishery College, Guangdong Ocean University, Zhanjiang, 524025, China; Pearl Breeding and Processing Engineering Technology Research Centre of Guangdong Province, Zhanjiang, 524088, China; Guangdong Science and Innovation Center for Pearl Culture, Zhanjiang, 524088, China.
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7
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Nowrousian M. The Role of Chromatin and Transcriptional Control in the Formation of Sexual Fruiting Bodies in Fungi. Microbiol Mol Biol Rev 2022; 86:e0010422. [PMID: 36409109 PMCID: PMC9769939 DOI: 10.1128/mmbr.00104-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Fungal fruiting bodies are complex, three-dimensional structures that arise from a less complex vegetative mycelium. Their formation requires the coordinated action of many genes and their gene products, and fruiting body formation is accompanied by major changes in the transcriptome. In recent years, numerous transcription factor genes as well as chromatin modifier genes that play a role in fruiting body morphogenesis were identified, and through research on several model organisms, the underlying regulatory networks that integrate chromatin structure, gene expression, and cell differentiation are becoming clearer. This review gives a summary of the current state of research on the role of transcriptional control and chromatin structure in fruiting body development. In the first part, insights from transcriptomics analyses are described, with a focus on comparative transcriptomics. In the second part, examples of more detailed functional characterizations of the role of chromatin modifiers and/or transcription factors in several model organisms (Neurospora crassa, Aspergillus nidulans, Sordaria macrospora, Coprinopsis cinerea, and Schizophyllum commune) that have led to a better understanding of regulatory networks at the level of chromatin structure and transcription are discussed.
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Affiliation(s)
- Minou Nowrousian
- Department of Molecular and Cellular Botany, Ruhr University Bochum, Bochum, Germany
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8
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Kim J, Park MJ, Shim D, Ryoo R. De novo genome assembly of the bioluminescent mushroom Omphalotus guepiniiformis reveals an Omphalotus-specific lineage of the luciferase gene block. Genomics 2022; 114:110514. [PMID: 36332840 DOI: 10.1016/j.ygeno.2022.110514] [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: 07/07/2022] [Revised: 10/04/2022] [Accepted: 10/23/2022] [Indexed: 11/05/2022]
Abstract
Omphalotus guepiniiformis, a bioluminescent mushroom species, is a source of the potentially valuable anticancer chemical. To provide genome information, we de novo assembled the high-quality O. guepiniiformis genome using two Next-Generation sequencing techniques, PacBio and Illumina sequencing. Our draft O. guepiniiformis genome comprises 42.5 Mbp of sequence with only 80 contigs and an N50 sequence length of over 1 Mbp. There were 15,554 predicted coding genes, and 7693 genes were functionally annotated with Gene Ontology terms. We performed a genomic study focusing on mushroom bioluminescent pathway cluster genes by comparing 17 luminescent and 23 non-luminescent Agaricales species belonging to 23 genera. Synteny analysis of genomic regions near the luminescent pathway cluster genes inferred that the Omphalotus lineage was genus-specific. In summary, our de novo assembled O. guepiniiformis genome provides significant biological insights into this organism, including the evolution of the luciferase gene block, and forms the basis for future analyses.
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Affiliation(s)
- Jaewook Kim
- Department of Biological Sciences, Chungnam National University, 34134 Daejeon, Republic of Korea
| | - Mi-Jeong Park
- Forest Microbiology Division, Department of Forest Bio-Resources, National Institute of Forest Science, 16631 Suwon, Republic of Korea
| | - Donghwan Shim
- Department of Biological Sciences, Chungnam National University, 34134 Daejeon, Republic of Korea.
| | - Rhim Ryoo
- Forest Microbiology Division, Department of Forest Bio-Resources, National Institute of Forest Science, 16631 Suwon, Republic of Korea.
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9
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Varotto S, Krugman T, Aiese Cigliano R, Kashkush K, Kondić-Špika A, Aravanopoulos FA, Pradillo M, Consiglio F, Aversano R, Pecinka A, Miladinović D. Exploitation of epigenetic variation of crop wild relatives for crop improvement and agrobiodiversity preservation. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:3987-4003. [PMID: 35678824 PMCID: PMC9729329 DOI: 10.1007/s00122-022-04122-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 05/04/2022] [Indexed: 05/05/2023]
Abstract
Crop wild relatives (CWRs) are recognized as the best potential source of traits for crop improvement. However, successful crop improvement using CWR relies on identifying variation in genes controlling desired traits in plant germplasms and subsequently incorporating them into cultivars. Epigenetic diversity may provide an additional layer of variation within CWR and can contribute novel epialleles for key traits for crop improvement. There is emerging evidence that epigenetic variants of functional and/or agronomic importance exist in CWR gene pools. This provides a rationale for the conservation of epigenotypes of interest, thus contributing to agrobiodiversity preservation through conservation and (epi)genetic monitoring. Concepts and techniques of classical and modern breeding should consider integrating recent progress in epigenetics, initially by identifying their association with phenotypic variations and then by assessing their heritability and stability in subsequent generations. New tools available for epigenomic analysis offer the opportunity to capture epigenetic variation and integrate it into advanced (epi)breeding programmes. Advances in -omics have provided new insights into the sources and inheritance of epigenetic variation and enabled the efficient introduction of epi-traits from CWR into crops using epigenetic molecular markers, such as epiQTLs.
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Affiliation(s)
- Serena Varotto
- Department of Agronomy Animal Food Natural Resources and Environment, University of Padova, Viale dell'Università, 16 35020, Legnaro, Italy.
| | - Tamar Krugman
- Institute of Evolution, University of Haifa, Abba Khoushy Ave 199, 3498838, Haifa, Israel
| | | | - Khalil Kashkush
- Department of Life Sciences, Ben-Gurion University, Beersheba, 84105, Israel
| | - Ankica Kondić-Špika
- Institute of Field and Vegetable Crops, Maksima Gorkog 30, 21000, Novi Sad, Serbia
| | - Fillipos A Aravanopoulos
- Faculty of Agriculture, Forest Science & Natural Environment, Aristotle University of Thessaloniki, Thessaloniki, GR54006, Greece
| | - Monica Pradillo
- Department of Genetics, Physiology and Microbiology, Faculty of Biology, Complutense University of Madrid, 28040, Madrid, Spain
| | - Federica Consiglio
- Institute of Biosciences and Bioresources, National Research Council (CNR), Via Università 133, 80055, Portici, Italy
| | - Riccardo Aversano
- Department of Agricultural Sciences, University of Naples Federico II, Via Università 100, 80055, Portici, Italy
| | - Ales Pecinka
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Czech Acad Sci, Šlechtitelů 31, 779 00, Olomouc, Czech Republic
| | - Dragana Miladinović
- Institute of Field and Vegetable Crops, Maksima Gorkog 30, 21000, Novi Sad, Serbia
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10
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Barrero-Gil J, Bouza-Morcillo L, Espinosa-Cores L, Piñeiro M, Jarillo JA. H4 acetylation by the NuA4 complex is required for plastid transcription and chloroplast biogenesis. NATURE PLANTS 2022; 8:1052-1063. [PMID: 36038656 DOI: 10.1038/s41477-022-01229-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 07/20/2022] [Indexed: 06/15/2023]
Abstract
Chloroplast biogenesis is crucial in plant development, as it is essential for the transition to autotrophic growth. This process is light-induced and relies on the orchestrated transcription of nuclear and plastid genes, enabling the effective assembly and regulation of the photosynthetic machinery. Here we reveal a new regulation level for this process by showing the involvement of chromatin remodelling in the nuclear control of plastid gene expression for proper chloroplast biogenesis and function. The two Arabidopsis homologues of yeast EPL1 protein, components of the NuA4 histone acetyltransferase complex, are essential for plastid transcription and correct chloroplast development and performance. We show that EPL1 proteins are light-regulated and necessary for concerted expression of nuclear genes encoding most components of chloroplast transcriptional machinery, directly mediating H4K5ac deposition at these loci and promoting the expression of plastid genes required for chloroplast biogenesis. These data unveil a NuA4-mediated mechanism regulating chloroplast biogenesis that links the transcription of nuclear and plastid genomes during chloroplast development.
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Affiliation(s)
- Javier Barrero-Gil
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)/CSIC, Campus Montegancedo UPM, Pozuelo de Alarcón (Madrid), Madrid, Spain
| | - Laura Bouza-Morcillo
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)/CSIC, Campus Montegancedo UPM, Pozuelo de Alarcón (Madrid), Madrid, Spain
| | - Loreto Espinosa-Cores
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)/CSIC, Campus Montegancedo UPM, Pozuelo de Alarcón (Madrid), Madrid, Spain
| | - Manuel Piñeiro
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)/CSIC, Campus Montegancedo UPM, Pozuelo de Alarcón (Madrid), Madrid, Spain.
| | - José A Jarillo
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)/CSIC, Campus Montegancedo UPM, Pozuelo de Alarcón (Madrid), Madrid, Spain.
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11
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Oberkofler V, Bäurle I. Inducible epigenome editing probes for the role of histone H3K4 methylation in Arabidopsis heat stress memory. PLANT PHYSIOLOGY 2022; 189:703-714. [PMID: 35285498 PMCID: PMC9157090 DOI: 10.1093/plphys/kiac113] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 02/15/2022] [Indexed: 05/26/2023]
Abstract
Histone modifications play a crucial role in the integration of environmental signals to mediate gene expression outcomes. However, genetic and pharmacological interference often causes pleiotropic effects, creating the urgent need for methods that allow locus-specific manipulation of histone modifications, preferably in an inducible manner. Here, we report an inducible system for epigenome editing in Arabidopsis (Arabidopsis thaliana) using a heat-inducible dCas9 to target a JUMONJI (JMJ) histone H3 lysine 4 (H3K4) demethylase domain to a locus of interest. As a model locus, we target the ASCORBATE PEROXIDASE2 (APX2) gene that shows transcriptional memory after heat stress (HS), correlating with H3K4 hyper-methylation. We show that dCas9-JMJ is targeted in a HS-dependent manner to APX2 and that the HS-induced overaccumulation of H3K4 trimethylation (H3K4me3) decreases when dCas9-JMJ binds to the locus. This results in reduced HS-mediated transcriptional memory at the APX2 locus. Targeting an enzymatically inactive JMJ protein in an analogous manner affected transcriptional memory less than the active JMJ protein; however, we still observed a decrease in H3K4 methylation levels. Thus, the inducible targeting of dCas9-JMJ to APX2 was effective in reducing H3K4 methylation levels. As the effect was not fully dependent on enzyme activity of the eraser domain, the dCas9-JMJ fusion protein may act in part independently of its demethylase activity. This underlines the need for caution in the design and interpretation of epigenome editing studies. We expect our versatile inducible epigenome editing system to be especially useful for studying temporal dynamics of chromatin modifications.
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Affiliation(s)
- Vicky Oberkofler
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, 14476, Germany
| | - Isabel Bäurle
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, 14476, Germany
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12
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Müller-Xing R, Ardiansyah R, Xing Q, Faivre L, Tian J, Wang G, Zheng Y, Wang X, Jing T, de Leau E, Chen S, Chen S, Schubert D, Goodrich J. Polycomb proteins control floral determinacy by H3K27me3-mediated repression of pluripotency genes in Arabidopsis thaliana. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:2385-2402. [PMID: 35045165 DOI: 10.1093/jxb/erac013] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 01/17/2022] [Indexed: 06/14/2023]
Abstract
Polycomb group (PcG) protein-mediated histone methylation (H3K27me3) controls the correct spatiotemporal expression of numerous developmental regulators in Arabidopsis. Epigenetic silencing of the stem cell factor gene WUSCHEL (WUS) in floral meristems (FMs) depends on H3K27me3 deposition by PcG proteins. However, the role of H3K27me3 in silencing of other meristematic regulator and pluripotency genes during FM determinacy has not yet been studied. To this end, we report the genome-wide dynamics of H3K27me3 levels during FM arrest and the consequences of strongly depleted PcG activity on early flower morphogenesis including enlarged and indeterminate FMs. Strong depletion of H3K27me3 levels results in misexpression of the FM identity gene AGL24, which partially causes floral reversion leading to ap1-like flowers and indeterminate FMs ectopically expressing WUS and SHOOT MERISTEMLESS (STM). Loss of STM can rescue supernumerary floral organs and FM indeterminacy in H3K27me3-deficient flowers, indicating that the hyperactivity of the FMs is at least partially a result of ectopic STM expression. Nonetheless, WUS remained essential for the FM activity. Our results demonstrate that PcG proteins promote FM determinacy at multiple levels of the floral gene regulatory network, silencing initially floral regulators such as AGL24 that promotes FM indeterminacy and, subsequently, meristematic pluripotency genes such as WUS and STM during FM arrest.
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Affiliation(s)
- Ralf Müller-Xing
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, China
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin, China
- Plant Epigenetics and Development, Institute of Genetics, College of Life Science, Northeast Forestry University, Harbin, China
- Institute of Molecular Plant Sciences, The University of Edinburgh, Edinburgh, UK
| | - Rhomi Ardiansyah
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, China
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin, China
- Plant Epigenetics and Development, Institute of Genetics, College of Life Science, Northeast Forestry University, Harbin, China
| | - Qian Xing
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, China
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin, China
- Plant Epigenetics and Development, Institute of Genetics, College of Life Science, Northeast Forestry University, Harbin, China
- Institute of Molecular Plant Sciences, The University of Edinburgh, Edinburgh, UK
| | - Léa Faivre
- Epigenetics of Plants, Freie Universität Berlin, Berlin, Germany
| | - Jingjing Tian
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, China
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin, China
- Plant Epigenetics and Development, Institute of Genetics, College of Life Science, Northeast Forestry University, Harbin, China
| | - Guohua Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- Information and Computer Engineering College, Northeast Forestry University, Harbin, China
| | - Yucai Zheng
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, China
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin, China
- Plant Epigenetics and Development, Institute of Genetics, College of Life Science, Northeast Forestry University, Harbin, China
| | - Xue Wang
- Plant Epigenetics and Development, Institute of Genetics, College of Life Science, Northeast Forestry University, Harbin, China
| | - Tingting Jing
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, China
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin, China
- Plant Epigenetics and Development, Institute of Genetics, College of Life Science, Northeast Forestry University, Harbin, China
| | - Erica de Leau
- Institute of Molecular Plant Sciences, The University of Edinburgh, Edinburgh, UK
| | - Song Chen
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Su Chen
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Daniel Schubert
- Epigenetics of Plants, Freie Universität Berlin, Berlin, Germany
| | - Justin Goodrich
- Institute of Molecular Plant Sciences, The University of Edinburgh, Edinburgh, UK
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13
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Yamaguchi N. The epigenetic mechanisms regulating floral hub genes and their potential for manipulation. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:1277-1287. [PMID: 34752611 DOI: 10.1093/jxb/erab490] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 11/05/2021] [Indexed: 06/13/2023]
Abstract
Gene regulatory networks formed by transcription factors play essential roles in the regulation of gene expression during plant reproductive development. These networks integrate endogenous, phytohormonal, and environmental cues. Molecular genetic, biochemical, and chemical analyses performed mainly in Arabidopsis have identified network hub genes and revealed the contributions of individual components to these networks. Here, I outline current understanding of key epigenetic regulatory circuits identified by research on plant reproduction, and highlight significant recent examples of genetic engineering and chemical applications to modulate the epigenetic regulation of gene expression. Furthermore, I discuss future prospects for applying basic plant science to engineer useful floral traits in a predictable manner as well as the potential side effects.
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Affiliation(s)
- Nobutoshi Yamaguchi
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5, Takayama, Ikoma, Nara, 630-0192, Japan
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14
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Allen JR, Wilkinson EG, Strader LC. Creativity comes from interactions: modules of protein interactions in plants. FEBS J 2022; 289:1492-1514. [PMID: 33774929 PMCID: PMC8476656 DOI: 10.1111/febs.15847] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 03/06/2021] [Accepted: 03/26/2021] [Indexed: 01/03/2023]
Abstract
Protein interactions are the foundation of cell biology. For robust signal transduction to occur, proteins interact selectively and modulate their behavior to direct specific biological outcomes. Frequently, modular protein interaction domains are central to these processes. Some of these domains bind proteins bearing post-translational modifications, such as phosphorylation, whereas other domains recognize and bind to specific amino acid motifs. Other modules act as diverse protein interaction scaffolds or can be multifunctional, forming head-to-head homodimers and binding specific peptide sequences or membrane phospholipids. Additionally, the so-called head-to-tail oligomerization domains (SAM, DIX, and PB1) can form extended polymers to regulate diverse aspects of biology. Although the mechanism and structures of these domains are diverse, they are united by their modularity. Together, these domains are versatile and facilitate the evolution of complex protein interaction networks. In this review, we will highlight the role of select modular protein interaction domains in various aspects of plant biology.
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Affiliation(s)
- Jeffrey R. Allen
- Department of Biology, Washington University in St. Louis, MO, USA,Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, MO, USA,Center for Engineering Mechanobiology (CEMB), Washington University in St. Louis, MO, USA,Department of Biology, Duke University, Durham, NC, USA
| | - Edward G. Wilkinson
- Department of Biology, Washington University in St. Louis, MO, USA,Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, MO, USA,Center for Engineering Mechanobiology (CEMB), Washington University in St. Louis, MO, USA,Department of Biology, Duke University, Durham, NC, USA
| | - Lucia C. Strader
- Department of Biology, Washington University in St. Louis, MO, USA,Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, MO, USA,Center for Engineering Mechanobiology (CEMB), Washington University in St. Louis, MO, USA,Department of Biology, Duke University, Durham, NC, USA
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15
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Matilla AJ. Exploring Breakthroughs in Three Traits Belonging to Seed Life. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11040490. [PMID: 35214823 PMCID: PMC8875957 DOI: 10.3390/plants11040490] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 02/02/2022] [Accepted: 02/09/2022] [Indexed: 05/06/2023]
Abstract
Based on prior knowledge and with the support of new methodology, solid progress in the understanding of seed life has taken place over the few last years. This update reflects recent advances in three key traits of seed life (i.e., preharvest sprouting, genomic imprinting, and stored-mRNA). The first breakthrough refers to cloning of the mitogen-activated protein kinase-kinase 3 (MKK3) gene in barley and wheat. MKK3, in cooperation with ABA signaling, controls seed dormancy. This advance has been determinant in producing improved varieties that are resistant to preharvest sprouting. The second advance concerns to uniparental gene expression (i.e., imprinting). Genomic imprinting primarily occurs in the endosperm. Although great advances have taken place in the last decade, there is still a long way to go to complete the puzzle regarding the role of genomic imprinting in seed development. This trait is probably one of the most important epigenetic facets of developing endosperm. An example of imprinting regulation is polycomb repressive complex 2 (PRC2). The mechanism of PRC2 recruitment to target endosperm with specific genes is, at present, robustly studied. Further progress in the knowledge of recruitment of PRC2 epigenetic machinery is considered in this review. The third breakthrough referred to in this update involves stored mRNA. The role of the population of this mRNA in germination is far from known. Its relations to seed aging, processing bodies (P bodies), and RNA binding proteins (RBPs), and how the stored mRNA is targeted to monosomes, are aspects considered here. Perhaps this third trait is the one that will require greater experimental dedication in the future. In order to make progress, herein are included some questions that are needed to be answered.
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Affiliation(s)
- Angel J Matilla
- Departamento de Biología Funcional (Área Fisiología Vegetal), Facultad de Farmacia, Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain
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16
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Dal Santo S, De Paoli E, Pagliarani C, Amato A, Celii M, Boccacci P, Zenoni S, Gambino G, Perrone I. Stress responses and epigenomic instability mark the loss of somatic embryogenesis competence in grapevine. PLANT PHYSIOLOGY 2022; 188:490-508. [PMID: 34726761 PMCID: PMC8774814 DOI: 10.1093/plphys/kiab477] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 09/17/2021] [Indexed: 06/13/2023]
Abstract
Somatic embryogenesis (SE) represents the most appropriate tool for next-generation breeding methods in woody plants such as grapevine (Vitis vinifera L.). However, in this species, the SE competence is strongly genotype-dependent and the molecular basis of this phenomenon is poorly understood. We explored the genetic and epigenetic basis of SE in grapevine by profiling the transcriptome, epigenome, and small RNAome of undifferentiated, embryogenic, and non-embryogenic callus tissues derived from two genotypes differing in competence for SE, Sangiovese and Cabernet Sauvignon. During the successful formation of embryonic callus, we observed the upregulation of epigenetic-related transcripts and short interfering RNAs in association with DNA hypermethylation at transposable elements in both varieties. Nevertheless, the switch to nonembryonic development matched the incomplete reinforcement of transposon silencing, and the evidence of such effect was more apparent in the recalcitrant Cabernet Sauvignon. Transcriptomic differences between the two genotypes were maximized already at early stage of culture where the recalcitrant variety expressed a broad panel of genes related to stress responses and secondary metabolism. Our data provide a different angle on the SE molecular dynamics that can be exploited to leverage SE as a biotechnological tool for fruit crop breeding.
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Affiliation(s)
- Silvia Dal Santo
- Department of Biotechnology, University of Verona, Verona 37134, Italy
| | - Emanuele De Paoli
- Department of Agri-Food, Environmental and Animal Sciences, University of Udine, Udine 33100, Italy
| | - Chiara Pagliarani
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Torino 10135, Italy
| | - Alessandra Amato
- Department of Biotechnology, University of Verona, Verona 37134, Italy
| | - Mirko Celii
- Department of Agri-Food, Environmental and Animal Sciences, University of Udine, Udine 33100, Italy
| | - Paolo Boccacci
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Torino 10135, Italy
| | - Sara Zenoni
- Department of Biotechnology, University of Verona, Verona 37134, Italy
| | - Giorgio Gambino
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Torino 10135, Italy
| | - Irene Perrone
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Torino 10135, Italy
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17
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Aamir M, Karmakar P, Singh VK, Kashyap SP, Pandey S, Singh BK, Singh PM, Singh J. A novel insight into transcriptional and epigenetic regulation underlying sex expression and flower development in melon (Cucumis melo L.). PHYSIOLOGIA PLANTARUM 2021; 173:1729-1764. [PMID: 33547804 DOI: 10.1111/ppl.13357] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 01/29/2021] [Accepted: 02/01/2021] [Indexed: 06/12/2023]
Abstract
Melon (Cucumis melo L.) is an important cucurbit and has been considered as a model plant for studying sex determination. The four most common sexual morphotypes in melon are monoecious (A-G-M), gynoecious (--ggM-), andromonoecious (A-G-mm), and hermaphrodite (--ggmm). Sex expression in melons is complex, as the genes and associated networks that govern the sex expression are not fully explored. Recently, RNA-seq transcriptomic profiling, ChIP-qPCR analysis integrated with gene ontology annotation and Kyoto Encyclopedia of Genes and Genomes pathways predicted the differentially expressed genes including sex-specific ACS and ACO genes, in regulating the sex-expression, phytohormonal cross-talk, signal transduction, and secondary metabolism in melons. Integration of transcriptional control through genetic interaction in between the ACS7, ACS11, and WIP1 in epistatic or hypostatic manner, along with the recruitment of H3K9ac and H3K27me3, epigenetically, overall determine sex expression. Alignment of protein sequences for establishing phylogenetic evolution, motif comparison, and protein-protein interaction supported the structural conservation while presence of the conserved hydrophilic and charged residues across the diverged evolutionary group predicted the functional conservation of the ACS protein. Presence of the putative cis-binding elements or DNA motifs, and its further comparison with DAP-seq-based cistrome and epicistrome of Arabidopsis, unraveled strong ancestry of melons with Arabidopsis. Motif comparison analysis also characterized putative genes and transcription factors involved in ethylene biosynthesis, signal transduction, and hormonal cross-talk related to sex expression. Overall, we have comprehensively reviewed research findings for a deeper insight into transcriptional and epigenetic regulation of sex expression and flower development in melons.
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Affiliation(s)
- Mohd Aamir
- Division of Crop Improvement, ICAR-Indian Institute of Vegetable Research (ICAR-IIVR), Varanasi, India
| | - Pradip Karmakar
- Division of Crop Improvement, ICAR-Indian Institute of Vegetable Research (ICAR-IIVR), Varanasi, India
| | - Vinay Kumar Singh
- Centre for Bioinformatics, School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Sarvesh Pratap Kashyap
- Division of Crop Improvement, ICAR-Indian Institute of Vegetable Research (ICAR-IIVR), Varanasi, India
| | - Sudhakar Pandey
- Division of Crop Improvement, ICAR-Indian Institute of Vegetable Research (ICAR-IIVR), Varanasi, India
| | - Binod Kumar Singh
- Division of Crop Improvement, ICAR-Indian Institute of Vegetable Research (ICAR-IIVR), Varanasi, India
| | - Prabhakar Mohan Singh
- Division of Crop Improvement, ICAR-Indian Institute of Vegetable Research (ICAR-IIVR), Varanasi, India
| | - Jagdish Singh
- Division of Crop Improvement, ICAR-Indian Institute of Vegetable Research (ICAR-IIVR), Varanasi, India
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18
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Tripathi DK, Rai P, Guerriero G, Sharma S, Corpas FJ, Singh VP. Silicon induces adventitious root formation in rice under arsenate stress with involvement of nitric oxide and indole-3-acetic acid. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:4457-4471. [PMID: 33095869 DOI: 10.1093/jxb/eraa488] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 10/18/2020] [Indexed: 05/04/2023]
Abstract
Arsenic (As) negatively affects plant development. This study evaluates how the application of silicon (Si) can favor the formation of adventitious roots in rice under arsenate stress (AsV) as a mechanism to mitigate its negative effects. The simultaneous application of AsV and Si up-regulated the expression of genes involved in nitric oxide (NO) metabolism, cell cycle progression, auxin (IAA, indole-3-acetic acid) biosynthesis and transport, and Si uptake which accompanied adventitious root formation. Furthermore, Si triggered the expression and activity of enzymes involved in ascorbate recycling. Treatment with L-NAME (NG-nitro L-arginine methyl ester), an inhibitor of NO generation, significantly suppressed adventitious root formation, even in the presence of Si; however, supplying NO in the growth media rescued its effects. Our data suggest that both NO and IAA are essential for Si-mediated adventitious root formation under AsV stress. Interestingly, TIBA (2,3,5-triiodobenzoic acid), a polar auxin transport inhibitor, suppressed adventitious root formation even in the presence of Si and SNP (sodium nitroprusside, an NO donor), suggesting that Si is involved in a mechanism whereby a cellular signal is triggered and that first requires NO formation, followed by IAA biosynthesis.
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Affiliation(s)
- Durgesh Kumar Tripathi
- Amity Institute of Organic Agriculture (AIOA), Amity University, Noida, Noida, Uttar Pradesh
| | - Padmaja Rai
- Department of Biotechnology, Motilal Nehru National Institute of Technology Allahabad, PrayagrajIndia
| | - Gea Guerriero
- Environmental Research and Innovation Department, Luxembourg Institute of Science and Technology, Hautcharage, Luxembourg
| | - Shivesh Sharma
- Department of Biotechnology, Motilal Nehru National Institute of Technology Allahabad, PrayagrajIndia
| | - Francisco J Corpas
- Group of Antioxidants, Free Radicals and Nitric Oxide in Biotechnology, Food and Agriculture, Department of Biochemistry and Cell and Molecular Biology of Plants, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Profesor Albareda 1, Granada, Spain
| | - Vijay Pratap Singh
- Plant Physiology Laboratory, Department of Botany, C.M.P. Degree College, A Constituent Post Graduate College of University of Allahabad, Allahabad-211002, India
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19
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Selinski J, Scheibe R. Central Metabolism in Mammals and Plants as a Hub for Controlling Cell Fate. Antioxid Redox Signal 2021; 34:1025-1047. [PMID: 32620064 PMCID: PMC8060724 DOI: 10.1089/ars.2020.8121] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 06/15/2020] [Accepted: 06/23/2020] [Indexed: 02/06/2023]
Abstract
Significance: The importance of oxidoreductases in energy metabolism together with the occurrence of enzymes of central metabolism in the nucleus gave rise to the active research field aiming to understand moonlighting enzymes that undergo post-translational modifications (PTMs) before carrying out new tasks. Recent Advances: Cytosolic enzymes were shown to induce gene transcription after PTM and concomitant translocation to the nucleus. Changed properties of the oxidized forms of cytosolic glyceraldehyde 3-phosphate dehydrogenase, and also malate dehydrogenases and others, are the basis for a hypothesis suggesting moonlighting functions that directly link energy metabolism to adaptive responses required for maintenance of redox-homeostasis in all eukaryotes. Critical Issues: Small molecules, such as metabolic intermediates, coenzymes, or reduced glutathione, were shown to fine-tune the redox switches, interlinking redox state, metabolism, and induction of new functions via nuclear gene expression. The cytosol with its metabolic enzymes connecting energy fluxes between the various cell compartments can be seen as a hub for redox signaling, integrating the different signals for graded and directed responses in stressful situations. Future Directions: Enzymes of central metabolism were shown to interact with p53 or the assumed plant homologue suppressor of gamma response 1 (SOG1), an NAM, ATAF, and CUC transcription factor involved in the stress response upon ultraviolet exposure. Metabolic enzymes serve as sensors for imbalances, their inhibition leading to changed energy metabolism, and the adoption of transcriptional coactivator activities. Depending on the intensity of the impact, rerouting of energy metabolism, proliferation, DNA repair, cell cycle arrest, immune responses, or cell death will be induced. Antioxid. Redox Signal. 34, 1025-1047.
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Affiliation(s)
- Jennifer Selinski
- Department of Biochemistry and Physiology of Plants, Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Renate Scheibe
- Department of Plant Physiology, Faculty of Biology/Chemistry, Osnabrueck University, Osnabrueck, Germany
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20
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Kumar A, Kondhare KR, Malankar NN, Banerjee AK. The Polycomb group methyltransferase StE(z)2 and deposition of H3K27me3 and H3K4me3 regulate the expression of tuberization genes in potato. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:426-444. [PMID: 33048134 DOI: 10.1093/jxb/eraa468] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 10/06/2020] [Indexed: 06/11/2023]
Abstract
Polycomb repressive complex (PRC) group proteins regulate various developmental processes in plants by repressing target genes via H3K27 trimethylation, and they function antagonistically with H3K4 trimethylation mediated by Trithorax group proteins. Tuberization in potato has been widely studied, but the role of histone modifications in this process is unknown. Recently, we showed that overexpression of StMSI1, a PRC2 member, alters the expression of tuberization genes in potato. As MSI1 lacks histone-modification activity, we hypothesized that this altered expression could be caused by another PRC2 member, StE(z)2, a potential H3K27 methyltransferase in potato. Here, we demonstrate that a short-day photoperiod influences StE(z)2 expression in the leaves and stolons. StE(z)2 overexpression alters plant architecture and reduces tuber yield, whereas its knockdown enhances yield. ChIP-sequencing using stolons induced by short-days indicated that several genes related to tuberization and phytohormones, such as StBEL5/11/29, StSWEET11B, StGA2OX1, and StPIN1 carry H3K4me3 or H3K27me3 marks and/or are StE(z)2 targets. Interestingly, we observed that another important tuberization gene, StSP6A, is targeted by StE(z)2 in leaves and that it has increased deposition of H3K27me3 under long-day (non-induced) conditions compared to short days. Overall, our results show that StE(z)2 and deposition of H3K27me3 and/or H3K4me3 marks might regulate the expression of key tuberization genes in potato.
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Affiliation(s)
- Amit Kumar
- Biology Division, Dr. Homi Bhabha Road, Indian Institute of Science Education and Research (IISER) Pune, Maharashtra - 411008, India
| | - Kirtikumar R Kondhare
- Biology Division, Dr. Homi Bhabha Road, Indian Institute of Science Education and Research (IISER) Pune, Maharashtra - 411008, India
| | - Nilam N Malankar
- Biology Division, Dr. Homi Bhabha Road, Indian Institute of Science Education and Research (IISER) Pune, Maharashtra - 411008, India
| | - Anjan K Banerjee
- Biology Division, Dr. Homi Bhabha Road, Indian Institute of Science Education and Research (IISER) Pune, Maharashtra - 411008, India
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21
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Yang X, Medford JI, Markel K, Shih PM, De Paoli HC, Trinh CT, McCormick AJ, Ployet R, Hussey SG, Myburg AA, Jensen PE, Hassan MM, Zhang J, Muchero W, Kalluri UC, Yin H, Zhuo R, Abraham PE, Chen JG, Weston DJ, Yang Y, Liu D, Li Y, Labbe J, Yang B, Lee JH, Cottingham RW, Martin S, Lu M, Tschaplinski TJ, Yuan G, Lu H, Ranjan P, Mitchell JC, Wullschleger SD, Tuskan GA. Plant Biosystems Design Research Roadmap 1.0. BIODESIGN RESEARCH 2020; 2020:8051764. [PMID: 37849899 PMCID: PMC10521729 DOI: 10.34133/2020/8051764] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Accepted: 10/30/2020] [Indexed: 10/19/2023] Open
Abstract
Human life intimately depends on plants for food, biomaterials, health, energy, and a sustainable environment. Various plants have been genetically improved mostly through breeding, along with limited modification via genetic engineering, yet they are still not able to meet the ever-increasing needs, in terms of both quantity and quality, resulting from the rapid increase in world population and expected standards of living. A step change that may address these challenges would be to expand the potential of plants using biosystems design approaches. This represents a shift in plant science research from relatively simple trial-and-error approaches to innovative strategies based on predictive models of biological systems. Plant biosystems design seeks to accelerate plant genetic improvement using genome editing and genetic circuit engineering or create novel plant systems through de novo synthesis of plant genomes. From this perspective, we present a comprehensive roadmap of plant biosystems design covering theories, principles, and technical methods, along with potential applications in basic and applied plant biology research. We highlight current challenges, future opportunities, and research priorities, along with a framework for international collaboration, towards rapid advancement of this emerging interdisciplinary area of research. Finally, we discuss the importance of social responsibility in utilizing plant biosystems design and suggest strategies for improving public perception, trust, and acceptance.
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Affiliation(s)
- Xiaohan Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - June I. Medford
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Kasey Markel
- Department of Plant Biology, University of California, Davis, Davis, CA, USA
| | - Patrick M. Shih
- Department of Plant Biology, University of California, Davis, Davis, CA, USA
- Feedstocks Division, Joint BioEnergy Institute, Emeryville, CA, USA
| | - Henrique C. De Paoli
- Department of Biodesign, Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Cong T. Trinh
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, TN 37996, USA
| | - Alistair J. McCormick
- SynthSys and Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Raphael Ployet
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa
| | - Steven G. Hussey
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa
| | - Alexander A. Myburg
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa
| | - Poul Erik Jensen
- Department of Food Science, University of Copenhagen, Rolighedsvej 26, DK-1858, Frederiksberg, Copenhagen, Denmark
| | - Md Mahmudul Hassan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Jin Zhang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China
| | - Wellington Muchero
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Udaya C. Kalluri
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Hengfu Yin
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang 311400, China
| | - Renying Zhuo
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang 311400, China
| | - Paul E. Abraham
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Jin-Gui Chen
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - David J. Weston
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Yinong Yang
- Department of Plant Pathology and Environmental Microbiology and the Huck Institute of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Degao Liu
- Department of Genetics, Cell Biology and Development, Center for Precision Plant Genomics and Center for Genome Engineering, University of Minnesota, Saint Paul, MN 55108, USA
| | - Yi Li
- Department of Plant Science and Landscape Architecture, University of Connecticut, Storrs, CT 06269, USA
| | - Jessy Labbe
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Bing Yang
- Division of Plant Sciences, Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - Jun Hyung Lee
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | | | - Stanton Martin
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Mengzhu Lu
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China
| | - Timothy J. Tschaplinski
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Guoliang Yuan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Haiwei Lu
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Priya Ranjan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Julie C. Mitchell
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Stan D. Wullschleger
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Gerald A. Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
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22
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Hummel G, Berr A, Graindorge S, Cognat V, Ubrig E, Pflieger D, Molinier J, Drouard L. Epigenetic silencing of clustered tRNA genes in Arabidopsis. Nucleic Acids Res 2020; 48:10297-10312. [PMID: 32941623 PMCID: PMC7544208 DOI: 10.1093/nar/gkaa766] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 07/21/2020] [Accepted: 09/03/2020] [Indexed: 12/12/2022] Open
Abstract
Beyond their key role in translation, cytosolic transfer RNAs (tRNAs) are involved in a wide range of other biological processes. Nuclear tRNA genes (tDNAs) are transcribed by the RNA polymerase III (RNAP III) and cis-elements, trans-factors as well as genomic features are known to influence their expression. In Arabidopsis, besides a predominant population of dispersed tDNAs spread along the 5 chromosomes, some clustered tDNAs have been identified. Here, we demonstrate that these tDNA clusters are transcriptionally silent and that pathways involved in the maintenance of DNA methylation play a predominant role in their repression. Moreover, we show that clustered tDNAs exhibit repressive chromatin features whilst their dispersed counterparts contain permissive euchromatic marks. This work demonstrates that both genomic and epigenomic contexts are key players in the regulation of tDNAs transcription. The conservation of most of these regulatory processes suggests that this pioneering work in Arabidopsis can provide new insights into the regulation of RNA Pol III transcription in other organisms, including vertebrates.
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Affiliation(s)
- Guillaume Hummel
- Institut de biologie moléculaire des plantes-CNRS, Université de Strasbourg, 12 rue du Général Zimmer, F-67084 Strasbourg, France
| | - Alexandre Berr
- Institut de biologie moléculaire des plantes-CNRS, Université de Strasbourg, 12 rue du Général Zimmer, F-67084 Strasbourg, France
| | - Stéfanie Graindorge
- Institut de biologie moléculaire des plantes-CNRS, Université de Strasbourg, 12 rue du Général Zimmer, F-67084 Strasbourg, France
| | - Valérie Cognat
- Institut de biologie moléculaire des plantes-CNRS, Université de Strasbourg, 12 rue du Général Zimmer, F-67084 Strasbourg, France
| | - Elodie Ubrig
- Institut de biologie moléculaire des plantes-CNRS, Université de Strasbourg, 12 rue du Général Zimmer, F-67084 Strasbourg, France
| | - David Pflieger
- Institut de biologie moléculaire des plantes-CNRS, Université de Strasbourg, 12 rue du Général Zimmer, F-67084 Strasbourg, France
| | - Jean Molinier
- Institut de biologie moléculaire des plantes-CNRS, Université de Strasbourg, 12 rue du Général Zimmer, F-67084 Strasbourg, France
| | - Laurence Drouard
- Institut de biologie moléculaire des plantes-CNRS, Université de Strasbourg, 12 rue du Général Zimmer, F-67084 Strasbourg, France
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23
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Carrera-Castaño G, Calleja-Cabrera J, Pernas M, Gómez L, Oñate-Sánchez L. An Updated Overview on the Regulation of Seed Germination. PLANTS 2020; 9:plants9060703. [PMID: 32492790 PMCID: PMC7356954 DOI: 10.3390/plants9060703] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 05/22/2020] [Accepted: 05/26/2020] [Indexed: 02/07/2023]
Abstract
The ability of a seed to germinate and establish a plant at the right time of year is of vital importance from an ecological and economical point of view. Due to the fragility of these early growth stages, their swiftness and robustness will impact later developmental stages and crop yield. These traits are modulated by a continuous interaction between the genetic makeup of the plant and the environment from seed production to germination stages. In this review, we have summarized the established knowledge on the control of seed germination from a molecular and a genetic perspective. This serves as a “backbone” to integrate the latest developments in the field. These include the link of germination to events occurring in the mother plant influenced by the environment, the impact of changes in the chromatin landscape, the discovery of new players and new insights related to well-known master regulators. Finally, results from recent studies on hormone transport, signaling, and biophysical and mechanical tissue properties are underscoring the relevance of tissue-specific regulation and the interplay of signals in this crucial developmental process.
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24
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Zander M, Lewsey MG, Clark NM, Yin L, Bartlett A, Saldierna Guzmán JP, Hann E, Langford AE, Jow B, Wise A, Nery JR, Chen H, Bar-Joseph Z, Walley JW, Solano R, Ecker JR. Integrated multi-omics framework of the plant response to jasmonic acid. NATURE PLANTS 2020; 6:290-302. [PMID: 32170290 PMCID: PMC7094030 DOI: 10.1038/s41477-020-0605-7] [Citation(s) in RCA: 113] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 01/23/2020] [Indexed: 05/17/2023]
Abstract
Understanding the systems-level actions of transcriptional responses to hormones provides insight into how the genome is reprogrammed in response to environmental stimuli. Here, we investigated the signalling pathway of the hormone jasmonic acid (JA), which controls a plethora of critically important processes in plants and is orchestrated by the transcription factor MYC2 and its closest relatives in Arabidopsis thaliana. We generated an integrated framework of the response to JA, which spans from the activity of master and secondary regulatory transcription factors, through gene expression outputs and alternative splicing, to protein abundance changes, protein phosphorylation and chromatin remodelling. We integrated time-series transcriptome analysis with (phospho)proteomic data to reconstruct gene regulatory network models. These enabled us to predict previously unknown points of crosstalk of JA to other signalling pathways and to identify new components of the JA regulatory mechanism, which we validated through targeted mutant analysis. These results provide a comprehensive understanding of how a plant hormone remodels cellular functions and plant behaviour, the general principles of which provide a framework for analyses of cross-regulation between other hormone and stress signalling pathways.
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Affiliation(s)
- Mark Zander
- Plant Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
- Genomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
- Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Mathew G Lewsey
- Centre for AgriBioscience, Department of Animal, Plant and Soil Sciences, School of Life Sciences, La Trobe University, Melbourne, Victoria, Australia.
- Australian Research Council Industrial Transformation Research Hub for Medicinal Agriculture, Centre for AgriBioscience, La Trobe University, Bundoora, Victoria, Australia.
| | - Natalie M Clark
- Plant Pathology and Microbiology, Iowa State University, Ames, IA, USA
| | - Lingling Yin
- Centre for AgriBioscience, Department of Animal, Plant and Soil Sciences, School of Life Sciences, La Trobe University, Melbourne, Victoria, Australia
- Australian Research Council Industrial Transformation Research Hub for Medicinal Agriculture, Centre for AgriBioscience, La Trobe University, Bundoora, Victoria, Australia
| | - Anna Bartlett
- Genomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - J Paola Saldierna Guzmán
- Plant Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
- School of Natural Sciences, University of California Merced, Merced, CA, USA
| | - Elizabeth Hann
- Plant Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
- Department of Chemical and Environmental Engineering, Department of Botany and Plant Sciences, University of California, Riverside, CA, USA
| | - Amber E Langford
- Plant Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Bruce Jow
- Genomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
- Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Aaron Wise
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Joseph R Nery
- Genomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Huaming Chen
- Genomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Ziv Bar-Joseph
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Justin W Walley
- Plant Pathology and Microbiology, Iowa State University, Ames, IA, USA
| | - Roberto Solano
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Madrid, Spain
| | - Joseph R Ecker
- Plant Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA.
- Genomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA.
- Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, CA, USA.
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25
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Zander M, Lewsey MG, Clark NM, Yin L, Bartlett A, Saldierna Guzmán JP, Hann E, Langford AE, Jow B, Wise A, Nery JR, Chen H, Bar-Joseph Z, Walley JW, Solano R, Ecker JR. Integrated multi-omics framework of the plant response to jasmonic acid. NATURE PLANTS 2020; 6:290-302. [PMID: 32170290 DOI: 10.1038/s41477-020-0605-607] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 01/23/2020] [Indexed: 05/26/2023]
Abstract
Understanding the systems-level actions of transcriptional responses to hormones provides insight into how the genome is reprogrammed in response to environmental stimuli. Here, we investigated the signalling pathway of the hormone jasmonic acid (JA), which controls a plethora of critically important processes in plants and is orchestrated by the transcription factor MYC2 and its closest relatives in Arabidopsis thaliana. We generated an integrated framework of the response to JA, which spans from the activity of master and secondary regulatory transcription factors, through gene expression outputs and alternative splicing, to protein abundance changes, protein phosphorylation and chromatin remodelling. We integrated time-series transcriptome analysis with (phospho)proteomic data to reconstruct gene regulatory network models. These enabled us to predict previously unknown points of crosstalk of JA to other signalling pathways and to identify new components of the JA regulatory mechanism, which we validated through targeted mutant analysis. These results provide a comprehensive understanding of how a plant hormone remodels cellular functions and plant behaviour, the general principles of which provide a framework for analyses of cross-regulation between other hormone and stress signalling pathways.
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Affiliation(s)
- Mark Zander
- Plant Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
- Genomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
- Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Mathew G Lewsey
- Centre for AgriBioscience, Department of Animal, Plant and Soil Sciences, School of Life Sciences, La Trobe University, Melbourne, Victoria, Australia.
- Australian Research Council Industrial Transformation Research Hub for Medicinal Agriculture, Centre for AgriBioscience, La Trobe University, Bundoora, Victoria, Australia.
| | - Natalie M Clark
- Plant Pathology and Microbiology, Iowa State University, Ames, IA, USA
| | - Lingling Yin
- Centre for AgriBioscience, Department of Animal, Plant and Soil Sciences, School of Life Sciences, La Trobe University, Melbourne, Victoria, Australia
- Australian Research Council Industrial Transformation Research Hub for Medicinal Agriculture, Centre for AgriBioscience, La Trobe University, Bundoora, Victoria, Australia
| | - Anna Bartlett
- Genomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - J Paola Saldierna Guzmán
- Plant Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
- School of Natural Sciences, University of California Merced, Merced, CA, USA
| | - Elizabeth Hann
- Plant Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
- Department of Chemical and Environmental Engineering, Department of Botany and Plant Sciences, University of California, Riverside, CA, USA
| | - Amber E Langford
- Plant Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Bruce Jow
- Genomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
- Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Aaron Wise
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Joseph R Nery
- Genomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Huaming Chen
- Genomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Ziv Bar-Joseph
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Justin W Walley
- Plant Pathology and Microbiology, Iowa State University, Ames, IA, USA
| | - Roberto Solano
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Madrid, Spain
| | - Joseph R Ecker
- Plant Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA.
- Genomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA.
- Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, CA, USA.
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26
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Vadla R, Chatterjee N, Haldar D. Cellular environment controls the dynamics of histone H3 lysine 56 acetylation in response to DNA damage in mammalian cells. J Biosci 2020. [DOI: 10.1007/s12038-019-9986-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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27
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Hugues A, Jacobs CS, Roudier F. Mitotic Inheritance of PRC2-Mediated Silencing: Mechanistic Insights and Developmental Perspectives. FRONTIERS IN PLANT SCIENCE 2020; 11:262. [PMID: 32211012 PMCID: PMC7075419 DOI: 10.3389/fpls.2020.00262] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Accepted: 02/19/2020] [Indexed: 05/20/2023]
Abstract
Maintenance of gene repression by Polycomb Repressive Complex 2 (PRC2) that catalyzes the trimethylation of histone H3 at lysine 27 (H3K27me3) is integral to the orchestration of developmental programs in most multicellular eukaryotes. Faithful inheritance of H3K27me3 patterns across replication ensures the stability of PRC2-mediated transcriptional silencing over cell generations, thereby safeguarding cellular identities. In this review, we discuss the molecular and mechanistic principles that underlie H3K27me3 restoration after the passage of the replication fork, considering recent advances in different model systems. In particular, we aim at emphasizing parallels and differences between plants and other organisms, focusing on the recycling of parental histones and the replenishment of H3K27me3 patterns post-replication thanks to the remarkable properties of the PRC2 complex. We then discuss the necessity for fine-tuning this genuine epigenetic memory system so as to allow for cell fate and developmental transitions. We highlight recent insights showing that genome-wide destabilization of the H3K27me3 landscape during chromatin replication participates in achieving this flexible stability and provides a window of opportunity for subtle transcriptional reprogramming.
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Affiliation(s)
- Alice Hugues
- Laboratoire Reproduction et Développement des Plantes, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, INRIA, Université de Lyon, Lyon, France
- Master de Biologie, École Normale Supérieure de Lyon, Université Claude Bernard Lyon I, Université de Lyon, Lyon, France
| | - Chean Sern Jacobs
- Laboratoire Reproduction et Développement des Plantes, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, INRIA, Université de Lyon, Lyon, France
| | - François Roudier
- Laboratoire Reproduction et Développement des Plantes, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, INRIA, Université de Lyon, Lyon, France
- *Correspondence: François Roudier,
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28
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Vadla R, Chatterjee N, Haldar D. Cellular environment controls the dynamics of histone H3 lysine 56 acetylation in response to DNA damage in mammalian cells. J Biosci 2020; 45:19. [PMID: 31965997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Epigenetic changes play a crucial role in sensing signals and responding to fluctuations in the extracellular environment. How the cellular micro-environment affects DNA damage response signalling in chromatin context is not extensively studied. Histone acetylation is dynamic and very sensitive to changes in the extracellular environment. Existing literature on H3 lysine 56 acetylation (H3K56ac) levels upon DNA damage in mammals presents a conflicting picture. The occurrence of both increased and decreased H3K56ac upon DNA damage in our experiments led us to investigate the role of the micro-environment on H3K56ac. Here, we show that the global levels of H3K56ac increase as cells grow from low density to high density while SIRT1 and SIRT6 expression decrease. Additionally, rising lactic acid levels increase H3K56ac. Our results show that cell density and accumulation of metabolites affect dynamics of H3K56ac in response to DNA damage. Upon DNA damage, H3K56ac increases in low density cells with low initial acetylation, while acetylation decreases in high cell density cells. These results highlight that H3K56ac levels upon DNA damage are dependent on the metabolites in the extracellular milieu which impact chromatin structure by regulating chromatin modifying enzymes. Accumulation of lactic acid at high cell density reflects conditions similar to the tumour micro-environment. As H3K56ac increases in tumours, lactic acid and low pH might alter H3K56ac in tumours, leading to deregulated gene expression, contributing to tumour progression.
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Affiliation(s)
- Raghavendra Vadla
- Centre for DNA Fingerprinting and Diagnostics, Uppal, Hyderabad 500 039, India
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29
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Espinosa-Cores L, Bouza-Morcillo L, Barrero-Gil J, Jiménez-Suárez V, Lázaro A, Piqueras R, Jarillo JA, Piñeiro M. Insights Into the Function of the NuA4 Complex in Plants. FRONTIERS IN PLANT SCIENCE 2020; 11:125. [PMID: 32153620 PMCID: PMC7047200 DOI: 10.3389/fpls.2020.00125] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 01/28/2020] [Indexed: 05/14/2023]
Abstract
Chromatin remodeling plays a key role in the establishment and maintenance of gene expression patterns essential for plant development and responses to environmental factors. Post-translational modification of histones, including acetylation, is one of the most relevant chromatin remodeling mechanisms that operate in eukaryotic cells. Histone acetylation is an evolutionarily conserved chromatin signature commonly associated with transcriptional activation. Histone acetylation levels are tightly regulated through the antagonistic activity of histone acetyltransferases (HATs) and histone deacetylases (HDACs). In plants, different families of HATs are present, including the MYST family, which comprises homologs of the catalytic subunit of the Nucleosome Acetyltransferase of H4 (NuA4) complex in yeast. This complex mediates acetylation of histones H4, H2A, and H2A.Z, and is involved in transcriptional regulation, heterochromatin silencing, cell cycle progression, and DNA repair in yeast. In Arabidopsis and, other plant species, homologs for most of the yeast NuA4 subunits are present and although the existence of this complex has not been demonstrated yet, compelling evidence supports the notion that this type of HAT complex functions from mosses to angiosperms. Recent proteomic studies show that several Arabidopsis homologs of NuA4 components, including the assembly platform proteins and the catalytic subunit, are associated in vivo with additional members of this complex suggesting that a NuA4-like HAT complex is present in plants. Furthermore, the functional characterization of some Arabidopsis NuA4 subunits has uncovered the involvement of these proteins in the regulation of different plant biological processes. Interestingly, for most of the mutant plants deficient in subunits of this complex characterized so far, conspicuous defects in flowering time are observed, suggesting a role for NuA4 in the control of this plant developmental program. Moreover, the participation of Arabidopsis NuA4 homologs in other developmental processes, such as gametophyte development, as well as in cell proliferation and stress and hormone responses, has also been reported. In this review, we summarize the current state of knowledge on plant putative NuA4 subunits and discuss the latest progress concerning the function of this chromatin modifying complex.
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30
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Srivastava AK, Dutta S, Chattopadhyay S. MYC2 regulates ARR16, a component of cytokinin signaling pathways, in Arabidopsis seedling development. PLANT DIRECT 2019; 3:e00177. [PMID: 31788657 PMCID: PMC6875704 DOI: 10.1002/pld3.177] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 09/07/2019] [Accepted: 09/22/2019] [Indexed: 06/10/2023]
Abstract
MYC2 is a basic helix-loop-helix transcription factor that acts as a repressor of blue light-mediated photomorphogenic growth; however, it promotes lateral root formation. MYC2 also regulates different phytohormone-signaling pathways in crucial manner. Arabidopsis response regulator 16 (ARR16) is a negative regulator of cytokinin signaling pathways. Here, we show that MYC2 directly binds to the E-box of ARR16 minimal promoter and negatively regulates its expression in a cytokinin-dependent manner. While ARR16 and MYC2 influence jasmonic acid and cytokinin signaling, the expression of ARR16 is regulated by cry1, GBF1, and HYH, the components of light signaling pathways. The transgenic studies show that the expression of ARR16 is regulated by MYC2 at various stages of development. The mutational studies reveal that ARR16 positively regulates the hypocotyl growth in blue light, and phenotypic analysis of atmyc2 arr16 double mutant further reveals that arr16 can suppress the short hypocotyl phenotype of atmyc2. Altogether, this work highlights MYC2-mediated transcriptional repression of ARR16 in Arabidopsis seedling development.
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Affiliation(s)
| | - Siddhartha Dutta
- Department of BiotechnologyNational Institute of TechnologyDurgapurIndia
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Liu Y, Tian T, Zhang K, You Q, Yan H, Zhao N, Yi X, Xu W, Su Z. PCSD: a plant chromatin state database. Nucleic Acids Res 2019; 46:D1157-D1167. [PMID: 29040761 PMCID: PMC5753246 DOI: 10.1093/nar/gkx919] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 09/28/2017] [Indexed: 01/06/2023] Open
Abstract
Genome-wide maps of chromatin states have become a powerful representation of genome annotation and regulatory activity. We collected public and in-house plant epigenomic data sets and applied a Hidden Markov Model to define chromatin states, which included 290 553 (36 chromatin states), 831 235 (38 chromatin states) and 3 936 844 (26 chromatin states) segments across the whole genome of Arabidopsis thaliana, Oryza sativa and Zea mays, respectively. We constructed a Plant Chromatin State Database (PCSD, http://systemsbiology.cau.edu.cn/chromstates) to integrate detailed information about chromatin states, including the features and distribution of states, segments in states and related genes with segments. The self-organization mapping (SOM) results for these different chromatin signatures and UCSC Genome Browser for visualization were also integrated into the PCSD database. We further provided differential SOM maps between two epigenetic marks for chromatin state comparison and custom tools for new data analysis. The segments and related genes in SOM maps can be searched and used for motif and GO analysis, respectively. In addition, multi-species integration can be used to discover conserved features at the epigenomic level. In summary, our PCSD database integrated the identified chromatin states with epigenetic features and may be beneficial for communities to discover causal functions hidden in plant chromatin.
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Affiliation(s)
- Yue Liu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Tian Tian
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Kang Zhang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Qi You
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Hengyu Yan
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Nannan Zhao
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Xin Yi
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Wenying Xu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Zhen Su
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
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Maury S, Sow MD, Le Gac AL, Genitoni J, Lafon-Placette C, Mozgova I. Phytohormone and Chromatin Crosstalk: The Missing Link For Developmental Plasticity? FRONTIERS IN PLANT SCIENCE 2019; 10:395. [PMID: 31024580 PMCID: PMC6459951 DOI: 10.3389/fpls.2019.00395] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 03/14/2019] [Indexed: 05/29/2023]
Affiliation(s)
- Stéphane Maury
- LBLGC, INRA, Université d'Orléans, EA1207 USC 1328, Orléans, France
| | - Mamadou Dia Sow
- LBLGC, INRA, Université d'Orléans, EA1207 USC 1328, Orléans, France
| | - Anne-Laure Le Gac
- BIOSS Centre for Biological Signaling Studies, Institute for Biology III, University of Freiburg, Freiburg, Germany
| | - Julien Genitoni
- LBLGC, INRA, Université d'Orléans, EA1207 USC 1328, Orléans, France
- ESE, Ecology and Ecosystem Health, Agrocampus Ouest, INRA, Rennes, France
| | | | - Iva Mozgova
- Centre Algatech, Institute of Microbiology of the Czech Academy of Sciences, Trebon, Czechia
- Faculty of Science, University of South Bohemia in Ceske Budejovice, Ceske Budejovice, Czechia
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Bourbousse C, Barneche F. A Dynamic Signaling Path to Chromatin-Level Control of Plant Drought Response. MOLECULAR PLANT 2019; 12:292-294. [PMID: 30738193 DOI: 10.1016/j.molp.2019.01.022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 01/18/2019] [Accepted: 01/28/2019] [Indexed: 06/09/2023]
Affiliation(s)
- Clara Bourbousse
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL University, 75005 Paris, France.
| | - Fredy Barneche
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL University, 75005 Paris, France.
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Wilhelmsson PKI, Chandler JO, Fernandez-Pozo N, Graeber K, Ullrich KK, Arshad W, Khan S, Hofberger JA, Buchta K, Edger PP, Pires JC, Schranz ME, Leubner-Metzger G, Rensing SA. Usability of reference-free transcriptome assemblies for detection of differential expression: a case study on Aethionema arabicum dimorphic seeds. BMC Genomics 2019; 20:95. [PMID: 30700268 PMCID: PMC6354389 DOI: 10.1186/s12864-019-5452-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 01/14/2019] [Indexed: 12/31/2022] Open
Abstract
Background RNA-sequencing analysis is increasingly utilized to study gene expression in non-model organisms without sequenced genomes. Aethionema arabicum (Brassicaceae) exhibits seed dimorphism as a bet-hedging strategy – producing both a less dormant mucilaginous (M+) seed morph and a more dormant non-mucilaginous (NM) seed morph. Here, we compared de novo and reference-genome based transcriptome assemblies to investigate Ae. arabicum seed dimorphism and to evaluate the reference-free versus -dependent approach for identifying differentially expressed genes (DEGs). Results A de novo transcriptome assembly was generated using sequences from M+ and NM Ae. arabicum dry seed morphs. The transcripts of the de novo assembly contained 63.1% complete Benchmarking Universal Single-Copy Orthologs (BUSCO) compared to 90.9% for the transcripts of the reference genome. DEG detection used the strict consensus of three methods (DESeq2, edgeR and NOISeq). Only 37% of 1533 differentially expressed de novo assembled transcripts paired with 1876 genome-derived DEGs. Gene Ontology (GO) terms distinguished the seed morphs: the terms translation and nucleosome assembly were overrepresented in DEGs higher in abundance in M+ dry seeds, whereas terms related to mRNA processing and transcription were overrepresented in DEGs higher in abundance in NM dry seeds. DEGs amongst these GO terms included ribosomal proteins and histones (higher in M+), RNA polymerase II subunits and related transcription and elongation factors (higher in NM). Expression of the inferred DEGs and other genes associated with seed maturation (e.g. those encoding late embryogenesis abundant proteins and transcription factors regulating seed development and maturation such as ABI3, FUS3, LEC1 and WRI1 homologs) were put in context with Arabidopsis thaliana seed maturation and indicated that M+ seeds may desiccate and mature faster than NM. The 1901 transcriptomic DEG set GO-terms had almost 90% overlap with the 2191 genome-derived DEG GO-terms. Conclusions Whilst there was only modest overlap of DEGs identified in reference-free versus -dependent approaches, the resulting GO analysis was concordant in both approaches. The identified differences in dry seed transcriptomes suggest mechanisms underpinning previously identified contrasts between morphology and germination behaviour of M+ and NM seeds. Electronic supplementary material The online version of this article (10.1186/s12864-019-5452-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Per K I Wilhelmsson
- Plant Cell Biology, Faculty of Biology, University of Marburg, 35043, Marburg, Germany
| | - Jake O Chandler
- School of Biological Sciences, Royal Holloway University of London, Egham, Surrey, TW20 0EX, UK
| | - Noe Fernandez-Pozo
- Plant Cell Biology, Faculty of Biology, University of Marburg, 35043, Marburg, Germany
| | - Kai Graeber
- School of Biological Sciences, Royal Holloway University of London, Egham, Surrey, TW20 0EX, UK
| | - Kristian K Ullrich
- Plant Cell Biology, Faculty of Biology, University of Marburg, 35043, Marburg, Germany.,Present Address: Max Planck Institute for Evolutionary Biology, August-Thienemann-Straße 2, 24306, Ploen, Germany
| | - Waheed Arshad
- School of Biological Sciences, Royal Holloway University of London, Egham, Surrey, TW20 0EX, UK
| | - Safina Khan
- School of Biological Sciences, Royal Holloway University of London, Egham, Surrey, TW20 0EX, UK
| | - Johannes A Hofberger
- Biosystematics Group, Wageningen University, Wageningen, 6708 PB, The Netherlands
| | - Karl Buchta
- Plant Cell Biology, Faculty of Biology, University of Marburg, 35043, Marburg, Germany
| | - Patrick P Edger
- Department of Horticulture, Michigan State University, East Lansing, MI, 48864, USA
| | - J Chris Pires
- Division of Biological Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - M Eric Schranz
- Biosystematics Group, Wageningen University, Wageningen, 6708 PB, The Netherlands
| | - Gerhard Leubner-Metzger
- School of Biological Sciences, Royal Holloway University of London, Egham, Surrey, TW20 0EX, UK. .,Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University and Institute of Experimental Botany, Academy of Sciences of the Czech Republic, 78371, Olomouc, Czech Republic.
| | - Stefan A Rensing
- Plant Cell Biology, Faculty of Biology, University of Marburg, 35043, Marburg, Germany. .,BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany.
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35
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Wilhelmsson PKI, Chandler JO, Fernandez-Pozo N, Graeber K, Ullrich KK, Arshad W, Khan S, Hofberger JA, Buchta K, Edger PP, Pires JC, Schranz ME, Leubner-Metzger G, Rensing SA. Usability of reference-free transcriptome assemblies for detection of differential expression: a case study on Aethionema arabicum dimorphic seeds. BMC Genomics 2019. [PMID: 30700268 DOI: 10.1186/s12864-019-5452-5454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023] Open
Abstract
BACKGROUND RNA-sequencing analysis is increasingly utilized to study gene expression in non-model organisms without sequenced genomes. Aethionema arabicum (Brassicaceae) exhibits seed dimorphism as a bet-hedging strategy - producing both a less dormant mucilaginous (M+) seed morph and a more dormant non-mucilaginous (NM) seed morph. Here, we compared de novo and reference-genome based transcriptome assemblies to investigate Ae. arabicum seed dimorphism and to evaluate the reference-free versus -dependent approach for identifying differentially expressed genes (DEGs). RESULTS A de novo transcriptome assembly was generated using sequences from M+ and NM Ae. arabicum dry seed morphs. The transcripts of the de novo assembly contained 63.1% complete Benchmarking Universal Single-Copy Orthologs (BUSCO) compared to 90.9% for the transcripts of the reference genome. DEG detection used the strict consensus of three methods (DESeq2, edgeR and NOISeq). Only 37% of 1533 differentially expressed de novo assembled transcripts paired with 1876 genome-derived DEGs. Gene Ontology (GO) terms distinguished the seed morphs: the terms translation and nucleosome assembly were overrepresented in DEGs higher in abundance in M+ dry seeds, whereas terms related to mRNA processing and transcription were overrepresented in DEGs higher in abundance in NM dry seeds. DEGs amongst these GO terms included ribosomal proteins and histones (higher in M+), RNA polymerase II subunits and related transcription and elongation factors (higher in NM). Expression of the inferred DEGs and other genes associated with seed maturation (e.g. those encoding late embryogenesis abundant proteins and transcription factors regulating seed development and maturation such as ABI3, FUS3, LEC1 and WRI1 homologs) were put in context with Arabidopsis thaliana seed maturation and indicated that M+ seeds may desiccate and mature faster than NM. The 1901 transcriptomic DEG set GO-terms had almost 90% overlap with the 2191 genome-derived DEG GO-terms. CONCLUSIONS Whilst there was only modest overlap of DEGs identified in reference-free versus -dependent approaches, the resulting GO analysis was concordant in both approaches. The identified differences in dry seed transcriptomes suggest mechanisms underpinning previously identified contrasts between morphology and germination behaviour of M+ and NM seeds.
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Affiliation(s)
- Per K I Wilhelmsson
- Plant Cell Biology, Faculty of Biology, University of Marburg, 35043, Marburg, Germany
| | - Jake O Chandler
- School of Biological Sciences, Royal Holloway University of London, Egham, Surrey, TW20 0EX, UK
| | - Noe Fernandez-Pozo
- Plant Cell Biology, Faculty of Biology, University of Marburg, 35043, Marburg, Germany
| | - Kai Graeber
- School of Biological Sciences, Royal Holloway University of London, Egham, Surrey, TW20 0EX, UK
| | - Kristian K Ullrich
- Plant Cell Biology, Faculty of Biology, University of Marburg, 35043, Marburg, Germany
- Present Address: Max Planck Institute for Evolutionary Biology, August-Thienemann-Straße 2, 24306, Ploen, Germany
| | - Waheed Arshad
- School of Biological Sciences, Royal Holloway University of London, Egham, Surrey, TW20 0EX, UK
| | - Safina Khan
- School of Biological Sciences, Royal Holloway University of London, Egham, Surrey, TW20 0EX, UK
| | - Johannes A Hofberger
- Biosystematics Group, Wageningen University, Wageningen, 6708 PB, The Netherlands
| | - Karl Buchta
- Plant Cell Biology, Faculty of Biology, University of Marburg, 35043, Marburg, Germany
| | - Patrick P Edger
- Department of Horticulture, Michigan State University, East Lansing, MI, 48864, USA
| | - J Chris Pires
- Division of Biological Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - M Eric Schranz
- Biosystematics Group, Wageningen University, Wageningen, 6708 PB, The Netherlands
| | - Gerhard Leubner-Metzger
- School of Biological Sciences, Royal Holloway University of London, Egham, Surrey, TW20 0EX, UK.
- Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University and Institute of Experimental Botany, Academy of Sciences of the Czech Republic, 78371, Olomouc, Czech Republic.
| | - Stefan A Rensing
- Plant Cell Biology, Faculty of Biology, University of Marburg, 35043, Marburg, Germany.
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany.
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36
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Bourbousse C, Barneche F, Laloi C. Plant Chromatin Catches the Sun. FRONTIERS IN PLANT SCIENCE 2019; 10:1728. [PMID: 32038692 PMCID: PMC6992579 DOI: 10.3389/fpls.2019.01728] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 12/09/2019] [Indexed: 05/08/2023]
Abstract
Plants use solar radiation as energy source for photosynthesis. They also take advantage of the information provided by the varying properties of sunlight, such as wavelength, orientation, and periodicity, to trigger physiological and developmental adaptations to a changing environment. After more than a century of research efforts in plant photobiology, multiple light signaling pathways converging onto chromatin-based mechanisms have now been identified, which in some instances play critical roles in plant phenotypic plasticity. In addition to locus-specific changes linked to transcription regulation, light signals impact higher-order chromatin organization. Here, we summarize current knowledge on how light can affect the global composition and the spatial distribution of chromatin domains. We introduce emerging questions on the functional links between light signaling and the epigenome, and further discuss how different chromatin regulatory layers may interconnect during plant adaptive responses to light.
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Affiliation(s)
- Clara Bourbousse
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
- *Correspondence: Clara Bourbousse, ; Fredy Barneche,
| | - Fredy Barneche
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
- *Correspondence: Clara Bourbousse, ; Fredy Barneche,
| | - Christophe Laloi
- Aix Marseille Univ, CEA, CNRS, BIAM, Luminy Génétique et Biophysique des Plantes, Marseille, France
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Baroux C, Grossniklaus U. Seeds-An evolutionary innovation underlying reproductive success in flowering plants. Curr Top Dev Biol 2018; 131:605-642. [PMID: 30612632 DOI: 10.1016/bs.ctdb.2018.11.017] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
"Seeds nourish, seeds unite, seeds endure, seeds defend, seeds travel," explains the science writer Thor Hanson in his book The Triumph of Seeds (2015). The seed is an ultimate product of land plant evolution. The nursing and protective organization of the seed enable a unique parental care of the progeny that has fueled seed plant radiation. Seeds promote dispersal and optimize offspring production and thus reproductive fitness through biological adaptations that integrate environmental and developmental cues. The composite structure of seeds, uniting tissues that originate from three distinct organisms, enables the partitioning of tasks during development, maturation, and storage, while a sophisticated interplay between the compartments allows the fine-tuning of embryonic growth, as well as seed maturation, dormancy, and germination. In this review, we will highlight peculiarities in the development and evolution of the different seed compartments and focus on the molecular mechanisms underlying the interactions between them.
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Affiliation(s)
- Célia Baroux
- Department of Plant and Microbial Biology & Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland.
| | - Ueli Grossniklaus
- Department of Plant and Microbial Biology & Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland
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38
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Deng X, Qiu Q, He K, Cao X. The seekers: how epigenetic modifying enzymes find their hidden genomic targets in Arabidopsis. CURRENT OPINION IN PLANT BIOLOGY 2018; 45:75-81. [PMID: 29864678 DOI: 10.1016/j.pbi.2018.05.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 05/03/2018] [Accepted: 05/12/2018] [Indexed: 05/23/2023]
Abstract
Epigenetic regulation plays fundamental roles in modulating chromatin-based processes and shaping the epigenome in multicellular eukaryotes, including plants. How epigenetic factors recognize their target loci hiding in the vast genomic DNA sequence remains a long-standing mystery. During the past several years, a growing body of work has revealed the complex, dynamic, and diverse chromatin-targeting mechanisms of these epigenetic factors. In this review, we focus on recent advances in understanding the recruitment of epigenetic factors to specific genomic regions, based on data from Arabidopsis thaliana.
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Affiliation(s)
- Xian Deng
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Qi Qiu
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Kaixuan He
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing, China
| | - Xiaofeng Cao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing, China.
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EBS is a bivalent histone reader that regulates floral phase transition in Arabidopsis. Nat Genet 2018; 50:1247-1253. [PMID: 30082787 DOI: 10.1038/s41588-018-0187-8] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 06/06/2018] [Indexed: 12/11/2022]
Abstract
The ability of cells to perceive and translate versatile cues into differential chromatin and transcriptional states is critical for many biological processes1-5. In plants, timely transition to a flowering state is crucial for successful reproduction6-9. EARLY BOLTING IN SHORT DAY (EBS) is a negative transcriptional regulator that prevents premature flowering in Arabidopsis thaliana10,11. We found that EBS contains bivalent bromo-adjacent homology (BAH)-plant homeodomain (PHD) reader modules that bind H3K27me3 and H3K4me3, respectively. We observed co-enrichment of a subset of EBS-associated genes with H3K4me3, H3K27me3, and Polycomb repressor complex 2 (PRC2). Notably, EBS adopted an autoinhibition mode to mediate its switch in binding preference between H3K27me3 and H3K4me3. This binding balance was critical because disruption of either EBS-H3K27me3 or EBS-H3K4me3 interaction induced early floral transition. Our results identify a bivalent chromatin reader capable of recognizing two antagonistic histone marks, and we propose a distinct mechanism of interaction between active and repressive chromatin states.
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Carter B, Bishop B, Ho KK, Huang R, Jia W, Zhang H, Pascuzzi PE, Deal RB, Ogas J. The Chromatin Remodelers PKL and PIE1 Act in an Epigenetic Pathway That Determines H3K27me3 Homeostasis in Arabidopsis. THE PLANT CELL 2018; 30:1337-1352. [PMID: 29802212 PMCID: PMC6048792 DOI: 10.1105/tpc.17.00867] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 05/07/2018] [Accepted: 05/24/2018] [Indexed: 05/20/2023]
Abstract
Selective, tissue-specific gene expression is facilitated by the epigenetic modification H3K27me3 (trimethylation of lysine 27 on histone H3) in plants and animals. Much remains to be learned about how H3K27me3-enriched chromatin states are constructed and maintained. Here, we identify a genetic interaction in Arabidopsis thaliana between the chromodomain helicase DNA binding chromatin remodeler PICKLE (PKL), which promotes H3K27me3 enrichment, and the SWR1-family remodeler PHOTOPERIOD INDEPENDENT EARLY FLOWERING1 (PIE1), which incorporates the histone variant H2A.Z. Chromatin immunoprecipitation-sequencing and RNA-sequencing reveal that PKL, PIE1, and the H3K27 methyltransferase CURLY LEAF act in a common gene expression pathway and are required for H3K27me3 levels genome-wide. Additionally, H3K27me3-enriched genes are largely a subset of H2A.Z-enriched genes, further supporting the functional linkage between these marks. We also found that recombinant PKL acts as a prenucleosome maturation factor, indicating that it promotes retention of H3K27me3. These data support the existence of an epigenetic pathway in which PIE1 promotes H2A.Z, which in turn promotes H3K27me3 deposition. After deposition, PKL promotes retention of H3K27me3 after DNA replication and/or transcription. Our analyses thus reveal roles for H2A.Z and ATP-dependent remodelers in construction and maintenance of H3K27me3-enriched chromatin in plants.
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Affiliation(s)
- Benjamin Carter
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907
| | - Brett Bishop
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907
| | - Kwok Ki Ho
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907
| | - Ru Huang
- Shanghai Center for Plant Stress Biology, Songjiang District, Shanghai 201602, China
| | - Wei Jia
- Shanghai Center for Plant Stress Biology, Songjiang District, Shanghai 201602, China
| | - Heng Zhang
- Shanghai Center for Plant Stress Biology, Songjiang District, Shanghai 201602, China
| | - Pete E Pascuzzi
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907
- Purdue University Libraries, Purdue University, West Lafayette, Indiana 47907
| | - Roger B Deal
- Department of Biology, Emory University, Atlanta, Georgia 30322
| | - Joe Ogas
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907
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Bräutigam K, Cronk Q. DNA Methylation and the Evolution of Developmental Complexity in Plants. FRONTIERS IN PLANT SCIENCE 2018; 9:1447. [PMID: 30349550 PMCID: PMC6186995 DOI: 10.3389/fpls.2018.01447] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 09/12/2018] [Indexed: 05/20/2023]
Abstract
All land plants so far examined use DNA methylation to silence transposons (TEs). DNA methylation therefore appears to have been co-opted in evolution from an original function in TE management to a developmental function (gene regulation) in both phenotypic plasticity and in normal development. The significance of DNA methylation to the evolution of developmental complexity in plants lies in its role in the management of developmental pathways. As such it is more important in fine tuning the presence, absence, and placement of organs rather than having a central role in the evolution of new organs. Nevertheless, its importance should not be underestimated as it contributes considerably to the range of phenotypic expression and complexity available to plants: the subject of the emerging field of epi-evodevo. Furthermore, changes in DNA methylation can function as a "soft" mutation that may be important in the early stages of major evolutionary novelty.
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Affiliation(s)
- Katharina Bräutigam
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, Canada
| | - Quentin Cronk
- Department of Botany, The University of British Columbia, Vancouver, BC, Canada
- *Correspondence: Quentin Cronk,
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