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Bidhendi AJ, Lampron O, Gosselin FP, Geitmann A. Cell geometry regulates tissue fracture. Nat Commun 2023; 14:8275. [PMID: 38092784 PMCID: PMC10719271 DOI: 10.1038/s41467-023-44075-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Accepted: 11/29/2023] [Indexed: 12/17/2023] Open
Abstract
In vascular plants, the epidermal surfaces of leaves and flower petals often display cells with wavy geometries forming intricate jigsaw puzzle patterns. The prevalence and diversity of these complex epidermal patterns, originating from simple polyhedral progenitor cells, suggest adaptive significance. However, despite multiple efforts to explain the evolutionary drivers behind these geometrical features, compelling validation remains elusive. Employing a multidisciplinary approach that integrates microscopic and macroscopic fracture experiments with computational fracture mechanics, we demonstrate that wavy epidermal cells toughen the plants' protective skin. Through a multi-scale framework, we demonstrate that this energy-efficient patterning mechanism is universally applicable for toughening biological and synthetic materials. Our findings reveal a tunable structural-mechanical strategy employed in the microscale design of plants to protect them from deleterious surface fissures while facilitating and strategically directing beneficial ones. These findings hold implications for targeted plant breeding aimed at enhancing resilience in fluctuating environmental conditions. From an engineering perspective, our work highlights the sophisticated design principles the plant kingdom offers to inspire metamaterials.
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Affiliation(s)
- Amir J Bidhendi
- Department of Plant Science, McGill University, Macdonald Campus, 21111 Lakeshore, Ste-Anne-de-Bellevue, Québec, H9X 3V9, Canada.
- EERS Global Technologies, Montreal, Canada.
| | - Olivier Lampron
- Laboratoire de Mécanique Multi-échelles, Département de génie mécanique, École Polytechnique de Montréal, Montreal, Québec, H3C 3A7, Canada
| | - Frédérick P Gosselin
- Laboratoire de Mécanique Multi-échelles, Département de génie mécanique, École Polytechnique de Montréal, Montreal, Québec, H3C 3A7, Canada
| | - Anja Geitmann
- Department of Plant Science, McGill University, Macdonald Campus, 21111 Lakeshore, Ste-Anne-de-Bellevue, Québec, H9X 3V9, Canada.
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2
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Chen C, Ge Y, Lu L. Opportunities and challenges in the application of single-cell and spatial transcriptomics in plants. FRONTIERS IN PLANT SCIENCE 2023; 14:1185377. [PMID: 37636094 PMCID: PMC10453814 DOI: 10.3389/fpls.2023.1185377] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 07/26/2023] [Indexed: 08/29/2023]
Abstract
Single-cell and spatial transcriptomics have diverted researchers' attention from the multicellular level to the single-cell level and spatial information. Single-cell transcriptomes provide insights into the transcriptome at the single-cell level, whereas spatial transcriptomes help preserve spatial information. Although these two omics technologies are helpful and mature, further research is needed to ensure their widespread applicability in plant studies. Reviewing recent research on plant single-cell or spatial transcriptomics, we compared the different experimental methods used in various plants. The limitations and challenges are clear for both single-cell and spatial transcriptomic analyses, such as the lack of applicability, spatial information, or high resolution. Subsequently, we put forth further applications, such as cross-species analysis of roots at the single-cell level and the idea that single-cell transcriptome analysis needs to be combined with other omics analyses to achieve superiority over individual omics analyses. Overall, the results of this review suggest that combining single-cell transcriptomics, spatial transcriptomics, and spatial element distribution can provide a promising research direction, particularly for plant research.
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Affiliation(s)
- Ce Chen
- Ministry of Education Key Laboratory of Environment Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Yining Ge
- Ministry of Education Key Laboratory of Environment Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Lingli Lu
- Ministry of Education Key Laboratory of Environment Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
- Key Laboratory of Agricultural Resource and Environment of Zhejiang Province, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
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3
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Neyaz M, Gardner DR, Creamer R, Cook D. Localization of the Swainsonine-Producing Chaetothyriales Symbiont in the Seed and Shoot Apical Meristem in Its Host Ipomoea carnea. Microorganisms 2022; 10:microorganisms10030545. [PMID: 35336121 PMCID: PMC8951018 DOI: 10.3390/microorganisms10030545] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 02/26/2022] [Accepted: 02/26/2022] [Indexed: 12/04/2022] Open
Abstract
Several species of fungi from the orders Chaetothyriales and Pleosporales have been reported to produce swainsonine and be associated as symbionts with plants of the Convolvulaceae and Fabaceae, respectively. An endosymbiont belonging to the Chaetothyriales produces swainsonine and grows as an epibiont on the adaxial leaf surfaces of Ipomoea carnea, but how the symbiont passes through plant growth and development is unknown. Herein, different types of microscopy were used to localize the symbiont in seeds and in cross sections of plant parts. The symbiont was found in several tissues including the hilum, the sclereids, and the hypocotyl of seeds. In five-day old seedlings and mature plants, the symbiont was found in the shoot apical meristem (SAM) and the adaxial surface of immature folded leaves. The mycelia generally formed a close association with peltate glandular trichomes. This report provides further data explaining the relationship between the seed transmitted Chaetothyriales symbiont and Ipomoea carnea. These results provide a possible explanation for how this symbiont, and others like Periglandula may persist and are transmitted over time.
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Affiliation(s)
- Marwa Neyaz
- Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM 88003, USA;
| | - Dale R. Gardner
- Poisonous Plant Research Laboratory, US Department of Agriculture, Logan, UT 84321, USA;
| | - Rebecca Creamer
- Department of Entomology, Plant Pathology, and Weed Science, New Mexico State University, Las Cruces, NM 88003, USA;
| | - Daniel Cook
- Poisonous Plant Research Laboratory, US Department of Agriculture, Logan, UT 84321, USA;
- Correspondence:
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4
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Dełeńko K, Nuc P, Kubiak D, Bielewicz D, Dolata J, Niedojadło K, Górka S, Jarmołowski A, Szweykowska-Kulińska Z, Niedojadło J. MicroRNA biogenesis and activity in plant cell dedifferentiation stimulated by cell wall removal. BMC PLANT BIOLOGY 2022; 22:9. [PMID: 34979922 PMCID: PMC8722089 DOI: 10.1186/s12870-021-03323-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Accepted: 11/05/2021] [Indexed: 06/14/2023]
Abstract
BACKGROUND Despite the frequent use of protoplast-to-plant system in in vitro cultures of plants, the molecular mechanisms regulating the first and most limiting stages of this process, i.e., protoplast dedifferentiation and the first divisions leading to the formation of a microcallus, have not been elucidated. RESULTS In this study, we investigated the function of miRNAs in the dedifferentiation of A. thaliana mesophyll cells in a process stimulated by the enzymatic removal of the cell wall. Leaf cells, protoplasts and CDPs (cells derived from protoplasts) cultured for 24, 72 and 120 h (first cell division). In protoplasts, a strong decrease in the amount of AGO1 in both the nucleus and the cytoplasm, as well as dicing bodies (DBs), which are considered to be sites of miRNA biogenesis, was shown. However during CDPs division, the amounts of AGO1 and DBs strongly increased. MicroRNA transcriptome studies demonstrated that lower amount of differentially expressed miRNAs are present in protoplasts than in CDPs cultured for 120 h. Then analysis of differentially expressed miRNAs, selected pri-miRNA and mRNA targets were performed. CONCLUSION This result indicates that miRNA function is not a major regulation of gene expression in the initial but in later steps of dedifferentiation during CDPs divisions. miRNAs participate in organogenesis, oxidative stress, nutrient deficiencies and cell cycle regulation in protoplasts and CDPs. The important role played by miRNAs in the process of dedifferentiation of mesophyll cells was confirmed by the increased mortality and reduced cell division of CDPs derived from mutants with defective miRNA biogenesis and miR319b expression.
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Affiliation(s)
- Konrad Dełeńko
- Department of Cellular and Molecular Biology, Nicolaus Copernicus University, Lwowska 1, 87-100, Toruń, Poland
- Centre For Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Wileńska 4, 87-100, Torun, Poland
| | - Przemysław Nuc
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 6, 61-614, Poznan, Poland
| | - Dawid Kubiak
- Department of Cellular and Molecular Biology, Nicolaus Copernicus University, Lwowska 1, 87-100, Toruń, Poland
- Centre For Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Wileńska 4, 87-100, Torun, Poland
| | - Dawid Bielewicz
- Center for Advanced Technology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 10, 61-614, Poznań, Poland
| | - Jakub Dolata
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 6, 61-614, Poznan, Poland
| | - Katarzyna Niedojadło
- Department of Cellular and Molecular Biology, Nicolaus Copernicus University, Lwowska 1, 87-100, Toruń, Poland
| | - Sylwia Górka
- Department of Cellular and Molecular Biology, Nicolaus Copernicus University, Lwowska 1, 87-100, Toruń, Poland
- Centre For Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Wileńska 4, 87-100, Torun, Poland
| | - Artur Jarmołowski
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 6, 61-614, Poznan, Poland
| | - Zofia Szweykowska-Kulińska
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 6, 61-614, Poznan, Poland
| | - Janusz Niedojadło
- Department of Cellular and Molecular Biology, Nicolaus Copernicus University, Lwowska 1, 87-100, Toruń, Poland.
- Centre For Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Wileńska 4, 87-100, Torun, Poland.
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5
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Space: the final frontier — achieving single-cell, spatially resolved transcriptomics in plants. Emerg Top Life Sci 2021; 5:179-188. [DOI: 10.1042/etls20200274] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 01/05/2021] [Accepted: 01/11/2021] [Indexed: 01/13/2023]
Abstract
Single-cell RNA-seq is a tool that generates a high resolution of transcriptional data that can be used to understand regulatory networks in biological systems. In plants, several methods have been established for transcriptional analysis in tissue sections, cell types, and/or single cells. These methods typically require cell sorting, transgenic plants, protoplasting, or other damaging or laborious processes. Additionally, the majority of these technologies lose most or all spatial resolution during implementation. Those that offer a high spatial resolution for RNA lack breadth in the number of transcripts characterized. Here, we briefly review the evolution of spatial transcriptomics methods and we highlight recent advances and current challenges in sequencing, imaging, and computational aspects toward achieving 3D spatial transcriptomics of plant tissues with a resolution approaching single cells. We also provide a perspective on the potential opportunities to advance this novel methodology in plants.
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6
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Abstract
There are various preparatory techniques for light microscopy permitting access to the inner structure of plant body and its development. Minute objects might be processed as whole-mount preparations, while voluminous ones should be separated into smaller pieces. Here we summarize some of the "classical" techniques to cut more voluminous objects into slices and access their inner structure either for simple anatomical analysis or for further processing (e.g., histochemistry, immunohistochemistry, in situ hybridization, enzyme histochemistry).
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Affiliation(s)
- Aleš Soukup
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Prague, Czech Republic.
| | - Edita Tylová
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Prague, Czech Republic
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7
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Sims J, Chouaref J, Schlögelhofer P. Whole-Mount Immuno-FISH on Arabidopsis Meiocytes (WhoMI-FISH). Methods Mol Biol 2020; 2061:59-66. [PMID: 31583653 DOI: 10.1007/978-1-4939-9818-0_6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Imaging cells, nuclei, and DNA in their natural spatial contexts and configurations is challenging yet required to understand the biology of genome organization, maintenance, and transmission. Live-cell imaging allows capturing dynamic changes of chromosomes in their nuclear and cellular context but lacks resolution. In contrast, imaging of fixed, spread chromosome samples provides unmatched resolution but potentially distorts configurations and spatial relations. Fixed whole-mount samples preserve chromosome configurations and cellular contexts and allow high-resolution imaging. Importantly the latter method allows simultaneous visualization of specific genomic regions (via fluorescent in situ hybridization-FISH) and proteins (via immune-localization using antibodies or tags). Here we present an advanced "whole-mount immuno-FISH" (WhoMI-FISH) method based on the published protocol by Bey Till et al. (Methods Mol Biol 1675:467-480, 2018) specifically optimized for pollen mother cells (PMCs) of Arabidopsis thaliana. It focuses on (1) specimen preparation that maintains meiocyte nuclei positions and genome organization in anthers and also on (2) simultaneous detection of specific genomic regions and meiotic proteins.
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Affiliation(s)
- Jason Sims
- Max Perutz Labs, Department of Chromosome Biology, Vienna Biocenter (VBC), University of Vienna, Vienna, Austria
| | - Jihed Chouaref
- Swammerdam Institute for Life Sciences, Universiteit van Amsterdam, Amsterdam, The Netherlands
| | - Peter Schlögelhofer
- Max Perutz Labs, Department of Chromosome Biology, Vienna Biocenter (VBC), University of Vienna, Vienna, Austria.
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8
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Yang W, Schuster C, Prunet N, Dong Q, Landrein B, Wightman R, Meyerowitz EM. Visualization of Protein Coding, Long Noncoding, and Nuclear RNAs by Fluorescence in Situ Hybridization in Sections of Shoot Apical Meristems and Developing Flowers. PLANT PHYSIOLOGY 2020; 182:147-158. [PMID: 31722974 PMCID: PMC6945838 DOI: 10.1104/pp.19.00980] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 11/05/2019] [Indexed: 05/31/2023]
Abstract
In addition to transcriptional regulation, gene expression is further modulated through mRNA spatiotemporal distribution, by RNA movement between cells, and by RNA localization within cells. Here, we have adapted RNA fluorescence in situ hybridization (FISH) to explore RNA localization in Arabidopsis (Arabidopsis thaliana). We show that RNA FISH on sectioned material can be applied to investigate the tissue and subcellular localization of meristem and flower development genes, cell cycle transcripts, and plant long noncoding RNAs. We also developed double RNA FISH to dissect the coexpression of different mRNAs at the shoot apex and nuclear-cytoplasmic separation of cell cycle gene transcripts in dividing cells. By coupling RNA FISH with fluorescence immunocytochemistry, we further demonstrate that a gene's mRNA and protein may be simultaneously detected, for example revealing uniform distribution of PIN-FORMED1 (PIN1) mRNA and polar localization of PIN1 protein in the same cells. Therefore, our method enables the visualization of gene expression at both transcriptional and translational levels with subcellular spatial resolution, opening up the possibility of systematically tracking the dynamics of RNA molecules and their cognate proteins in plant cells.
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Affiliation(s)
- Weibing Yang
- Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, United Kingdom
| | - Christoph Schuster
- Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, United Kingdom
| | - Nathanaël Prunet
- Howard Hughes Medical Institute and Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125
| | - Qingkun Dong
- Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, United Kingdom
- State Key Laboratory for Conservation and Utilization of Subtropical Agrobioresources, South China Agricultural University, Guangzhou 510642, China
| | - Benoit Landrein
- Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, United Kingdom
| | - Raymond Wightman
- Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, United Kingdom
| | - Elliot M Meyerowitz
- Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, United Kingdom
- Howard Hughes Medical Institute and Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125
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9
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Millar AJ, Urquiza U, Freeman PL, Hume A, Plotkin GD, Sorokina O, Zardilis A, Zielinski T. Practical steps to digital organism models, from laboratory model species to 'Crops in silico. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:2403-2418. [PMID: 30615184 DOI: 10.1093/jxb/ery435] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 11/28/2018] [Indexed: 05/20/2023]
Abstract
A recent initiative named 'Crops in silico' proposes that multi-scale models 'have the potential to fill in missing mechanistic details and generate new hypotheses to prioritize directed engineering efforts' in plant science, particularly directed to crop species. To that end, the group called for 'a paradigm shift in plant modelling, from largely isolated efforts to a connected community'. 'Wet' (experimental) research has been especially productive in plant science, since the adoption of Arabidopsis thaliana as a laboratory model species allowed the emergence of an Arabidopsis research community. Parts of this community invested in 'dry' (theoretical) research, under the rubric of Systems Biology. Our past research combined concepts from Systems Biology and crop modelling. Here we outline the approaches that seem most relevant to connected, 'digital organism' initiatives. We illustrate the scale of experimental research required, by collecting the kinetic parameter values that are required for a quantitative, dynamic model of a gene regulatory network. By comparison with the Systems Biology Markup Language (SBML) community, we note computational resources and community structures that will help to realize the potential for plant Systems Biology to connect with a broader crop science community.
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Affiliation(s)
- Andrew J Millar
- SynthSys and School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Uriel Urquiza
- SynthSys and School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | | | - Alastair Hume
- SynthSys and School of Biological Sciences, University of Edinburgh, Edinburgh, UK
- EPCC, Bayes Centre, University of Edinburgh, Edinburgh, UK
| | - Gordon D Plotkin
- Laboratory for the Foundations of Computer Science, School of Informatics, University of Edinburgh, Edinburgh, UK
| | - Oxana Sorokina
- Institute for Adaptive and Neural Computation, School of Informatics, University of Edinburgh, Edinburgh, UK
| | - Argyris Zardilis
- SynthSys and School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Tomasz Zielinski
- SynthSys and School of Biological Sciences, University of Edinburgh, Edinburgh, UK
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10
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Skorupa M, Gołębiewski M, Kurnik K, Niedojadło J, Kęsy J, Klamkowski K, Wójcik K, Treder W, Tretyn A, Tyburski J. Salt stress vs. salt shock - the case of sugar beet and its halophytic ancestor. BMC PLANT BIOLOGY 2019; 19:57. [PMID: 30727960 PMCID: PMC6364445 DOI: 10.1186/s12870-019-1661-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 01/24/2019] [Indexed: 05/20/2023]
Abstract
BACKGROUND Sugar beet is a highly salt-tolerant crop. However, its ability to withstand high salinity is reduced compared to sea beet, a wild ancestor of all beet crops. The aim of this study was to investigate transcriptional patterns associated with physiological, cytological and biochemical mechanisms involved in salt response in these closely related subspecies. Salt acclimation strategies were assessed in plants subjected to either gradually increasing salt levels (salt-stress) or in excised leaves, exposed instantly to salinity (salt-shock). RESULT The majority of DEGs was down-regulated under stress, which may lead to certain aspects of metabolism being reduced in this treatment, as exemplified by lowered transpiration and photosynthesis. This effect was more pronounced in sugar beet. Additionally, sugar beet, but not sea beet, growth was restricted. Silencing of genes encoding numerous transcription factors and signaling proteins was observed, concomitantly with the up-regulation of lipid transfer protein-encoding genes and those coding for NRTs. Bark storage protein genes were up-regulated in sugar beet to the level observed in unstressed sea beet. Osmotic adjustment, manifested by increased water and proline content, occurred in salt-shocked leaves of both genotypes, due to the concerted activation of genes encoding aquaporins, ion channels and osmoprotectants synthesizing enzymes. bHLH137 was the only TF-encoding gene induced by salt in a dose-dependent manner irrespective of the mode of salt treatment. Moreover, the incidence of bHLH-binding motives in promoter regions of salinity-regulated genes was significantly greater than in non-regulated ones. CONCLUSIONS Maintaining homeostasis under salt stress requires deeper transcriptomic changes in the sugar beet than in the sea beet. In both genotypes salt shock elicits greater transcriptomic changes than stress and it results in greater number of up-regulated genes compared to the latter. NRTs and bark storage protein may play a yet undefined role in salt stress-acclimation in beet. bHLH is a putative regulator of salt response in beet leaves and a promising candidate for further studies.
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Affiliation(s)
- Monika Skorupa
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Toruń, Poland
| | - Marcin Gołębiewski
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Toruń, Poland
- Chair of Plant Physiology and Biotechnology, Faculty of Biology and Environment Protection, Nicolaus Copernicus University, Toruń, Poland
| | - Katarzyna Kurnik
- Chair of Plant Physiology and Biotechnology, Faculty of Biology and Environment Protection, Nicolaus Copernicus University, Toruń, Poland
| | - Janusz Niedojadło
- Department of Cellular and Molecular Biology, Faculty of Biology and Environment Protection, Nicolaus Copernicus University, Toruń, Poland
| | - Jacek Kęsy
- Chair of Plant Physiology and Biotechnology, Faculty of Biology and Environment Protection, Nicolaus Copernicus University, Toruń, Poland
| | | | | | | | - Andrzej Tretyn
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Toruń, Poland
- Chair of Plant Physiology and Biotechnology, Faculty of Biology and Environment Protection, Nicolaus Copernicus University, Toruń, Poland
| | - Jarosław Tyburski
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Toruń, Poland
- Chair of Plant Physiology and Biotechnology, Faculty of Biology and Environment Protection, Nicolaus Copernicus University, Toruń, Poland
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11
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Hasegawa J, Sakamoto T, Fujimoto S, Yamashita T, Suzuki T, Matsunaga S. Auxin decreases chromatin accessibility through the TIR1/AFBs auxin signaling pathway in proliferative cells. Sci Rep 2018; 8:7773. [PMID: 29773913 PMCID: PMC5958073 DOI: 10.1038/s41598-018-25963-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Accepted: 05/02/2018] [Indexed: 11/09/2022] Open
Abstract
Chromatin accessibility is closely associated with chromatin functions such as gene expression, DNA replication, and maintenance of DNA integrity. However, the relationship between chromatin accessibility and plant hormone signaling has remained elusive. Here, based on the correlation between chromatin accessibility and DNA damage, we used the sensitivity to DNA double strand breaks (DSBs) as an indicator of chromatin accessibility and demonstrated that auxin regulates chromatin accessibility through the TIR1/AFBs signaling pathway in proliferative cells. Treatment of proliferating plant cells with an inhibitor of the TIR1/AFBs auxin signaling pathway, PEO-IAA, caused chromatin loosening, indicating that auxin signaling functions to decrease chromatin accessibility. In addition, a transcriptome analysis revealed that several histone H4 genes and a histone chaperone gene, FAS1, are positively regulated through the TIR1/AFBs signaling pathway, suggesting that auxin plays a role in promoting nucleosome assembly. Analysis of the fas1 mutant of Arabidopsis thaliana confirmed that FAS1 is required for the auxin-dependent decrease in chromatin accessibility. These results suggest that the positive regulation of chromatin-related genes mediated by the TIR1/AFBs auxin signaling pathway enhances nucleosome assembly, resulting in decreased chromatin accessibility in proliferative cells.
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Affiliation(s)
- Junko Hasegawa
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, 278-8510, Japan
| | - Takuya Sakamoto
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, 278-8510, Japan
| | - Satoru Fujimoto
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, 278-8510, Japan
| | - Tomoe Yamashita
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, 278-8510, Japan
| | - Takamasa Suzuki
- College of Bioscience and Biotechnology, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi, 487-8501, Japan
| | - Sachihiro Matsunaga
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, 278-8510, Japan.
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12
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Arpòn J, Gaudin V, Andrey P. A Method for Testing Random Spatial Models on Nuclear Object Distributions. Methods Mol Biol 2018; 1675:493-507. [PMID: 29052210 DOI: 10.1007/978-1-4939-7318-7_29] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The cell nucleus is a structurally complex and dynamic organelle ensuring key biological functions. Complex relationships between nuclear structure and functions require a better understanding of the three-dimensional organization of the genome and of the subnuclear compartments. Quantitative image analysis coupled with spatial statistics and modeling is a relevant approach to address these questions. In this chapter, we describe a step-by-step procedure to process images and to test a spatial random model for the distribution of nuclear objects using chromocenters as an example. More elaborate models can be designed on the basis of the random model by introducing additional and more complex constraints to better fit observations and to question determinants of these spatial organizations.
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Affiliation(s)
- Javier Arpòn
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, F-78000, Versailles, France
| | - Valérie Gaudin
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, F-78000, Versailles, France
| | - Philippe Andrey
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, F-78000, Versailles, France.
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13
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Abstract
The long linear chromosomes of eukaryotic organisms are tightly packed into the nucleus of the cell. Beyond a first organization into nucleosomes and higher-order chromatin fibers, the positioning of nuclear DNA within the three-dimensional space of the nucleus plays a critical role in genome function and gene expression. Different techniques have been developed to assess nanoscale chromatin organization, nuclear position of genomic regions or specific chromatin features and binding proteins as well as higher-order chromatin organization. Here, I present an overview of imaging and molecular techniques applied to study nuclear architecture in plants, with special attention to the related protocols published in the "Plant Chromatin Dynamics" edition from Methods in Molecular Biology.
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Affiliation(s)
- Aline V Probst
- GReD, Université Clermont Auvergne, CNRS, INSERM, 63001, Clermont-Ferrand, France.
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14
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Bey TD, Koini M, Fransz P. Fluorescence In Situ Hybridization (FISH) and Immunolabeling on 3D Preserved Nuclei. Methods Mol Biol 2018; 1675:467-480. [PMID: 29052208 DOI: 10.1007/978-1-4939-7318-7_27] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The spatial distribution of genes in the nucleus emerges as an important factor in gene regulation and epigenetics. The position of loci relative to each other, to nuclear landmarks such as the nucleolus and chromocenters, as well as to chromatin proteins is therefore highly interesting. With fluorescent in situ hybridization (FISH) specific DNA sequences can be stained and antibodies allow the detection of specific proteins. Here, we present two protocols that preserve the 3D structure of nuclei. With whole-mount FISH, specific sequences can be stained in intact tissues and, secondly, a combined immunolabeling and FISH protocol on acrylamide-embedded nuclei makes it possible to stain DNA sequences and proteins simultaneously.
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Affiliation(s)
- Till David Bey
- Plant Development and (Epi)Genetics, Swammerdam Institute for Life Sciences, University of Amsterdam, Postbus 94215, 1090, GE, Amsterdam, The Netherlands
| | - Maria Koini
- Plant Development and (Epi)Genetics, Swammerdam Institute for Life Sciences, University of Amsterdam, Postbus 94215, 1090, GE, Amsterdam, The Netherlands
| | - Paul Fransz
- Plant Development and (Epi)Genetics, Swammerdam Institute for Life Sciences, University of Amsterdam, Postbus 94215, 1090, GE, Amsterdam, The Netherlands.
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Desset S, Poulet A, Tatout C. Quantitative 3D Analysis of Nuclear Morphology and Heterochromatin Organization from Whole-Mount Plant Tissue Using NucleusJ. Methods Mol Biol 2018; 1675:615-632. [PMID: 29052214 DOI: 10.1007/978-1-4939-7318-7_33] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Image analysis is a classical way to study nuclear organization. While nuclear organization used to be investigated by colorimetric or fluorescent labeling of DNA or specific nuclear compartments, new methods in microscopy imaging now enable qualitative and quantitative analyses of chromatin pattern, and nuclear size and shape. Several procedures have been developed to prepare samples in order to collect 3D images for the analysis of spatial chromatin organization, but only few preserve the positional information of the cell within its tissue context. Here, we describe a whole mount tissue preparation procedure coupled to DNA staining using the PicoGreen® intercalating agent suitable for image analysis of the nucleus in living and fixed tissues. 3D Image analysis is then performed using NucleusJ, an open source ImageJ plugin, which allows for quantifying variations in nuclear morphology such as nuclear volume, sphericity, elongation, and flatness as well as in heterochromatin content and position in respect to the nuclear periphery.
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Affiliation(s)
- Sophie Desset
- Université Clermont Auvergne, CNRS, INSERM, GReD, 63000, Clermont-Ferrand, France
| | - Axel Poulet
- Université Clermont Auvergne, CNRS, INSERM, GReD, 63000, Clermont-Ferrand, France
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, OX3 0BP, UK
| | - Christophe Tatout
- Université Clermont Auvergne, CNRS, INSERM, GReD, 63000, Clermont-Ferrand, France.
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16
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Sas-Nowosielska H, Bernas T. Spatial relationship between chromosomal domains in diploid and autotetraploid Arabidopsis thaliana nuclei. Nucleus 2017; 7:216-31. [PMID: 27310308 DOI: 10.1080/19491034.2016.1182277] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Polyploids constitute more than 80% of angiosperm plant species. Their DNA content is often further increased by endoreplication, which occurs as a part of cell differentiation. Here, we explore the relationship between 3D chromatin architecture, number of genome copies and their origin in the model plant, Arabidopsis thaliana. Spatial proximity between pericentromeric, interstitial and subtelomeric domains of chromosomes 1 and 4 was quantified over a range of distances. The results indicate that average nuclear volume as well as chromatin density increase with the genome copy number. Similar dependence is observed when association of homologous chromosomes (in 2C/ endopolyploid nuclei) and sister chromatid separation (in endopolyploid nuclei) is studied. Moreover, clusters of chromosomal domains are detectable at the spatial scale above microscopy resolution. Subtelomeric, interstitial and pericentromeric chromosomal domains are affected to different extent by these processes, which are modulated by endopolyploidy. This factor influences fusion of heterochromatin as well. Nonetheless, local chromatin architecture of Arabidopsis thaliana depends mainly on endopolyploidy level, and to lesser extend on polyploidy.
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Affiliation(s)
- H Sas-Nowosielska
- a Laboratory of Imaging Tissue Structure and Function , Nencki Institute of Experimental Biology , Polish Academy of Sciences , Warszawa , Poland.,b Department of Plant Anatomy and Cytology , Faculty of Biology , University of Silesia , Katowice , Poland
| | - T Bernas
- b Department of Plant Anatomy and Cytology , Faculty of Biology , University of Silesia , Katowice , Poland
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17
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Fujimoto S, Sugano SS, Kuwata K, Osakabe K, Matsunaga S. Visualization of specific repetitive genomic sequences with fluorescent TALEs in Arabidopsis thaliana. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:6101-6110. [PMID: 27811079 PMCID: PMC5100022 DOI: 10.1093/jxb/erw371] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Live imaging of the dynamics of nuclear organization provides the opportunity to uncover the mechanisms responsible for four-dimensional genome architecture. Here, we describe the use of fluorescent protein (FP) fusions of transcription activator-like effectors (TALEs) to visualize endogenous genomic sequences in Arabidopsis thaliana. The ability to engineer sequence-specific TALEs permits the investigation of precise genomic sequences. We could detect TALE-FP signals associated with centromeric, telomeric, and rDNA repeats and the signal distribution was consistent with that observed by fluorescent in situ hybridization. TALE-FPs are advantageous because they permit the observation of intact tissues. We used our TALE-FP method to investigate the nuclei of several multicellular plant tissues including roots, hypocotyls, leaves, and flowers. Because TALE-FPs permit live-cell imaging, we successfully observed the temporal dynamics of centromeres and telomeres in plant organs. Fusing TALEs to multimeric FPs enhanced the signal intensity when observing telomeres. We found that the mobility of telomeres was different in sub-nuclear regions. Transgenic plants stably expressing TALE-FPs will provide new insights into chromatin organization and dynamics in multicellular organisms.
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Affiliation(s)
- Satoru Fujimoto
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Noda, Chiba 278-8510, Japan
| | - Shigeo S Sugano
- Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
- PRESTO, JST, Saitama 332-0012, Japan
| | - Keiko Kuwata
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya 464-8601, Japan
| | - Keishi Osakabe
- Faculty of Bioscience and Bioindustry, Tokushima University, Tokushima 770-8513, Japan
| | - Sachihiro Matsunaga
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Noda, Chiba 278-8510, Japan
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18
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Tu Y, Liu F, Guo D, Fan L, Zhu Z, Xue Y, Gao Y, Guo M. Molecular characterization of flavanone 3-hydroxylase gene and flavonoid accumulation in two chemotyped safflower lines in response to methyl jasmonate stimulation. BMC PLANT BIOLOGY 2016; 16:132. [PMID: 27286810 PMCID: PMC4902928 DOI: 10.1186/s12870-016-0813-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 05/18/2016] [Indexed: 05/08/2023]
Abstract
BACKGROUND Among secondary metabolites, flavonoids are particularly crucial for plant growth, development, and reproduction, as well as beneficial for maintenance of human health. As a flowering plant, safflower has synthesized a striking variety of flavonoids with various pharmacologic properties. However, far less research has been carried out on the genes involved in the biosynthetic pathways that generate these amazing flavonoids, especially characterized quinochalcones. In this study, we first cloned and investigated the participation of a presumed flavanone 3-hydroxylase gene (F3H) from safflower (CtF3H) in a flavonoid biosynthetic pathway. RESULTS Bioinformation analysis showed that CtF3H shared high conserved residues and confidence with F3H from other plants. Subcellular localization uncovered the nuclear and cytosol localization of CtF3H in onion epidermal cells. The functional expressions of CtF3H in Escherichia coli BL21(DE3)pLysS cells in the pMAL-C5x vector led to the production of dihydrokaempferol when naringenin was the substrate. Furthermore, the transcriptome expression of CtF3H showed a diametrically opposed expression pattern in a quinochalcone-type safflower line (with orange-yellow flowers) and a flavonol-type safflower line (with white flowers) under external stimulation by methyl jasmonate (MeJA), which has been identified as an elicitor of flavonoid metabolites. Further metabolite analysis showed the increasing tendency of quinochalcones and flavonols, such as hydroxysafflor yellow A, kaempferol-3-O-β-D-glucoside, kaempferol-3-O-β-rutinoside, rutin, carthamin, and luteolin, in the quinochalcone-type safflower line. Also, the accumulation of kaempferol-3-O-β-rutinoside and kaempferol-3-O-β-D-glucoside in flavonols-typed safflower line showed enhanced accumulation pattern after MeJA treatment. However, other flavonols, such as kaempferol, dihydrokaempferol and quercetin-3-O-β-D-glucoside, in flavonols-typed safflower line presented down accumulation respond to MeJA stimulus. CONCLUSIONS Our results showed that the high expression of CtF3H in quinochalcone-type safflower line was associated with the accumulation of both quinochalcones and flavonols, whereas its low expression did not affect the increased accumulation of glycosylated derivatives (kaempferol-3-O-β-rutinoside and rutin) in flavonols-typed safflower line but affect the upstream precursors (D-phenylalanine, dihydrokaempferol, kaempferol), which partly revealed the function of CtF3H in different phenotypes and chemotypes of safflower lines.
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Affiliation(s)
- YanHua Tu
- School of Pharmacy, Second Military Medical University, Shanghai, 200433, People's Republic of China
| | - Fei Liu
- School of Pharmacy, Second Military Medical University, Shanghai, 200433, People's Republic of China
| | - DanDan Guo
- School of Pharmacy, Second Military Medical University, Shanghai, 200433, People's Republic of China
| | - LiJiao Fan
- School of Pharmacy, Second Military Medical University, Shanghai, 200433, People's Republic of China
| | - ZhenXian Zhu
- School of Biological and Environmental Sciences, Nanjing Forestry University, Nanjing, 210095, People's Republic of China
| | - YingRu Xue
- School of Pharmacy, Second Military Medical University, Shanghai, 200433, People's Republic of China
| | - Yue Gao
- School of Pharmacy, Second Military Medical University, Shanghai, 200433, People's Republic of China.
| | - MeiLi Guo
- School of Pharmacy, Second Military Medical University, Shanghai, 200433, People's Republic of China.
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19
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Tamayo-Ordóñez MC, Rodriguez-Zapata LC, Narváez-Zapata JA, Tamayo-Ordóñez YJ, Ayil-Gutiérrez BA, Barredo-Pool F, Sánchez-Teyer LF. Morphological features of different polyploids for adaptation and molecular characterization of CC-NBS-LRR and LEA gene families in Agave L. JOURNAL OF PLANT PHYSIOLOGY 2016; 195:80-94. [PMID: 27016883 DOI: 10.1016/j.jplph.2016.03.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 03/12/2016] [Accepted: 03/18/2016] [Indexed: 05/21/2023]
Abstract
Polyploidy has been widely described in many Agave L. species, but its influence on environmental response to stress is still unknown. With the objective of knowing the morphological adaptations and regulation responses of genes related to biotic (LEA) and abiotic (NBS-LRR) stress in species of Agave with different levels of ploidy, and how these factors contribute to major response of Agave against environmental stresses, we analyzed 16 morphological trials on five accessions of three species (Agave tequilana Weber, Agave angustifolia Haw. and Agave fourcroydes Lem.) with different ploidy levels (2n=2x=60 2n=3x=90, 2n=5x=150, 2n=6x=180) and evaluated the expression of NBS-LRR and LEA genes regulated by biotic and abiotic stress. It was possible to associate some morphological traits (spines, nuclei, and stomata) to ploidy level. The genetic characterization of stress-related genes NBS-LRR induced by pathogenic infection and LEA by heat or saline stresses indicated that amino acid sequence analysis in these genes showed more substitutions in higher ploidy level accessions of A. fourcroydes Lem. 'Sac Ki' (2n=5x=150) and A. angustifolia Haw. 'Chelem Ki' (2n=6x=180), and a higher LEA and NBS-LRR representativeness when compared to their diploid and triploid counterparts. In all studied Agave accessions expression of LEA and NBS-LRR genes was induced by saline or heat stresses or by infection with Erwinia carotovora, respectively. The transcriptional activation was also higher in A. angustifolia Haw. 'Chelem Ki' (2n=6x=180) and A. fourcroydes 'Sac Ki' (2n=5x=150) than in their diploid and triploid counterparts, which suggests higher adaptation to stress. Finally, the diploid accession A. tequilana Weber 'Azul' showed a differentiated genetic profile relative to other Agave accessions. The differences include similar or higher genetic representativeness and transcript accumulation of LEA and NBS-LRR genes than in polyploid (2n=5x=150 and 2n=6x=180) Agave accessions, thus suggesting a differentiated selection pressure for overcoming the lower ploidy level of the diploid A. tequilana Weber 'Azul'.
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Affiliation(s)
- M C Tamayo-Ordóñez
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán. Calle 43 No. 130, Colonia Chuburná de Hidalgo, Mérida, Yucatán, Mexico
| | - L C Rodriguez-Zapata
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán. Calle 43 No. 130, Colonia Chuburná de Hidalgo, Mérida, Yucatán, Mexico
| | - J A Narváez-Zapata
- Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Blvd. del Maestro, s/n, Esq. Elías Piña, Reynosa 88710, Mexico
| | - Y J Tamayo-Ordóñez
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán. Calle 43 No. 130, Colonia Chuburná de Hidalgo, Mérida, Yucatán, Mexico
| | - B A Ayil-Gutiérrez
- Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Blvd. del Maestro, s/n, Esq. Elías Piña, Reynosa 88710, Mexico
| | - F Barredo-Pool
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán. Calle 43 No. 130, Colonia Chuburná de Hidalgo, Mérida, Yucatán, Mexico
| | - L F Sánchez-Teyer
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán. Calle 43 No. 130, Colonia Chuburná de Hidalgo, Mérida, Yucatán, Mexico.
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20
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Dełeńko K, Niedojadło J, Łabędzka A, Wiśniewska E, Bednarska-Kozakiewicz E. Dedifferentiation of Arabidopsis thaliana cells is accompanied by a strong decrease in RNA polymerase II transcription activity and poly(A+) RNA and 25S rRNA eradication from the cytoplasm. PROTOPLASMA 2015; 252:537-46. [PMID: 25248757 PMCID: PMC4335095 DOI: 10.1007/s00709-014-0700-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Accepted: 09/09/2014] [Indexed: 05/09/2023]
Abstract
The mechanisms of plant cell dedifferentiation and the acquisition of totipotency are poorly understood. One of the methods to induce the dedifferentiation process in plant cells is simple and requires the removal of the cell wall. After cell wall removal in protoplasts, large-scale chromatin decondensation is observed (Tessadori et al. in J Cell Sci 120:1200-1208, 2007). Here, we show that in Arabidopsis thaliana protoplasts, despite chromatin decondensation, RNA polymerase II transcriptional activity is reduced. The subsequent investigated stages displayed a clear decrease in the quantity of 25S ribosomal RNA (rRNA) first and then poly(A+) RNA, particularly in the cytoplasm. Therefore, the reduced transcription activity and the removal of these RNA transcripts from the cytoplasm is a crucial process in obtaining totipotency in plant cells. After the cytoplasm cleaning of transcripts derived from mesophyll cells, we observed the resynthesis of these RNAs. An increase in the amount of examined molecules to a level similar to that in differentiated mesophyll cells precedes the divisions of already undifferentiated cells. In this work, we show changes in RNA polymerase II transcription dynamics and the quantity of poly(A+) RNA and 25S rRNA during dedifferentiation and re-entry into the cell cycle.
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Affiliation(s)
- Konrad Dełeńko
- Department of Cell Biology, Faculty of Biology and Environment Protection, Nicolaus Copernicus University, Gagarina 9, 87-100 Toruń, Poland
| | - Janusz Niedojadło
- Department of Cell Biology, Faculty of Biology and Environment Protection, Nicolaus Copernicus University, Gagarina 9, 87-100 Toruń, Poland
| | - Agata Łabędzka
- Department of Cell Biology, Faculty of Biology and Environment Protection, Nicolaus Copernicus University, Gagarina 9, 87-100 Toruń, Poland
| | - Ewa Wiśniewska
- Department of Clinical Pathomorphology, Ludwik Rydygier Collegium Medium Bydgoszcz, Nicolaus Copernicus University in Toruń, Skłodowskiej-Curie 9, 85-094 Bydgoszcz, Poland
| | - Elżbieta Bednarska-Kozakiewicz
- Department of Cell Biology, Faculty of Biology and Environment Protection, Nicolaus Copernicus University, Gagarina 9, 87-100 Toruń, Poland
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21
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Abstract
There are various preparatory techniques for light microscopy permitting access to the inner structure of plant body and its development. Minute objects might be processed as whole-mount preparations, while voluminous ones should be separated into smaller pieces. Hereby we summarize some of the "classical" techniques to cut more voluminous objects into slices and access their inner structure either for simple anatomical analysis or for further processing (e.g., histochemistry, immunohistochemistry, in situ hybridization, enzyme histochemistry).
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Affiliation(s)
- Aleš Soukup
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Prague, Czech Republic
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22
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Wang LC, Wu JR, Chang WL, Yeh CH, Ke YT, Lu CA, Wu SJ. Arabidopsis HIT4 encodes a novel chromocentre-localized protein involved in the heat reactivation of transcriptionally silent loci and is essential for heat tolerance in plants. JOURNAL OF EXPERIMENTAL BOTANY 2013; 64:1689-701. [PMID: 23408827 DOI: 10.1093/jxb/ert030] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The Arabidopsis mutant heat-intolerant 4-1 (hit4-1) was isolated from an ethyl methanesulphonate-mutagenized M2 population on the basis of its inability to withstand prolonged heat stress (4 days at 37°C). Further characterization indicated that hit4-1 was impaired specifically in terms of basal but not acquired thermotolerance. Map-based cloning revealed that the HIT4 gene encoded a plant-specific protein for which the molecular function has yet to be studied. To investigate the cellular role of HIT4 and hence elucidate better its protective function in heat tolerance in plants, a GFP-HIT4 reporter construct was created for a protoplast transient expression assay. Results showed that fluorescently tagged HIT4 was localized to the chromocentre, a condensed heterochromatin domain that harbours repetitive elements for which transcription is normally suppressed by transcriptional gene silencing (TGS). DAPI-staining analysis and FISH with a probe that targeted centromeric repeats showed that heat-induced chromocentre decondensation was inhibited in nuclei of hit4-1 subjected to direct heat treatment, but not in those that were allowed to acquire thermotolerance. Moreover, heat reactivation of various TGS loci, regardless of whether they were endogenous or transgenic, or existed as a single copy or as repeats, was found to be attenuated in hit4-1. Meanwhile, the levels of transcripts of heat shock protein genes in response to heat stress were similar in both hit4-1 and wild-type plants. Collectively, these results demonstrated that HIT4 defines a new TGS regulator that acts at the level of heterochromatin organization and is essential for basal thermotolerance in plants.
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Affiliation(s)
- Lian-Chin Wang
- Department of Life Sciences, National Central University, 300 Jhong-Da Road, Jhong-Li City, Taoyuan County 32001, Taiwan
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23
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Vieira P, Engler G, de Almeida Engler J. Whole-mount confocal imaging of nuclei in giant feeding cells induced by root-knot nematodes in Arabidopsis. THE NEW PHYTOLOGIST 2012; 195:488-496. [PMID: 22616777 DOI: 10.1111/j.1469-8137.2012.04175.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
• Excellent visualization of nuclei was obtained here using a whole-mount procedure adapted to provide high-resolution images of large, irregularly shaped nuclei. The procedure is based on tissue clearing, and fluorescent staining of nuclear DNA with the dye propidium iodide. • The method developed for standard confocal imaging was applied to large multicellular root swellings, named galls, induced in plant hosts by the root-knot nematode Meloidogyne incognita. • Here, we performed a functional analysis, and examined the nuclear structure in giant feeding cells overexpressing the cell cycle inhibitor Kip-related protein 4 (KRP4). Ectopic KRP4 expression in galls led to aberrant nuclear structure, disturbing giant cell expansion and nematode reproduction. In vivo live-cell imaging of GFP-KRP4 demonstrated that this protein co-localizes to chromosomes from prophase to late anaphase during cell cycle progression. • The data presented here suggest the involvement of KRP4 during mitotic progression in plant cells. The detailed results obtained using confocal analysis also demonstrate the potential utility of a rapid, easy-to-use clearing method for the analysis of the nuclei of certain Arabidopsis mutants and other complex plant nuclei.
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Affiliation(s)
- Paulo Vieira
- Institut National de la Recherche Agronomique, UMR 1355 ISA, 400 route des Chappes, Sophia-Antipolis, France
- Centre National de la Recherche Scientifique, UMR 7254 ISA, 400 route des Chappes, Sophia-Antipolis, France
- Université de Nice-Sophia Antipolis, UMR ISA, 400 route des Chappes, Sophia-Antipolis, France
| | - Gilbert Engler
- Institut National de la Recherche Agronomique, UMR 1355 ISA, 400 route des Chappes, Sophia-Antipolis, France
- Centre National de la Recherche Scientifique, UMR 7254 ISA, 400 route des Chappes, Sophia-Antipolis, France
- Université de Nice-Sophia Antipolis, UMR ISA, 400 route des Chappes, Sophia-Antipolis, France
| | - Janice de Almeida Engler
- Institut National de la Recherche Agronomique, UMR 1355 ISA, 400 route des Chappes, Sophia-Antipolis, France
- Centre National de la Recherche Scientifique, UMR 7254 ISA, 400 route des Chappes, Sophia-Antipolis, France
- Université de Nice-Sophia Antipolis, UMR ISA, 400 route des Chappes, Sophia-Antipolis, France
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24
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Grassl J, Taylor NL, Millar AH. Matrix-assisted laser desorption/ionisation mass spectrometry imaging and its development for plant protein imaging. PLANT METHODS 2011; 7:21. [PMID: 21726462 PMCID: PMC3141805 DOI: 10.1186/1746-4811-7-21] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2011] [Accepted: 07/05/2011] [Indexed: 05/17/2023]
Abstract
Matrix-Assisted Laser Desorption/Ionisation (MALDI) mass spectrometry imaging (MSI) uses the power of high mass resolution time of flight (ToF) mass spectrometry coupled to the raster of lasers shots across the cut surface of tissues to provide new insights into the spatial distribution of biomolecules within biological tissues. The history of this technique in animals and plants is considered and the potential for analysis of proteins by this technique in plants is discussed. Protein biomarker identification from MALDI-MSI is a challenge and a number of different approaches to address this bottleneck are discussed. The technical considerations needed for MALDI-MSI are reviewed and these are presented alongside examples from our own work and a protocol for MALDI-MSI of proteins in plant samples.
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Affiliation(s)
- Julia Grassl
- ARC Centre of Excellence in Plant Energy Biology and Centre for Comparative Analysis of Biomolecular Networks, M316, The University of Western Australia, Crawley, WA 6009, Australia
| | - Nicolas L Taylor
- ARC Centre of Excellence in Plant Energy Biology and Centre for Comparative Analysis of Biomolecular Networks, M316, The University of Western Australia, Crawley, WA 6009, Australia
| | - A Harvey Millar
- ARC Centre of Excellence in Plant Energy Biology and Centre for Comparative Analysis of Biomolecular Networks, M316, The University of Western Australia, Crawley, WA 6009, Australia
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25
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Immunofluorescence microscopy for localization of Arabidopsis chloroplast proteins. Methods Mol Biol 2011; 774:33-58. [PMID: 21822831 DOI: 10.1007/978-1-61779-234-2_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Immunofluorescence microscopy reveals localization of proteins in cells and tissues by means of highly specific, fluorescently labeled antibodies. This technique is an important complement to localization methods that use genetically encoded fluorescent tags. This chapter describes the five stages of immunofluorescence localization of proteins in plant chloroplasts in sectioned leaf tissue: (1) fixation, (2) tissue embedding and sectioning, (3) treatment of sections prior to immunolabeling, (4) immunostaining, and (5) fluorescence microscopy and image capture. Protocols for both cryosectioning and sectioning of low-melting-point wax-embedded samples are described. Immunofluorescence localization in chloroplasts is complicated by their intense autofluorescence background. Measures to suppress nonspecific background staining, confirm specificity of the fluorescence signal, and optimize imaging conditions are described.
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26
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Stitt M, Sulpice R, Keurentjes J. Metabolic networks: how to identify key components in the regulation of metabolism and growth. PLANT PHYSIOLOGY 2010; 152:428-44. [PMID: 20018593 PMCID: PMC2815907 DOI: 10.1104/pp.109.150821] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2009] [Accepted: 12/08/2009] [Indexed: 05/18/2023]
Affiliation(s)
- Mark Stitt
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany.
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