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Iyer RR, Žurauskas M, Rao Y, Chaney EJ, Boppart SA. Bichromatic tetraphasic full-field optical coherence microscopy. JOURNAL OF BIOMEDICAL OPTICS 2024; 29:S22704. [PMID: 38584966 PMCID: PMC10996847 DOI: 10.1117/1.jbo.29.s2.s22704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 02/29/2024] [Accepted: 03/05/2024] [Indexed: 04/09/2024]
Abstract
Significance Full-field optical coherence microscopy (FF-OCM) is a prevalent technique for backscattering and phase imaging with epi-detection. Traditional methods have two limitations: suboptimal utilization of functional information about the sample and complicated optical design with several moving parts for phase contrast. Aim We report an OCM setup capable of generating dynamic intensity, phase, and pseudo-spectroscopic contrast with single-shot full-field video-rate imaging called bichromatic tetraphasic (BiTe) full-field OCM with no moving parts. Approach BiTe OCM resourcefully uses the phase-shifting properties of anti-reflection (AR) coatings outside the rated bandwidths to create four unique phase shifts, which are detected with two emission filters for spectroscopic contrast. Results BiTe OCM overcomes the disadvantages of previous FF-OCM setup techniques by capturing both the intensity and phase profiles without any artifacts or speckle noise for imaging scattering samples in three-dimensional (3D). BiTe OCM also utilizes the raw data effectively to generate three complementary contrasts: intensity, phase, and color. We demonstrate BiTe OCM to observe cellular dynamics, image live, and moving micro-animals in 3D, capture the spectroscopic hemodynamics of scattering tissues along with dynamic intensity and phase profiles, and image the microstructure of fall foliage with two different colors. Conclusions BiTe OCM can maximize the information efficiency of FF-OCM while maintaining overall simplicity in design for quantitative, dynamic, and spectroscopic characterization of biological samples.
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Affiliation(s)
- Rishyashring R. Iyer
- University of Illinois Urbana-Champaign, Beckman Institute for Advanced Science and Technology, Urbana, Illinois, United States
- University of Illinois Urbana-Champaign, Department of Electrical and Computer Engineering, Urbana, Illinois, United States
| | - Mantas Žurauskas
- University of Illinois Urbana-Champaign, Beckman Institute for Advanced Science and Technology, Urbana, Illinois, United States
| | - Yug Rao
- University of Illinois Urbana-Champaign, Beckman Institute for Advanced Science and Technology, Urbana, Illinois, United States
- University of Illinois Urbana-Champaign, Department of Electrical and Computer Engineering, Urbana, Illinois, United States
| | - Eric J. Chaney
- University of Illinois Urbana-Champaign, Beckman Institute for Advanced Science and Technology, Urbana, Illinois, United States
| | - Stephen A. Boppart
- University of Illinois Urbana-Champaign, Beckman Institute for Advanced Science and Technology, Urbana, Illinois, United States
- University of Illinois Urbana-Champaign, Department of Electrical and Computer Engineering, Urbana, Illinois, United States
- University of Illinois Urbana-Champaign, Department of Bioengineering, Urbana, Illinois, United States
- University of Illinois Urbana Champaign, NIH/NIBIB P41 Center for Label-free Imaging and Multiscale Biophotonics (CLIMB), Urbana, Illinois, United States
- University of Illinois Urbana-Champaign, Cancer Center at Illinois, Urbana, Illinois, United States
- University of Illinois Urbana-Champaign, Carle Illinois College of Medicine, Urbana, Illinois, United States
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2
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Koenig AM, Liu B, Hu J. Visualizing the dynamics of plant energy organelles. Biochem Soc Trans 2023; 51:2029-2040. [PMID: 37975429 PMCID: PMC10754284 DOI: 10.1042/bst20221093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 11/06/2023] [Accepted: 11/08/2023] [Indexed: 11/19/2023]
Abstract
Plant organelles predominantly rely on the actin cytoskeleton and the myosin motors for long-distance trafficking, while using microtubules and the kinesin motors mostly for short-range movement. The distribution and motility of organelles in the plant cell are fundamentally important to robust plant growth and defense. Chloroplasts, mitochondria, and peroxisomes are essential organelles in plants that function independently and coordinately during energy metabolism and other key metabolic processes. In response to developmental and environmental stimuli, these energy organelles modulate their metabolism, morphology, abundance, distribution and motility in the cell to meet the need of the plant. Consistent with their metabolic links in processes like photorespiration and fatty acid mobilization is the frequently observed inter-organellar physical interaction, sometimes through organelle membranous protrusions. The development of various organelle-specific fluorescent protein tags has allowed the simultaneous visualization of organelle movement in living plant cells by confocal microscopy. These energy organelles display an array of morphology and movement patterns and redistribute within the cell in response to changes such as varying light conditions, temperature fluctuations, ROS-inducible treatments, and during pollen tube development and immune response, independently or in association with one another. Although there are more reports on the mechanism of chloroplast movement than that of peroxisomes and mitochondria, our knowledge of how and why these three energy organelles move and distribute in the plant cell is still scarce at the functional and mechanistic level. It is critical to identify factors that control organelle motility coupled with plant growth, development, and stress response.
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Affiliation(s)
- Amanda M. Koenig
- Michigan State University-Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, MI, U.S.A
| | - Bo Liu
- Department of Plant Biology, University of California, Davis, CA, U.S.A
| | - Jianping Hu
- Michigan State University-Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, MI, U.S.A
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3
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Hlaváčková K, Šamaj J, Ovečka M. Cytoskeleton as a roadmap navigating rhizobia to establish symbiotic root nodulation in legumes. Biotechnol Adv 2023; 69:108263. [PMID: 37775072 DOI: 10.1016/j.biotechadv.2023.108263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 08/28/2023] [Accepted: 09/24/2023] [Indexed: 10/01/2023]
Abstract
Legumes enter into symbiotic associations with soil nitrogen-fixing rhizobia, culminating in the creation of new organs, root nodules. This complex process relies on chemical and physical interaction between legumes and rhizobia, including early signalling events informing the host legume plant of a potentially beneficial microbe and triggering the nodulation program. The great significance of this plant-microbe interaction rests upon conversion of atmospheric dinitrogen not accessible to plants into a biologically active form of ammonia available to plants. The plant cytoskeleton consists in a highly dynamic network and undergoes rapid remodelling upon sensing various developmental and environmental cues, including response to attachment, internalization, and accommodation of rhizobia in plant root and nodule cells. This dynamic nature is governed by cytoskeleton-associated proteins that modulate cytoskeletal behaviour depending on signal perception and transduction. Precisely localized cytoskeletal rearrangements are therefore essential for the uptake of rhizobia, their targeted delivery, and establishing beneficial root nodule symbiosis. This review summarizes current knowledge about rhizobia-dependent rearrangements and functions of the cytoskeleton in legume roots and nodules. General patterns and nodule type-, nodule stage-, and species-specific aspects of actin filaments and microtubules remodelling are discussed. Moreover, emerging evidence is provided about fine-tuning the root nodulation process through cytoskeleton-associated proteins. We also consider future perspectives on dynamic localization studies of the cytoskeleton during early symbiosis utilizing state of the art molecular and advanced microscopy approaches. Based on acquired detailed knowledge of the mutualistic interactions with microbes, these approaches could contribute to broader biotechnological crop improvement.
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Affiliation(s)
- Kateřina Hlaváčková
- Department of Biotechnology, Faculty of Science, Palacký University Olomouc, Olomouc, Czech Republic.
| | - Jozef Šamaj
- Department of Biotechnology, Faculty of Science, Palacký University Olomouc, Olomouc, Czech Republic.
| | - Miroslav Ovečka
- Department of Biotechnology, Faculty of Science, Palacký University Olomouc, Olomouc, Czech Republic.
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4
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Yuan G, Gao H, Yang T. Exploring the Role of the Plant Actin Cytoskeleton: From Signaling to Cellular Functions. Int J Mol Sci 2023; 24:15480. [PMID: 37895158 PMCID: PMC10607326 DOI: 10.3390/ijms242015480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 10/06/2023] [Accepted: 10/21/2023] [Indexed: 10/29/2023] Open
Abstract
The plant actin cytoskeleton is characterized by the basic properties of dynamic array, which plays a central role in numerous conserved processes that are required for diverse cellular functions. Here, we focus on how actins and actin-related proteins (ARPs), which represent two classical branches of a greatly diverse superfamily of ATPases, are involved in fundamental functions underlying signal regulation of plant growth and development. Moreover, we review the structure, assembly dynamics, and biological functions of filamentous actin (F-actin) from a molecular perspective. The various accessory proteins known as actin-binding proteins (ABPs) partner with F-actin to finely tune actin dynamics, often in response to various cell signaling pathways. Our understanding of the significance of the actin cytoskeleton in vital cellular activities has been furthered by comparison of conserved functions of actin filaments across different species combined with advanced microscopic techniques and experimental methods. We discuss the current model of the plant actin cytoskeleton, followed by examples of the signaling mechanisms under the supervision of F-actin related to cell morphogenesis, polar growth, and cytoplasmic streaming. Determination of the theoretical basis of how the cytoskeleton works is important in itself and is beneficial to future applications aimed at improving crop biomass and production efficiency.
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Affiliation(s)
| | | | - Tao Yang
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China; (G.Y.); (H.G.)
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5
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Light Microscopy Technologies and the Plant Cytoskeleton. Methods Mol Biol 2023; 2604:337-352. [PMID: 36773248 DOI: 10.1007/978-1-0716-2867-6_28] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
The cytoskeleton is a dynamic and diverse subcellular filament network, and as such microscopy is an essential technology to enable researchers to study and characterize these systems. Microscopy has a long history of observing the plant world not least as the subject where Robert Hooke coined the term "cell" in his publication Micrographia. From early observations of plant morphology to today's advanced super-resolution technologies, light microscopy is the indispensable tool for the plant cell biologist. In this mini review, we will discuss some of the major modalities used to examine the plant cytoskeleton and the theory behind them.
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6
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Zhang L, Liang X, Takáč T, Komis G, Li X, Zhang Y, Ovečka M, Chen Y, Šamaj J. Spatial proteomics of vesicular trafficking: coupling mass spectrometry and imaging approaches in membrane biology. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:250-269. [PMID: 36204821 PMCID: PMC9884029 DOI: 10.1111/pbi.13929] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 08/14/2022] [Accepted: 09/08/2022] [Indexed: 06/16/2023]
Abstract
In plants, membrane compartmentalization requires vesicle trafficking for communication among distinct organelles. Membrane proteins involved in vesicle trafficking are highly dynamic and can respond rapidly to changes in the environment and to cellular signals. Capturing their localization and dynamics is thus essential for understanding the mechanisms underlying vesicular trafficking pathways. Quantitative mass spectrometry and imaging approaches allow a system-wide dissection of the vesicular proteome, the characterization of ligand-receptor pairs and the determination of secretory, endocytic, recycling and vacuolar trafficking pathways. In this review, we highlight major proteomics and imaging methods employed to determine the location, distribution and abundance of proteins within given trafficking routes. We focus in particular on methodologies for the elucidation of vesicle protein dynamics and interactions and their connections to downstream signalling outputs. Finally, we assess their biological applications in exploring different cellular and subcellular processes.
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Affiliation(s)
- Liang Zhang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological SciencesChina Agricultural UniversityBeijingChina
- College of Life ScienceHenan Normal UniversityXinxiangChina
| | - Xinlin Liang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Tomáš Takáč
- Department of Biotechnology, Faculty of SciencePalacky University OlomoucOlomoucCzech Republic
| | - George Komis
- Department of Cell Biology, Centre of the Region Hana for Biotechnological and Agricultural Research, Faculty of SciencePalacky University OlomoucOlomoucCzech Republic
| | - Xiaojuan Li
- College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Yuan Zhang
- College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Miroslav Ovečka
- Department of Biotechnology, Faculty of SciencePalacky University OlomoucOlomoucCzech Republic
| | - Yanmei Chen
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Jozef Šamaj
- Department of Biotechnology, Faculty of SciencePalacky University OlomoucOlomoucCzech Republic
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7
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Super-resolution microscopy reveals the number and distribution of topoisomerase IIα and CENH3 molecules within barley metaphase chromosomes. Chromosoma 2023; 132:19-29. [PMID: 36719450 PMCID: PMC9981516 DOI: 10.1007/s00412-023-00785-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 10/25/2022] [Accepted: 12/13/2022] [Indexed: 02/01/2023]
Abstract
Topoisomerase IIα (Topo IIα) and the centromere-specific histone H3 variant CENH3 are key proteins involved in chromatin condensation and centromere determination, respectively. Consequently, they are required for proper chromosome segregation during cell divisions. We combined two super-resolution techniques, structured illumination microscopy (SIM) to co-localize Topo IIα and CENH3, and photoactivated localization microscopy (PALM) to determine their molecule numbers in barley metaphase chromosomes. We detected a dispersed Topo IIα distribution along chromosome arms but an accumulation at centromeres, telomeres, and nucleolus-organizing regions. With a precision of 10-50 nm, we counted ~ 20,000-40,000 Topo IIα molecules per chromosome, 28% of them within the (peri)centromere. With similar precision, we identified ~13,500 CENH3 molecules per centromere where Topo IIα proteins and CENH3-containing chromatin intermingle. In short, we demonstrate PALM as a useful method to count and localize single molecules with high precision within chromosomes. The ultrastructural distribution and the detected amount of Topo IIα and CENH3 are instrumental for a better understanding of their functions during chromatin condensation and centromere determination.
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8
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Davis W, Endo M, Locke JCW. Spatially specific mechanisms and functions of the plant circadian clock. PLANT PHYSIOLOGY 2022; 190:938-951. [PMID: 35640123 PMCID: PMC9516738 DOI: 10.1093/plphys/kiac236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 04/22/2022] [Indexed: 06/15/2023]
Abstract
Like many organisms, plants have evolved a genetic network, the circadian clock, to coordinate processes with day/night cycles. In plants, the clock is a pervasive regulator of development and modulates many aspects of physiology. Clock-regulated processes range from the correct timing of growth and cell division to interactions with the root microbiome. Recently developed techniques, such as single-cell time-lapse microscopy and single-cell RNA-seq, are beginning to revolutionize our understanding of this clock regulation, revealing a surprising degree of organ, tissue, and cell-type specificity. In this review, we highlight recent advances in our spatial view of the clock across the plant, both in terms of how it is regulated and how it regulates a diversity of output processes. We outline how understanding these spatially specific functions will help reveal the range of ways that the clock provides a fitness benefit for the plant.
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Affiliation(s)
- William Davis
- Sainsbury Laboratory, University of Cambridge, Cambridge, UK
| | - Motomu Endo
- Authors for correspondence: (M.E.); (J.C.W.L.)
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9
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Donaldson LA. Super-resolution imaging of Douglas fir xylem cell wall nanostructure using SRRF microscopy. PLANT METHODS 2022; 18:27. [PMID: 35246172 PMCID: PMC8897896 DOI: 10.1186/s13007-022-00865-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 02/26/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND The nanostructure of plant cell walls is of significant biological and technological interest, but methods suited to imaging cell walls at the nanoscale while maintaining the natural water-saturated state are limited. Light microscopy allows imaging of wet cell walls but with spatial resolution limited to the micro-scale. Most super-resolution techniques require expensive hardware and/or special stains so are less applicable to some applications such as autofluorescence imaging of plant tissues. RESULTS A protocol was developed for super-resolution imaging of xylem cell walls using super-resolution radial fluctuations (SRRF) microscopy combined with confocal fluorescence imaging (CLSM). We compared lignin autofluorescence imaging with acriflavin or rhodamine B staining. The SRRF technique allows imaging of wet or dry tissue with moderate improvement in resolution for autofluorescence and acriflavin staining, and a large improvement for rhodamine B staining, achieving sub 100 nm resolution based on comparison with measurements from electron microscopy. Rhodamine B staining, which represents a convolution of lignin staining and cell wall accessibility, provided remarkable new details of cell wall structural features including both circumferential and radial lamellae demonstrating nanoscale variations in lignification and cell wall porosity within secondary cell walls. CONCLUSIONS SRRF microscopy can be combined with confocal fluorescence microscopy to provide nanoscale imaging of plant cell walls using conventional stains or autofluorescence in either the wet or dry state.
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10
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Cox Jr KL, Gurazada SGR, Duncan KE, Czymmek KJ, Topp CN, Meyers BC. Organizing your space: The potential for integrating spatial transcriptomics and 3D imaging data in plants. PLANT PHYSIOLOGY 2022; 188:703-712. [PMID: 34726737 PMCID: PMC8825300 DOI: 10.1093/plphys/kiab508] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 10/04/2021] [Indexed: 05/31/2023]
Abstract
Plant cells communicate information for the regulation of development and responses to external stresses. A key form of this communication is transcriptional regulation, accomplished via complex gene networks operating both locally and systemically. To fully understand how genes are regulated across plant tissues and organs, high resolution, multi-dimensional spatial transcriptional data must be acquired and placed within a cellular and organismal context. Spatial transcriptomics (ST) typically provides a two-dimensional spatial analysis of gene expression of tissue sections that can be stacked to render three-dimensional data. For example, X-ray and light-sheet microscopy provide sub-micron scale volumetric imaging of cellular morphology of tissues, organs, or potentially entire organisms. Linking these technologies could substantially advance transcriptomics in plant biology and other fields. Here, we review advances in ST and 3D microscopy approaches and describe how these technologies could be combined to provide high resolution, spatially organized plant tissue transcript mapping.
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Affiliation(s)
- Kevin L Cox Jr
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
| | - Sai Guna Ranjan Gurazada
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA
- Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19711, USA
| | - Keith E Duncan
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA
| | - Kirk J Czymmek
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA
- Advanced Bioimaging Laboratory, Donald Danforth Plant Science Center, St Louis, Missouri 63132, USA
| | | | - Blake C Meyers
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA
- Division of Plant Sciences and Technology, University of Missouri–Columbia, Columbia, MO 65211, USA
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11
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Ovečka M, Sojka J, Tichá M, Komis G, Basheer J, Marchetti C, Šamajová O, Kuběnová L, Šamaj J. Imaging plant cells and organs with light-sheet and super-resolution microscopy. PLANT PHYSIOLOGY 2022; 188:683-702. [PMID: 35235660 PMCID: PMC8825356 DOI: 10.1093/plphys/kiab349] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Accepted: 07/12/2021] [Indexed: 05/05/2023]
Abstract
The documentation of plant growth and development requires integrative and scalable approaches to investigate and spatiotemporally resolve various dynamic processes at different levels of plant body organization. The present update deals with vigorous developments in mesoscopy, microscopy and nanoscopy methods that have been translated to imaging of plant subcellular compartments, cells, tissues and organs over the past 3 years with the aim to report recent applications and reasonable expectations from current light-sheet fluorescence microscopy (LSFM) and super-resolution microscopy (SRM) modalities. Moreover, the shortcomings and limitations of existing LSFM and SRM are discussed, particularly for their ability to accommodate plant samples and regarding their documentation potential considering spherical aberrations or temporal restrictions prohibiting the dynamic recording of fast cellular processes at the three dimensions. For a more comprehensive description, advances in living or fixed sample preparation methods are also included, supported by an overview of developments in labeling strategies successfully applied in plants. These strategies are practically documented by current applications employing model plant Arabidopsis thaliana (L.) Heynh., but also robust crop species such as Medicago sativa L. and Hordeum vulgare L. Over the past few years, the trend towards designing of integrative microscopic modalities has become apparent and it is expected that in the near future LSFM and SRM will be bridged to achieve broader multiscale plant imaging with a single platform.
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Affiliation(s)
- Miroslav Ovečka
- Department of Cell Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University Olomouc, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
| | - Jiří Sojka
- Department of Cell Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University Olomouc, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
| | - Michaela Tichá
- Department of Cell Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University Olomouc, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
| | - George Komis
- Department of Cell Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University Olomouc, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
| | - Jasim Basheer
- Department of Cell Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University Olomouc, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
| | - Cintia Marchetti
- Centre of the Region Haná for Biotechnological and Agricultural Research, Czech Advanced Technology and Research Institute, Palacký University Olomouc, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
| | - Olga Šamajová
- Department of Cell Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University Olomouc, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
| | - Lenka Kuběnová
- Department of Cell Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University Olomouc, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
| | - Jozef Šamaj
- Department of Cell Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University Olomouc, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
- Author for communication:
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12
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Kümpers BMC, Han J, Vaughan-Hirsch J, Redman N, Ware A, Atkinson JA, Leftley N, Janes G, Castiglione G, Tarr PT, Pyke K, Voß U, Wells DM, Bishopp A. Dual expression and anatomy lines allow simultaneous visualization of gene expression and anatomy. PLANT PHYSIOLOGY 2022; 188:56-69. [PMID: 34718789 PMCID: PMC8774739 DOI: 10.1093/plphys/kiab503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 10/04/2021] [Indexed: 06/13/2023]
Abstract
Studying the developmental genetics of plant organs requires following gene expression in specific tissues. To facilitate this, we have developed dual expression anatomy lines, which incorporate a red plasma membrane marker alongside a fluorescent reporter for a gene of interest in the same vector. Here, we adapted the GreenGate cloning vectors to create two destination vectors showing strong marking of cell membranes in either the whole root or specifically in the lateral roots. This system can also be used in both embryos and whole seedlings. As proof of concept, we follow both gene expression and anatomy in Arabidopsis (Arabidopsis thaliana) during lateral root organogenesis for a period of over 24 h. Coupled with the development of a flow cell and perfusion system, we follow changes in activity of the DII auxin sensor following application of auxin.
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Affiliation(s)
- Britta M C Kümpers
- School of Biosciences, University of Nottingham, Loughborough, LE12 5RD, UK
| | - Jingyi Han
- School of Biosciences, University of Nottingham, Loughborough, LE12 5RD, UK
| | | | - Nicholas Redman
- School of Biosciences, University of Nottingham, Loughborough, LE12 5RD, UK
| | - Alexander Ware
- School of Biosciences, University of Nottingham, Loughborough, LE12 5RD, UK
| | | | - Nicola Leftley
- School of Biosciences, University of Nottingham, Loughborough, LE12 5RD, UK
| | - George Janes
- School of Biosciences, University of Nottingham, Loughborough, LE12 5RD, UK
| | | | - Paul T Tarr
- Howard Hughes Medical Institute, California Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, USA
- Division of Biology and Biological Engineering 156-29, California Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, USA
| | - Kevin Pyke
- School of Biosciences, University of Nottingham, Loughborough, LE12 5RD, UK
| | - Ute Voß
- School of Biosciences, University of Nottingham, Loughborough, LE12 5RD, UK
| | - Darren M Wells
- School of Biosciences, University of Nottingham, Loughborough, LE12 5RD, UK
| | - Anthony Bishopp
- School of Biosciences, University of Nottingham, Loughborough, LE12 5RD, UK
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13
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Colin L, Martin-Arevalillo R, Bovio S, Bauer A, Vernoux T, Caillaud MC, Landrein B, Jaillais Y. Imaging the living plant cell: From probes to quantification. THE PLANT CELL 2022; 34:247-272. [PMID: 34586412 PMCID: PMC8774089 DOI: 10.1093/plcell/koab237] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 09/20/2021] [Indexed: 05/20/2023]
Abstract
At the center of cell biology is our ability to image the cell and its various components, either in isolation or within an organism. Given its importance, biological imaging has emerged as a field of its own, which is inherently highly interdisciplinary. Indeed, biologists rely on physicists and engineers to build new microscopes and imaging techniques, chemists to develop better imaging probes, and mathematicians and computer scientists for image analysis and quantification. Live imaging collectively involves all the techniques aimed at imaging live samples. It is a rapidly evolving field, with countless new techniques, probes, and dyes being continuously developed. Some of these new methods or reagents are readily amenable to image plant samples, while others are not and require specific modifications for the plant field. Here, we review some recent advances in live imaging of plant cells. In particular, we discuss the solutions that plant biologists use to live image membrane-bound organelles, cytoskeleton components, hormones, and the mechanical properties of cells or tissues. We not only consider the imaging techniques per se, but also how the construction of new fluorescent probes and analysis pipelines are driving the field of plant cell biology.
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Affiliation(s)
- Leia Colin
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, CNRS, INRAE, 69342 Lyon, France
| | - Raquel Martin-Arevalillo
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, CNRS, INRAE, 69342 Lyon, France
| | - Simone Bovio
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, CNRS, INRAE, 69342 Lyon, France
- LYMIC-PLATIM imaging and microscopy core facility, Univ Lyon, SFR Biosciences, ENS de Lyon, Inserm US8, CNRS UMS3444, UCBL-50 Avenue Tony Garnier, 69007 Lyon, France
| | - Amélie Bauer
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, CNRS, INRAE, 69342 Lyon, France
| | - Teva Vernoux
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, CNRS, INRAE, 69342 Lyon, France
| | - Marie-Cecile Caillaud
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, CNRS, INRAE, 69342 Lyon, France
| | - Benoit Landrein
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, CNRS, INRAE, 69342 Lyon, France
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14
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Kumar S, Kaur S, Seem K, Kumar S, Mohapatra T. Understanding 3D Genome Organization and Its Effect on Transcriptional Gene Regulation Under Environmental Stress in Plant: A Chromatin Perspective. Front Cell Dev Biol 2021; 9:774719. [PMID: 34957106 PMCID: PMC8692796 DOI: 10.3389/fcell.2021.774719] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 11/23/2021] [Indexed: 01/17/2023] Open
Abstract
The genome of a eukaryotic organism is comprised of a supra-molecular complex of chromatin fibers and intricately folded three-dimensional (3D) structures. Chromosomal interactions and topological changes in response to the developmental and/or environmental stimuli affect gene expression. Chromatin architecture plays important roles in DNA replication, gene expression, and genome integrity. Higher-order chromatin organizations like chromosome territories (CTs), A/B compartments, topologically associating domains (TADs), and chromatin loops vary among cells, tissues, and species depending on the developmental stage and/or environmental conditions (4D genomics). Every chromosome occupies a separate territory in the interphase nucleus and forms the top layer of hierarchical structure (CTs) in most of the eukaryotes. While the A and B compartments are associated with active (euchromatic) and inactive (heterochromatic) chromatin, respectively, having well-defined genomic/epigenomic features, TADs are the structural units of chromatin. Chromatin architecture like TADs as well as the local interactions between promoter and regulatory elements correlates with the chromatin activity, which alters during environmental stresses due to relocalization of the architectural proteins. Moreover, chromatin looping brings the gene and regulatory elements in close proximity for interactions. The intricate relationship between nucleotide sequence and chromatin architecture requires a more comprehensive understanding to unravel the genome organization and genetic plasticity. During the last decade, advances in chromatin conformation capture techniques for unravelling 3D genome organizations have improved our understanding of genome biology. However, the recent advances, such as Hi-C and ChIA-PET, have substantially increased the resolution, throughput as well our interest in analysing genome organizations. The present review provides an overview of the historical and contemporary perspectives of chromosome conformation capture technologies, their applications in functional genomics, and the constraints in predicting 3D genome organization. We also discuss the future perspectives of understanding high-order chromatin organizations in deciphering transcriptional regulation of gene expression under environmental stress (4D genomics). These might help design the climate-smart crop to meet the ever-growing demands of food, feed, and fodder.
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Affiliation(s)
- Suresh Kumar
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Simardeep Kaur
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Karishma Seem
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, India
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15
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Higashiyama T, Maizel A, Simon R. Seeing is Believing: Advances in Plant Imaging Technologies. PLANT & CELL PHYSIOLOGY 2021; 62:1217-1220. [PMID: 34510209 DOI: 10.1093/pcp/pcab133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 08/28/2021] [Accepted: 09/11/2021] [Indexed: 06/13/2023]
Affiliation(s)
- Tetsuya Higashiyama
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Alexis Maizel
- Center for Organismal Studies (COS), University of Heidelberg, Im Neuenheimer Feld 230, Heidelberg 69120, Germany
| | - Rüdiger Simon
- Cluster of Excellence on Plant Sciences, Heinrich Heine University, Universitätsstraße 1, Düsseldorf 40225, Germany
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16
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Dhungana SR, Braun DM. Sugar transporters in grasses: Function and modulation in source and storage tissues. JOURNAL OF PLANT PHYSIOLOGY 2021; 266:153541. [PMID: 34634553 DOI: 10.1016/j.jplph.2021.153541] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 09/11/2021] [Accepted: 09/29/2021] [Indexed: 06/13/2023]
Abstract
Carbohydrate partitioning, the process of transporting carbohydrates from photosynthetic (source) tissues, such as leaves, to non-photosynthetic (sink) tissues, such as stems, roots, and reproductive structures, is vital not only for the growth and development of plants but also for withstanding biotic and abiotic stress. In many plants, sucrose is the primary form of carbohydrate loaded into the phloem for long-distance transport and unloaded into the sink tissues for utilization or storage. We highlight recent findings about 1) phloem loading in grasses, 2) the principal families of sugar transporters involved in sucrose transport, and 3) novel mechanisms by which the activities of sugar transporters are modulated. We discuss exciting discoveries from eudicot species that provide valuable insights regarding the regulation of these sugar transporters, which may be translatable to monocot species. As we better understand the intricate pathways that control the activities of various sugar transporters, we can utilize this knowledge for developing improved crop varieties.
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Affiliation(s)
- Singha R Dhungana
- Divisions of Biological Sciences, Interdisciplinary Plant Group, and Missouri Maize Center, University of Missouri-Columbia, USA
| | - David M Braun
- Divisions of Biological Sciences, Interdisciplinary Plant Group, and Missouri Maize Center, University of Missouri-Columbia, USA; Plant Science and Technology, Interdisciplinary Plant Group, and Missouri Maize Center, University of Missouri-Columbia, USA.
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17
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Stelate A, Tihlaříková E, Schwarzerová K, Neděla V, Petrášek J. Correlative Light-Environmental Scanning Electron Microscopy of Plasma Membrane Efflux Carriers of Plant Hormone Auxin. Biomolecules 2021; 11:1407. [PMID: 34680040 PMCID: PMC8533460 DOI: 10.3390/biom11101407] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 09/21/2021] [Accepted: 09/22/2021] [Indexed: 12/17/2022] Open
Abstract
Fluorescence light microscopy provided convincing evidence for the domain organization of plant plasma membrane (PM) proteins. Both peripheral and integral PM proteins show an inhomogeneous distribution within the PM. However, the size of PM nanodomains and protein clusters is too small to accurately determine their dimensions and nano-organization using routine confocal fluorescence microscopy and super-resolution methods. To overcome this limitation, we have developed a novel correlative light electron microscopy method (CLEM) using total internal reflection fluorescence microscopy (TIRFM) and advanced environmental scanning electron microscopy (A-ESEM). Using this technique, we determined the number of auxin efflux carriers from the PINFORMED (PIN) family (NtPIN3b-GFP) within PM nanodomains of tobacco cell PM ghosts. Protoplasts were attached to coverslips and immunostained with anti-GFP primary antibody and secondary antibody conjugated to fluorochrome and gold nanoparticles. After imaging the nanodomains within the PM with TIRFM, the samples were imaged with A-ESEM without further processing, and quantification of the average number of molecules within the nanodomain was performed. Without requiring any post-fixation and coating procedures, this method allows to study details of the organization of auxin carriers and other plant PM proteins.
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Affiliation(s)
- Ayoub Stelate
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Viničná 5, 128 44 Prague 2, Czech Republic; (A.S.); (K.S.)
| | - Eva Tihlaříková
- Institute of Scientific Instruments, Academy of Sciences of the Czech Republic, Královopolská 147, 612 64 Brno, Czech Republic; (E.T.); (V.N.)
| | - Kateřina Schwarzerová
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Viničná 5, 128 44 Prague 2, Czech Republic; (A.S.); (K.S.)
| | - Vilém Neděla
- Institute of Scientific Instruments, Academy of Sciences of the Czech Republic, Královopolská 147, 612 64 Brno, Czech Republic; (E.T.); (V.N.)
| | - Jan Petrášek
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Viničná 5, 128 44 Prague 2, Czech Republic; (A.S.); (K.S.)
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18
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Imaging the Cytoskeleton in Living Plant Roots. Methods Mol Biol 2021; 2364:139-148. [PMID: 34542851 DOI: 10.1007/978-1-0716-1661-1_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Abstract
For the past two decades, genetically encoded fluorescent proteins have emerged as the most popular method to image the plant cytoskeleton. Because fluorescent protein technology involves handling living plant cells, it is important to implement protocols that enable these delicate plant specimens to maintain optimal growth for the entire duration of the imaging experiment. To this end, we rely on a system that consists of a large coverslip coated with nutrient-supplemented agar. This agar-coverslip system is planted with surface-sterilized Arabidopsis thaliana seeds expressing cytoskeletal fluorescent protein reporters. The agar-coverslip system with planted seeds is then maintained in an environmentally controlled growth chamber. The entire setup is transferred onto the stage of a confocal microscope for imaging when roots of germinated seedlings reach a desired length. For plants with larger roots such as Medicago truncatula, the polymerized nutrient-supplemented agar is gently lifted or cut and used to secure pre-germinated seeds on the coverslip prior to root imaging. The agar-coverslip system we use for imaging the cytoskeleton in living roots along with general methods for expressing green fluorescent protein (GFP)-based cytoskeletal reporters in hairy roots of Medicago truncatula is described here.
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19
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McGaley J, Paszkowski U. Visualising an invisible symbiosis. PLANTS, PEOPLE, PLANET 2021; 3:462-470. [PMID: 34938955 PMCID: PMC8651000 DOI: 10.1002/ppp3.10180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Revised: 12/17/2020] [Accepted: 12/17/2020] [Indexed: 06/14/2023]
Abstract
Despite the vast abundance and global importance of plant and microbial species, the large majority go unnoticed and unappreciated by humans, contributing to pressing issues including the neglect of study and research of these organisms, the lack of interest and support for their protection and conservation, low microbial and botanical literacy in society, and a growing disconnect between people and nature. The invisibility of many of these organisms is a key factor in their oversight by society, but also points to a solution: sharing the wealth of visual data produced during scientific research with a broader audience. Here, we discuss how the invisible can be visualised for a public audience, and the benefits it can bring. SUMMARY Whether too small, slow or concealed, the majority of species on Earth go unseen by humans. One such rather unobservable group of organisms are the arbuscular mycorrhizal (AM) fungi, who form beneficial symbioses with plants. AM symbiosis is ubiquitous and vitally important globally in ecosystem functioning, but partly as a consequence of its invisibility, it receives disproportionally little attention and appreciation. Yet AM fungi, and other unseen organisms, need not remain overlooked: from decades of scientific research there exists a goldmine of visual data, which if shared effectively we believe can alleviate the issues of low awareness. Here, we use examples from our experience of public engagement with AM symbiosis as well as evidence from the literature to outline the diverse ways in which invisible organisms can be visualised for a broad audience. We highlight outcomes and knock-on consequences of this visualisation, ranging from improved human mental health to environmental protection, making the case for researchers to share their images more widely for the benefit of plants (and fungi and other overlooked organisms), people and planet.
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Affiliation(s)
| | - Uta Paszkowski
- Department of Plant SciencesUniversity of CambridgeCambridgeUK
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20
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Sims J, Schlögelhofer P, Kurzbauer MT. From Microscopy to Nanoscopy: Defining an Arabidopsis thaliana Meiotic Atlas at the Nanometer Scale. FRONTIERS IN PLANT SCIENCE 2021; 12:672914. [PMID: 34084178 PMCID: PMC8167036 DOI: 10.3389/fpls.2021.672914] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 04/27/2021] [Indexed: 06/12/2023]
Abstract
Visualization of meiotic chromosomes and the proteins involved in meiotic recombination have become essential to study meiosis in many systems including the model plant Arabidopsis thaliana. Recent advances in super-resolution technologies changed how microscopic images are acquired and analyzed. New technologies enable observation of cells and nuclei at a nanometer scale and hold great promise to the field since they allow observing complex meiotic molecular processes with unprecedented detail. Here, we provide an overview of classical and advanced sample preparation and microscopy techniques with an updated Arabidopsis meiotic atlas based on super-resolution microscopy. We review different techniques, focusing on stimulated emission depletion (STED) nanoscopy, to offer researchers guidance for selecting the optimal protocol and equipment to address their scientific question.
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21
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Liu Z, Gao J, Cui Y, Klumpe S, Xiang Y, Erdmann PS, Jiang L. Membrane imaging in the plant endomembrane system. PLANT PHYSIOLOGY 2021; 185:562-576. [PMID: 33793889 PMCID: PMC8133680 DOI: 10.1093/plphys/kiaa040] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 08/11/2020] [Indexed: 05/10/2023]
Abstract
Recent studies on membrane imaging in the plant endomembrane system by 2-D/3-D CLSM and TEM provide future perspectives of whole-cell ET and cryo-FIB-aided cryo-ET analysis.
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Affiliation(s)
- Zhiqi Liu
- State Key Laboratory of Agrobiotechnology, School of Life Sciences, Centre for Cell and Developmental Biology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Jiayang Gao
- State Key Laboratory of Agrobiotechnology, School of Life Sciences, Centre for Cell and Developmental Biology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Yong Cui
- State Key Laboratory of Agrobiotechnology, School of Life Sciences, Centre for Cell and Developmental Biology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Sven Klumpe
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Yun Xiang
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Philipp S Erdmann
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
- Author for communication: (L.J.)
| | - Liwen Jiang
- State Key Laboratory of Agrobiotechnology, School of Life Sciences, Centre for Cell and Developmental Biology, The Chinese University of Hong Kong, Shatin, Hong Kong
- CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen 518057, China
- Author for communication: (L.J.)
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22
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Hrbáčková M, Luptovčiak I, Hlaváčková K, Dvořák P, Tichá M, Šamajová O, Novák D, Bednarz H, Niehaus K, Ovečka M, Šamaj J. Overexpression of alfalfa SIMK promotes root hair growth, nodule clustering and shoot biomass production. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:767-784. [PMID: 33112469 PMCID: PMC8051612 DOI: 10.1111/pbi.13503] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 10/08/2020] [Accepted: 10/15/2020] [Indexed: 05/03/2023]
Abstract
Nitrogen-fixing rhizobia and legumes have developed complex mutualistic mechanism that allows to convert atmospheric nitrogen into ammonia. Signalling by mitogen-activated protein kinases (MAPKs) seems to be involved in this symbiotic interaction. Previously, we reported that stress-induced MAPK (SIMK) shows predominantly nuclear localization in alfalfa root epidermal cells. Nevertheless, SIMK is activated and relocalized to the tips of growing root hairs during their development. SIMK kinase (SIMKK) is a well-known upstream activator of SIMK. Here, we characterized production parameters of transgenic alfalfa plants with genetically manipulated SIMK after infection with Sinorhizobium meliloti. SIMKK RNAi lines, causing strong downregulation of both SIMKK and SIMK, showed reduced root hair growth and lower capacity to form infection threads and nodules. In contrast, constitutive overexpression of GFP-tagged SIMK promoted root hair growth as well as infection thread and nodule clustering. Moreover, SIMKK and SIMK downregulation led to decrease, while overexpression of GFP-tagged SIMK led to increase of biomass in above-ground part of plants. These data suggest that genetic manipulations causing downregulation or overexpression of SIMK affect root hair, nodule and shoot formation patterns in alfalfa, and point to the new biotechnological potential of this MAPK.
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Affiliation(s)
- Miroslava Hrbáčková
- Faculty of ScienceDepartment of Cell BiologyCentre of the Region Haná for Biotechnological and Agricultural ResearchPalacký University OlomoucOlomoucCzech Republic
| | - Ivan Luptovčiak
- Faculty of ScienceDepartment of Cell BiologyCentre of the Region Haná for Biotechnological and Agricultural ResearchPalacký University OlomoucOlomoucCzech Republic
| | - Kateřina Hlaváčková
- Faculty of ScienceDepartment of Cell BiologyCentre of the Region Haná for Biotechnological and Agricultural ResearchPalacký University OlomoucOlomoucCzech Republic
| | - Petr Dvořák
- Faculty of ScienceDepartment of Cell BiologyCentre of the Region Haná for Biotechnological and Agricultural ResearchPalacký University OlomoucOlomoucCzech Republic
| | - Michaela Tichá
- Faculty of ScienceDepartment of Cell BiologyCentre of the Region Haná for Biotechnological and Agricultural ResearchPalacký University OlomoucOlomoucCzech Republic
| | - Olga Šamajová
- Faculty of ScienceDepartment of Cell BiologyCentre of the Region Haná for Biotechnological and Agricultural ResearchPalacký University OlomoucOlomoucCzech Republic
| | - Dominik Novák
- Faculty of ScienceDepartment of Cell BiologyCentre of the Region Haná for Biotechnological and Agricultural ResearchPalacký University OlomoucOlomoucCzech Republic
| | - Hanna Bednarz
- Faculty of BiologyCenter for Biotechnology – CeBiTecUniversität BielefeldBielefeldGermany
| | - Karsten Niehaus
- Faculty of BiologyCenter for Biotechnology – CeBiTecUniversität BielefeldBielefeldGermany
| | - Miroslav Ovečka
- Faculty of ScienceDepartment of Cell BiologyCentre of the Region Haná for Biotechnological and Agricultural ResearchPalacký University OlomoucOlomoucCzech Republic
| | - Jozef Šamaj
- Faculty of ScienceDepartment of Cell BiologyCentre of the Region Haná for Biotechnological and Agricultural ResearchPalacký University OlomoucOlomoucCzech Republic
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23
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DeVree BT, Steiner LM, Głazowska S, Ruhnow F, Herburger K, Persson S, Mravec J. Current and future advances in fluorescence-based visualization of plant cell wall components and cell wall biosynthetic machineries. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:78. [PMID: 33781321 PMCID: PMC8008654 DOI: 10.1186/s13068-021-01922-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 03/05/2021] [Indexed: 05/18/2023]
Abstract
Plant cell wall-derived biomass serves as a renewable source of energy and materials with increasing importance. The cell walls are biomacromolecular assemblies defined by a fine arrangement of different classes of polysaccharides, proteoglycans, and aromatic polymers and are one of the most complex structures in Nature. One of the most challenging tasks of cell biology and biomass biotechnology research is to image the structure and organization of this complex matrix, as well as to visualize the compartmentalized, multiplayer biosynthetic machineries that build the elaborate cell wall architecture. Better knowledge of the plant cells, cell walls, and whole tissue is essential for bioengineering efforts and for designing efficient strategies of industrial deconstruction of the cell wall-derived biomass and its saccharification. Cell wall-directed molecular probes and analysis by light microscopy, which is capable of imaging with a high level of specificity, little sample processing, and often in real time, are important tools to understand cell wall assemblies. This review provides a comprehensive overview about the possibilities for fluorescence label-based imaging techniques and a variety of probing methods, discussing both well-established and emerging tools. Examples of applications of these tools are provided. We also list and discuss the advantages and limitations of the methods. Specifically, we elaborate on what are the most important considerations when applying a particular technique for plants, the potential for future development, and how the plant cell wall field might be inspired by advances in the biomedical and general cell biology fields.
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Affiliation(s)
- Brian T DeVree
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg, Denmark
| | - Lisa M Steiner
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg, Denmark
| | - Sylwia Głazowska
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg, Denmark
| | - Felix Ruhnow
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg, Denmark
| | - Klaus Herburger
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg, Denmark
| | - Staffan Persson
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg, Denmark
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Jozef Mravec
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg, Denmark
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24
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Biosensors: A Sneak Peek into Plant Cell's Immunity. Life (Basel) 2021; 11:life11030209. [PMID: 33800034 PMCID: PMC7999283 DOI: 10.3390/life11030209] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 02/23/2021] [Accepted: 03/03/2021] [Indexed: 12/26/2022] Open
Abstract
Biosensors are indispensable tools to understand a plant’s immunity as its spatiotemporal dimension is key in withstanding complex plant immune signaling. The diversity of genetically encoded biosensors in plants is expanding, covering new analytes with ever higher sensitivity and robustness, but their assortment is limited in some respects, such as their use in following biotic stress response, employing more than one biosensor in the same chassis, and their implementation into crops. In this review, we focused on the available biosensors that encompass these aspects. We show that in vivo imaging of calcium and reactive oxygen species is satisfactorily covered with the available genetically encoded biosensors, while on the other hand they are still underrepresented when it comes to imaging of the main three hormonal players in the immune response: salicylic acid, ethylene and jasmonic acid. Following more than one analyte in the same chassis, upon one or more conditions, has so far been possible by using the most advanced genetically encoded biosensors in plants which allow the monitoring of calcium and the two main hormonal pathways involved in plant development, auxin and cytokinin. These kinds of biosensor are also the most evolved in crops. In the last section, we examine the challenges in the use of biosensors and demonstrate some strategies to overcome them.
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25
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Kubalová I, Němečková A, Weisshart K, Hřibová E, Schubert V. Comparing Super-Resolution Microscopy Techniques to Analyze Chromosomes. Int J Mol Sci 2021; 22:ijms22041903. [PMID: 33672992 PMCID: PMC7917581 DOI: 10.3390/ijms22041903] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 02/04/2021] [Accepted: 02/10/2021] [Indexed: 12/21/2022] Open
Abstract
The importance of fluorescence light microscopy for understanding cellular and sub-cellular structures and functions is undeniable. However, the resolution is limited by light diffraction (~200–250 nm laterally, ~500–700 nm axially). Meanwhile, super-resolution microscopy, such as structured illumination microscopy (SIM), is being applied more and more to overcome this restriction. Instead, super-resolution by stimulated emission depletion (STED) microscopy achieving a resolution of ~50 nm laterally and ~130 nm axially has not yet frequently been applied in plant cell research due to the required specific sample preparation and stable dye staining. Single-molecule localization microscopy (SMLM) including photoactivated localization microscopy (PALM) has not yet been widely used, although this nanoscopic technique allows even the detection of single molecules. In this study, we compared protein imaging within metaphase chromosomes of barley via conventional wide-field and confocal microscopy, and the sub-diffraction methods SIM, STED, and SMLM. The chromosomes were labeled by DAPI (4′,6-diamidino-2-phenylindol), a DNA-specific dye, and with antibodies against topoisomerase IIα (Topo II), a protein important for correct chromatin condensation. Compared to the diffraction-limited methods, the combination of the three different super-resolution imaging techniques delivered tremendous additional insights into the plant chromosome architecture through the achieved increased resolution.
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Affiliation(s)
- Ivona Kubalová
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, D-06466 Seeland, Germany;
| | - Alžběta Němečková
- Centre of the Region Hana for Biotechnological and Agricultural Research, Institute of Experimental Botany of the Czech Academy of Sciences, 77900 Olomouc, Czech Republic; (A.N.); (E.H.)
| | | | - Eva Hřibová
- Centre of the Region Hana for Biotechnological and Agricultural Research, Institute of Experimental Botany of the Czech Academy of Sciences, 77900 Olomouc, Czech Republic; (A.N.); (E.H.)
| | - Veit Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, D-06466 Seeland, Germany;
- Correspondence: ; Tel.: +49-394-825-212
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26
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Davaritouchaee M, Chen S, Mancini RJ. Delignification and Enzyme-Diffusion Kinetics of Radical Systems Treating Wheat Straw. Ind Eng Chem Res 2020. [DOI: 10.1021/acs.iecr.0c04107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Maryam Davaritouchaee
- The Gene & Linda Voiland School of Chemical Engineering and Bioengineering, Washington State University, 1505 NE Stadium Way, Pullman, Washington 99164, United States
- Department of Chemistry, Washington State University, 1470 NE College Avenue, Pullman, Washington 99164, United States
| | - Shulin Chen
- The Gene & Linda Voiland School of Chemical Engineering and Bioengineering, Washington State University, 1505 NE Stadium Way, Pullman, Washington 99164, United States
- Department of Biological Systems Engineering, Washington State University, 1935 E. Grimes Way, Pullman, Washington 99164, United States
| | - Rock J. Mancini
- The Gene & Linda Voiland School of Chemical Engineering and Bioengineering, Washington State University, 1505 NE Stadium Way, Pullman, Washington 99164, United States
- Department of Chemistry, Washington State University, 1470 NE College Avenue, Pullman, Washington 99164, United States
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27
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Abstract
A transition from qualitative to quantitative descriptors of morphology has been facilitated through the growing field of morphometrics, representing the conversion of shapes and patterns into numbers. The analysis of plant form at the macromorphological scale using morphometric approaches quantifies what is commonly referred to as a phenotype. Quantitative phenotypic analysis of individuals with contrasting genotypes in turn provides a means to establish links between genes and shapes. The path from a gene to a morphological phenotype is, however, not direct, with instructive information progressing both across multiple scales of biological complexity and through nonintuitive feedback, such as mechanical signals. In this review, we explore morphometric approaches used to perform whole-plant phenotyping and quantitative approaches in capture processes in the mesoscales, which bridge the gaps between genes and shapes in plants. Quantitative frameworks involving both the computational simulation and the discretization of data into networks provide a putative path to predicting emergent shape from underlying genetic programs.
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Affiliation(s)
- Hao Xu
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom;
| | - George W Bassel
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom;
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Rae AE, Wei X, Flores-Rodriguez N, McCurdy DW, Collings DA. Super-Resolution Fluorescence Imaging of Arabidopsis thaliana Transfer Cell Wall Ingrowths using Pseudo-Schiff Labelling Adapted for the Use of Different Dyes. PLANT & CELL PHYSIOLOGY 2020; 61:1775-1787. [PMID: 32761075 DOI: 10.1093/pcp/pcaa102] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 07/28/2020] [Indexed: 05/23/2023]
Abstract
To understand plant growth and development, it is often necessary to investigate the organization of plant cells and plant cell walls. Plant cell walls are often fluorescently labeled for confocal imaging with the dye propidium iodide using a pseudo-Schiff reaction. This reaction binds free amine groups on dye molecules to aldehyde groups on cellulose that result from oxidation with periodic acid. We tested a range of fluorescent dyes carrying free amine groups for their ability to act as pseudo-Schiff reagents. Using the low-pH solution historically used for the Schiff reaction, these alternative dyes failed to label cell walls of Arabidopsis cotyledon vascular tissue as strongly as propidium iodide but replacing the acidic solution with water greatly improved fluorescence labeling. Under these conditions, rhodamine-123 provided improved staining of plant cell walls compared to propidium iodide. We also developed protocols for pseudo-Schiff labeling with ATTO 647N-amine, a dye compatible for super-resolution Stimulated Emission Depletion (STED) imaging. ATTO 647N-amine was used for super-resolution imaging of cell wall ingrowths that occur in phloem parenchyma transfer cells of Arabidopsis, structures whose small size is only slightly larger than the resolution limit of conventional confocal microscopy. Application of surface-rendering software demonstrated the increase in plasma membrane surface area as a consequence of wall ingrowth deposition and suggests that STED-based approaches will be useful for more detailed morphological analysis of wall ingrowth formation. These improvements in pseudo-Schiff labeling for conventional confocal microscopy and STED imaging will be broadly applicable for high-resolution imaging of plant cell walls.
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Affiliation(s)
- Angus E Rae
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW 2308, Australia
- Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
| | - Xiaoyang Wei
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW 2308, Australia
| | - Neftali Flores-Rodriguez
- Australian Centre for Microscopy and Microanalysis, University of Sydney, Sydney, NSW 2006, Australia
| | - David W McCurdy
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW 2308, Australia
| | - David A Collings
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW 2308, Australia
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29
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Tichá M, Illésová P, Hrbáčková M, Basheer J, Novák D, Hlaváčková K, Šamajová O, Niehaus K, Ovečka M, Šamaj J. Tissue culture, genetic transformation, interaction with beneficial microbes, and modern bio-imaging techniques in alfalfa research. Crit Rev Biotechnol 2020; 40:1265-1280. [PMID: 32942912 DOI: 10.1080/07388551.2020.1814689] [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: 12/23/2022]
Abstract
Current research needs to be more focused on agronomical plants to effectively utilize the knowledge obtained from model plant species. Efforts to improve legumes have long employed common breeding tools. Recently, biotechnological approaches facilitated the development of improved legumes with new traits, allowing them to withstand climatic changes and biotic stress. Owing to its multiple uses and profits, alfalfa (Medicago sativa L.) has become a prominent forage crop worldwide. This review provides a comprehensive research summary of tissue culture-based genetic transformation methods, which could be exploited for the development of transgenic alfalfa with agronomically desirable traits. Moreover, advanced bio-imaging approaches, including cutting-edge microscopy and phenotyping, are outlined here. Finally, characterization and the employment of beneficial microbes should help to produce biotechnologically improved and sustainable alfalfa cultivars.
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Affiliation(s)
- Michaela Tichá
- Department of Cell Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Olomouc, Czech Republic
| | - Petra Illésová
- Department of Cell Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Olomouc, Czech Republic
| | - Miroslava Hrbáčková
- Department of Cell Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Olomouc, Czech Republic
| | - Jasim Basheer
- Department of Cell Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Olomouc, Czech Republic
| | - Dominik Novák
- Department of Cell Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Olomouc, Czech Republic
| | - Kateřina Hlaváčková
- Department of Cell Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Olomouc, Czech Republic
| | - Olga Šamajová
- Department of Cell Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Olomouc, Czech Republic
| | - Karsten Niehaus
- Faculty of Biology, Center for Biotechnology - CeBiTec, Universität Bielefeld, Bielefeld, Germany
| | - Miroslav Ovečka
- Department of Cell Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Olomouc, Czech Republic
| | - Jozef Šamaj
- Department of Cell Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Olomouc, Czech Republic
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30
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Schnorrenberg S, Ghareeb H, Frahm L, Grotjohann T, Jensen N, Teichmann T, Hell SW, Lipka V, Jakobs S. Live-cell RESOLFT nanoscopy of transgenic Arabidopsis thaliana. PLANT DIRECT 2020; 4:e00261. [PMID: 32995700 PMCID: PMC7507094 DOI: 10.1002/pld3.261] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 07/20/2020] [Accepted: 08/03/2020] [Indexed: 05/04/2023]
Abstract
Subdiffraction super-resolution fluorescence microscopy, or nanoscopy, has seen remarkable developments in the last two decades. Yet, for the visualization of plant cells, nanoscopy is still rarely used. In this study, we established RESOLFT nanoscopy on living green plant tissue. Live-cell RESOLFT nanoscopy requires and utilizes comparatively low light doses and intensities to overcome the diffraction barrier. We generated a transgenic Arabidopsis thaliana plant line expressing the reversibly switchable fluorescent protein rsEGFP2 fused to the mammalian microtubule-associated protein 4 (MAP4) in order to ubiquitously label the microtubule cytoskeleton. We demonstrate the use of RESOLFT nanoscopy for extended time-lapse imaging of cortical microtubules in Arabidopsis leaf discs. By combining our approach with fluorescence lifetime gating, we were able to acquire live-cell RESOLFT images even close to chloroplasts, which exhibit very strong autofluorescence. The data demonstrate the feasibility of subdiffraction resolution imaging in transgenic plant material with minimal requirements for sample preparation.
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Affiliation(s)
- Sebastian Schnorrenberg
- Department of NanoBiophotonicsMax Planck Institute for Biophysical ChemistryGöttingenGermany
| | - Hassan Ghareeb
- Department of Plant Cell BiologyAlbrecht‐von‐Haller Institute of Plant SciencesUniversity of GöttingenGöttingenGermany
- Present address:
Department of Plant BiotechnologyNational Research CentreCairoEgypt
| | - Lars Frahm
- Department of NanoBiophotonicsMax Planck Institute for Biophysical ChemistryGöttingenGermany
| | - Tim Grotjohann
- Department of NanoBiophotonicsMax Planck Institute for Biophysical ChemistryGöttingenGermany
| | - Nickels Jensen
- Department of NanoBiophotonicsMax Planck Institute for Biophysical ChemistryGöttingenGermany
| | - Thomas Teichmann
- Department of Plant Cell BiologyAlbrecht‐von‐Haller Institute of Plant SciencesUniversity of GöttingenGöttingenGermany
| | - Stefan W. Hell
- Department of NanoBiophotonicsMax Planck Institute for Biophysical ChemistryGöttingenGermany
| | - Volker Lipka
- Department of Plant Cell BiologyAlbrecht‐von‐Haller Institute of Plant SciencesUniversity of GöttingenGöttingenGermany
- Central Microscopy Facility of the Faculty of Biology and PsychologyUniversity of GöttingenGöttingenGermany
| | - Stefan Jakobs
- Department of NanoBiophotonicsMax Planck Institute for Biophysical ChemistryGöttingenGermany
- Clinic of NeurologyUniversity Medical Center of GöttingenGöttingenGermany
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31
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Prunet N, Duncan K. Imaging flowers: a guide to current microscopy and tomography techniques to study flower development. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:2898-2909. [PMID: 32383442 PMCID: PMC7260710 DOI: 10.1093/jxb/eraa094] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 05/06/2020] [Indexed: 05/20/2023]
Abstract
Developmental biology relies heavily on our ability to generate three-dimensional images of live biological specimens through time, and to map gene expression and hormone response in these specimens as they undergo development. The last two decades have seen an explosion of new bioimaging technologies that have pushed the limits of spatial and temporal resolution and provided biologists with invaluable new tools. However, plant tissues are difficult to image, and no single technology fits all purposes; choosing between many bioimaging techniques is not trivial. Here, we review modern light microscopy and computed projection tomography methods, their capabilities and limitations, and we discuss their current and potential applications to the study of flower development and fertilization.
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Affiliation(s)
| | - Keith Duncan
- Donald Danforth Plant Science Center, St. Louis, MO, USA
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32
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Seerangan K, van Spoordonk R, Sampathkumar A, Eng RC. Long-term live-cell imaging techniques for visualizing pavement cell morphogenesis. Methods Cell Biol 2020; 160:365-380. [PMID: 32896328 DOI: 10.1016/bs.mcb.2020.04.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Recent advancements in microscopy and biological technologies have allowed scientists to study dynamic plant developmental processes with high temporal and spatial resolution. Pavement cells, epidermal cells found on leaf tissue, form complex shapes with alternating regions of indentations and outgrowths that are postulated to be driven by the microtubule cytoskeleton. Given their complex shapes, pavement cells and the microtubule contribution towards morphogenesis have been of great interest in the field of developmental biology. Here, we focus on two live-cell imaging methods that allow for early and long-term imaging of the cotyledon (embryonic leaf-like tissue) and leaf epidermis with minimal invasiveness in order to study microtubules throughout pavement cell morphogenesis. The methods described in this chapter can be applied to studying other developmental processes associated with cotyledon and leaf tissue.
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Affiliation(s)
- Kumar Seerangan
- Plant Cell Biology & Microscopy, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Ruben van Spoordonk
- Plant Cell Biology & Microscopy, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Arun Sampathkumar
- Plant Cell Biology & Microscopy, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany.
| | - Ryan Christopher Eng
- Plant Cell Biology & Microscopy, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany.
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33
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Clark NM, Van den Broeck L, Guichard M, Stager A, Tanner HG, Blilou I, Grossmann G, Iyer-Pascuzzi AS, Maizel A, Sparks EE, Sozzani R. Novel Imaging Modalities Shedding Light on Plant Biology: Start Small and Grow Big. ANNUAL REVIEW OF PLANT BIOLOGY 2020; 71:789-816. [PMID: 32119794 DOI: 10.1146/annurev-arplant-050718-100038] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
The acquisition of quantitative information on plant development across a range of temporal and spatial scales is essential to understand the mechanisms of plant growth. Recent years have shown the emergence of imaging methodologies that enable the capture and analysis of plant growth, from the dynamics of molecules within cells to the measurement of morphometricand physiological traits in field-grown plants. In some instances, these imaging methods can be parallelized across multiple samples to increase throughput. When high throughput is combined with high temporal and spatial resolution, the resulting image-derived data sets could be combined with molecular large-scale data sets to enable unprecedented systems-level computational modeling. Such image-driven functional genomics studies may be expected to appear at an accelerating rate in the near future given the early success of the foundational efforts reviewed here. We present new imaging modalities and review how they have enabled a better understanding of plant growth from the microscopic to the macroscopic scale.
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Affiliation(s)
- Natalie M Clark
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina 27695, USA; ,
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa 50010, USA;
| | - Lisa Van den Broeck
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina 27695, USA; ,
| | - Marjorie Guichard
- Center for Organismal Studies (COS), University of Heidelberg, 69120 Heidelberg, Germany; , ,
- CellNetworks Cluster of Excellence, Heidelberg University, 69120 Heidelberg, Germany
| | - Adam Stager
- Department of Mechanical Engineering, University of Delaware, Newark, Delaware 19711, USA; ,
| | - Herbert G Tanner
- Department of Mechanical Engineering, University of Delaware, Newark, Delaware 19711, USA; ,
| | - Ikram Blilou
- Department of Plant Cell and Developmental Biology, Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia;
| | - Guido Grossmann
- Center for Organismal Studies (COS), University of Heidelberg, 69120 Heidelberg, Germany; , ,
- CellNetworks Cluster of Excellence, Heidelberg University, 69120 Heidelberg, Germany
| | - Anjali S Iyer-Pascuzzi
- Department of Botany and Plant Pathology and Center for Plant Biology, Purdue University, West Lafayette, Indiana 47907, USA;
| | - Alexis Maizel
- Center for Organismal Studies (COS), University of Heidelberg, 69120 Heidelberg, Germany; , ,
| | - Erin E Sparks
- Department of Plant and Soil Sciences and the Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19711, USA;
| | - Rosangela Sozzani
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina 27695, USA; ,
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34
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Tichá M, Hlaváčková K, Hrbáčková M, Ovečka M, Šamajová O, Šamaj J. Super-resolution imaging of microtubules in Medicago sativa. Methods Cell Biol 2020; 160:237-251. [PMID: 32896319 DOI: 10.1016/bs.mcb.2020.03.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Study of microtubules on cellular and subcellular levels is compromised by limited resolution of conventional fluorescence microscopy. However, it is possible to improve Abbe's diffraction-limited resolution by employment of super-resolution microscopy methods. Two of them, described herein, are structured-illumination microscopy (SIM) and Airyscan laser scanning microscopy (AM). Both methods allow high-resolution imaging of cortical microtubules in plant cells, thus contributing to the current knowledge on plant morphogenesis, growth and development. Both SIM and AM provide certain advantages and characteristic features, which are described here. We present immunofluorescence localization methods for microtubules in fixed plant cells achieving high signal efficiency, superb sample stability and sub-diffraction resolution. These protocols were developed for whole-mount immunolabeling of root samples of legume crop species Medicago sativa. They also contain tips for optimal sample preparation of plants germinated from seeds as well as plantlets regenerated from somatic embryos in vitro. We describe in detail all steps of optimized protocols for sample preparation, microtubule immunolabeling and super-resolution imaging.
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Affiliation(s)
- Michaela Tichá
- Department of Cell Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University Olomouc, Olomouc, Czech Republic
| | - Kateřina Hlaváčková
- Department of Cell Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University Olomouc, Olomouc, Czech Republic
| | - Miroslava Hrbáčková
- Department of Cell Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University Olomouc, Olomouc, Czech Republic
| | - Miroslav Ovečka
- Department of Cell Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University Olomouc, Olomouc, Czech Republic
| | - Olga Šamajová
- Department of Cell Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University Olomouc, Olomouc, Czech Republic
| | - Jozef Šamaj
- Department of Cell Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University Olomouc, Olomouc, Czech Republic.
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35
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Kunishima N, Takeda Y, Hirose R, Kalasová D, Šalplachta J, Omote K. Visualization of internal 3D structure of small live seed on germination by laboratory-based X-ray microscopy with phase contrast computed tomography. PLANT METHODS 2020; 16:7. [PMID: 32021643 PMCID: PMC6995115 DOI: 10.1186/s13007-020-0557-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 01/22/2020] [Indexed: 05/05/2023]
Abstract
BACKGROUND The visualization of internal 3D-structure of tissues at micron resolutions without staining by contrast reagents is desirable in plant researches, and it can be achieved by an X-ray computed tomography (CT) with a phase-retrieval technique. Recently, a laboratory-based X-ray microscope adopting the phase contrast CT was developed as a powerful tool for the observation of weakly absorbing biological samples. Here we report the observation of unstained pansy seeds using the laboratory-based X-ray phase-contrast CT. RESULTS A live pansy seed within 2 mm in size was simply mounted inside a plastic tube and irradiated by in-house X-rays to collect projection images using a laboratory-based X-ray microscope. The phase-retrieval technique was applied to enhance contrasts in the projection images. In addition to a dry seed, wet seeds on germination with the poorer contrasts were tried. The phase-retrieved tomograms from both the dry and the wet seeds revealed a cellular level of spatial resolutions that were enough to resolve cells in the seeds, and provided enough contrasts to delineate the boundary of embryos manually. The manual segmentation allowed a 3D rendering of embryos at three different stages in the germination, which visualized an overall morphological change of the embryo upon germination as well as a spatial arrangement of cells inside the embryo. CONCLUSIONS Our results confirmed an availability of the laboratory-based X-ray phase-contrast CT for a 3D-structural study on the development of small seeds. The present method may provide a unique way to observe live plant tissues at micron resolutions without structural perturbations due to the sample preparation.
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Affiliation(s)
- Naoki Kunishima
- X-Ray Research Laboratory, Rigaku Corporation, 3-9-12 Matsubara-cho, Akishima, Tokyo, 196-8666 Japan
| | - Yoshihiro Takeda
- X-Ray Research Laboratory, Rigaku Corporation, 3-9-12 Matsubara-cho, Akishima, Tokyo, 196-8666 Japan
| | - Raita Hirose
- X-Ray Research Laboratory, Rigaku Corporation, 3-9-12 Matsubara-cho, Akishima, Tokyo, 196-8666 Japan
| | - Dominika Kalasová
- CEITEC-Central European Institute of Technology, Brno University of Technology, Purkynova 123, 612 00 Brno, Czech Republic
| | - Jakub Šalplachta
- CEITEC-Central European Institute of Technology, Brno University of Technology, Purkynova 123, 612 00 Brno, Czech Republic
| | - Kazuhiko Omote
- X-Ray Research Laboratory, Rigaku Corporation, 3-9-12 Matsubara-cho, Akishima, Tokyo, 196-8666 Japan
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Vavrdová T, Křenek P, Ovečka M, Šamajová O, Floková P, Illešová P, Šnaurová R, Šamaj J, Komis G. Complementary Superresolution Visualization of Composite Plant Microtubule Organization and Dynamics. FRONTIERS IN PLANT SCIENCE 2020; 11:693. [PMID: 32582243 PMCID: PMC7290007 DOI: 10.3389/fpls.2020.00693] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Accepted: 05/01/2020] [Indexed: 05/04/2023]
Abstract
Microtubule bundling is an essential mechanism underlying the biased organization of interphase and mitotic microtubular systems of eukaryotes in ordered arrays. Microtubule bundle formation can be exemplified in plants, where the formation of parallel microtubule systems in the cell cortex or the spindle midzone is largely owing to the microtubule crosslinking activity of a family of microtubule associated proteins, designated as MAP65s. Among the nine members of this family in Arabidopsis thaliana, MAP65-1 and MAP65-2 are ubiquitous and functionally redundant. Crosslinked microtubules can form high-order arrays, which are difficult to track using widefield or confocal laser scanning microscopy approaches. Here, we followed spatiotemporal patterns of MAP65-2 localization in hypocotyl cells of Arabidopsis stably expressing fluorescent protein fusions of MAP65-2 and tubulin. To circumvent imaging difficulties arising from the density of cortical microtubule bundles, we use different superresolution approaches including Airyscan confocal laser scanning microscopy (ACLSM), structured illumination microscopy (SIM), total internal reflection SIM (TIRF-SIM), and photoactivation localization microscopy (PALM). We provide insights into spatiotemporal relations between microtubules and MAP65-2 crossbridges by combining SIM and ACLSM. We obtain further details on MAP65-2 distribution by single molecule localization microscopy (SMLM) imaging of either mEos3.2-MAP65-2 stochastic photoconversion, or eGFP-MAP65-2 stochastic emission fluctuations under specific illumination conditions. Time-dependent dynamics of MAP65-2 were tracked at variable time resolution using SIM, TIRF-SIM, and ACLSM and post-acquisition kymograph analysis. ACLSM imaging further allowed to track end-wise dynamics of microtubules labeled with TUA6-GFP and to correlate them with concomitant fluctuations of MAP65-2 tagged with tagRFP. All different microscopy modules examined herein are accompanied by restrictions in either the spatial resolution achieved, or in the frame rates of image acquisition. PALM imaging is compromised by speed of acquisition. This limitation was partially compensated by exploiting emission fluctuations of eGFP which allowed much higher photon counts at substantially smaller time series compared to mEos3.2. SIM, TIRF-SIM, and ACLSM were the methods of choice to follow the dynamics of MAP65-2 in bundles of different complexity. Conclusively, the combination of different superresolution methods allowed for inferences on the distribution and dynamics of MAP65-2 within microtubule bundles of living A. thaliana cells.
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de Bang L, Paez-Garcia A, Cannon AE, Chin S, Kolape J, Liao F, Sparks JA, Jiang Q, Blancaflor EB. Brassinosteroids Inhibit Autotropic Root Straightening by Modifying Filamentous-Actin Organization and Dynamics. FRONTIERS IN PLANT SCIENCE 2020; 11:5. [PMID: 32117357 PMCID: PMC7010715 DOI: 10.3389/fpls.2020.00005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 01/06/2020] [Indexed: 05/12/2023]
Abstract
When positioned horizontally, roots grow down toward the direction of gravity. This phenomenon, called gravitropism, is influenced by most of the major plant hormones including brassinosteroids. Epi-brassinolide (eBL) was previously shown to enhance root gravitropism, a phenomenon similar to the response of roots exposed to the actin inhibitor, latrunculin B (LatB). This led us to hypothesize that eBL might enhance root gravitropism through its effects on filamentous-actin (F-actin). This hypothesis was tested by comparing gravitropic responses of maize (Zea mays) roots treated with eBL or LatB. LatB- and eBL-treated roots displayed similar enhanced downward growth compared with controls when vertical roots were oriented horizontally. Moreover, the effects of the two compounds on root growth directionality were more striking on a slowly-rotating two-dimensional clinostat. Both compounds inhibited autotropism, a process in which the root straightened after the initial gravistimulus was withdrawn by clinorotation. Although eBL reduced F-actin density in chemically-fixed Z. mays roots, the impact was not as strong as that of LatB. Modification of F-actin organization after treatment with both compounds was also observed in living roots of barrel medic (Medicago truncatula) seedlings expressing genetically encoded F-actin reporters. Like in fixed Z. mays roots, eBL effects on F-actin in living M. truncatula roots were modest compared with those of LatB. Furthermore, live cell imaging revealed a decrease in global F-actin dynamics in hypocotyls of etiolated M. truncatula seedlings treated with eBL compared to controls. Collectively, our data indicate that eBL-and LatB-induced enhancement of root gravitropism can be explained by inhibited autotropic root straightening, and that eBL affects this process, in part, by modifying F-actin organization and dynamics.
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Affiliation(s)
- Louise de Bang
- Noble Research Institute LLC, Ardmore, OK, United States
- Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Ashley E. Cannon
- Noble Research Institute LLC, Ardmore, OK, United States
- Department of Biological Sciences, University of North Texas, Denton, TX, United States
| | - Sabrina Chin
- Noble Research Institute LLC, Ardmore, OK, United States
| | - Jaydeep Kolape
- Noble Research Institute LLC, Ardmore, OK, United States
- Center for Biotechnology, University of Nebraska—Lincoln, Lincoln, NE, United States
| | - Fuqi Liao
- Noble Research Institute LLC, Ardmore, OK, United States
| | - J. Alan Sparks
- Noble Research Institute LLC, Ardmore, OK, United States
| | - Qingzhen Jiang
- Noble Research Institute LLC, Ardmore, OK, United States
| | - Elison B. Blancaflor
- Noble Research Institute LLC, Ardmore, OK, United States
- *Correspondence: Elison B. Blancaflor,
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Dumur T, Duncan S, Graumann K, Desset S, Randall RS, Scheid OM, Prodanov D, Tatout C, Baroux C. Probing the 3D architecture of the plant nucleus with microscopy approaches: challenges and solutions. Nucleus 2019; 10:181-212. [PMID: 31362571 PMCID: PMC6682351 DOI: 10.1080/19491034.2019.1644592] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 06/24/2019] [Accepted: 07/01/2019] [Indexed: 12/18/2022] Open
Abstract
The eukaryotic cell nucleus is a central organelle whose architecture determines genome function at multiple levels. Deciphering nuclear organizing principles influencing cellular responses and identity is a timely challenge. Despite many similarities between plant and animal nuclei, plant nuclei present intriguing specificities. Complementary to molecular and biochemical approaches, 3D microscopy is indispensable for resolving nuclear architecture. However, novel solutions are required for capturing cell-specific, sub-nuclear and dynamic processes. We provide a pointer for utilising high-to-super-resolution microscopy and image processing to probe plant nuclear architecture in 3D at the best possible spatial and temporal resolution and at quantitative and cell-specific levels. High-end imaging and image-processing solutions allow the community now to transcend conventional practices and benefit from continuously improving approaches. These promise to deliver a comprehensive, 3D view of plant nuclear architecture and to capture spatial dynamics of the nuclear compartment in relation to cellular states and responses. Abbreviations: 3D and 4D: Three and Four dimensional; AI: Artificial Intelligence; ant: antipodal nuclei (ant); CLSM: Confocal Laser Scanning Microscopy; CTs: Chromosome Territories; DL: Deep Learning; DLIm: Dynamic Live Imaging; ecn: egg nucleus; FACS: Fluorescence-Activated Cell Sorting; FISH: Fluorescent In Situ Hybridization; FP: Fluorescent Proteins (GFP, RFP, CFP, YFP, mCherry); FRAP: Fluorescence Recovery After Photobleaching; GPU: Graphics Processing Unit; KEEs: KNOT Engaged Elements; INTACT: Isolation of Nuclei TAgged in specific Cell Types; LADs: Lamin-Associated Domains; ML: Machine Learning; NA: Numerical Aperture; NADs: Nucleolar Associated Domains; PALM: Photo-Activated Localization Microscopy; Pixel: Picture element; pn: polar nuclei; PSF: Point Spread Function; RHF: Relative Heterochromatin Fraction; SIM: Structured Illumination Microscopy; SLIm: Static Live Imaging; SMC: Spore Mother Cell; SNR: Signal to Noise Ratio; SRM: Super-Resolution Microscopy; STED: STimulated Emission Depletion; STORM: STochastic Optical Reconstruction Microscopy; syn: synergid nuclei; TADs: Topologically Associating Domains; Voxel: Volumetric pixel.
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Affiliation(s)
- Tao Dumur
- Gregor Mendel Institute (GMI) of Molecular Plant Biology, Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria
| | - Susan Duncan
- Norwich Research Park, Earlham Institute, Norwich, UK
| | - Katja Graumann
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
| | - Sophie Desset
- GReD, Université Clermont Auvergne, CNRS, INSERM, Clermont–Ferrand, France
| | - Ricardo S Randall
- Department of Plant and Microbial Biology, Zürich-Basel Plant Science Center, University of Zürich, Zürich, Switzerland
| | - Ortrun Mittelsten Scheid
- Gregor Mendel Institute (GMI) of Molecular Plant Biology, Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria
| | - Dimiter Prodanov
- Environment, Health and Safety, Neuroscience Research Flanders, Leuven, Belgium
| | - Christophe Tatout
- GReD, Université Clermont Auvergne, CNRS, INSERM, Clermont–Ferrand, France
| | - Célia Baroux
- Department of Plant and Microbial Biology, Zürich-Basel Plant Science Center, University of Zürich, Zürich, Switzerland
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Mironova V, Xu J. A single-cell view of tissue regeneration in plants. CURRENT OPINION IN PLANT BIOLOGY 2019; 52:149-154. [PMID: 31655397 DOI: 10.1016/j.pbi.2019.09.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 09/16/2019] [Accepted: 09/17/2019] [Indexed: 06/10/2023]
Abstract
With the development of advanced molecular-genetic and computational technologies it becomes possible to tackle individual cells within a regenerating tissue, to define morphogenetic and cellular changes in space and time by live imaging, to acquire transcriptome status with single-cell RNA sequencing (ScRNA-seq), and to delineate the candidate mechanisms by iterative computational and experimental approaches. Here, we review recent findings and current knowledge on tissue regeneration in plants, focusing on four evolutionarily conserved scenarios that a cell may embark on to facilitate the regeneration of a plant tissue structure lost by injury, namely cell death, division, dedifferentiation, and transdifferentiation. Understanding of these scenarios at single-cell resolution, singularly and in combination, could provide an unprecedented view of tissue regeneration in plants.
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Affiliation(s)
- Victoria Mironova
- Institute of Cytology and Genetics, Novosibirsk, 630090, Russia; Novosibirsk State University, LCT&EB, Novosibirsk, 630090, Russia.
| | - Jian Xu
- Department of Plant Systems Physiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands; Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, Singapore, 117543, Singapore.
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40
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Zhu D, Zhang M, Gao C, Shen J. Protein trafficking in plant cells: Tools and markers. SCIENCE CHINA-LIFE SCIENCES 2019; 63:343-363. [DOI: 10.1007/s11427-019-9598-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2019] [Accepted: 07/22/2019] [Indexed: 12/26/2022]
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41
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Schloetel JG, Heine J, Cowman AF, Pasternak M. Guided STED nanoscopy enables super-resolution imaging of blood stage malaria parasites. Sci Rep 2019; 9:4674. [PMID: 30886187 PMCID: PMC6423018 DOI: 10.1038/s41598-019-40718-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 02/19/2019] [Indexed: 12/27/2022] Open
Abstract
Malaria remains a major burden world-wide, but the disease-causing parasites from the genus Plasmodium are difficult to study in vitro. Owing to the small size of the parasites, subcellular imaging poses a major challenge and the use of super-resolution techniques has been hindered by the parasites' sensitivity to light. This is particularly apparent during the blood-stage of the Plasmodium life cycle, which presents an important target for drug research. The iron-rich food vacuole of the parasite undergoes disintegration when illuminated with high-power lasers such as those required for high resolution in Stimulated Emission Depletion (STED) microscopy. This causes major damage to the sample precluding the use of this super-resolution technique. Here we present guided STED, a novel adaptive illumination (AI) STED approach, which takes advantage of the highly-reflective nature of the iron deposit in the cell to identify the most light-sensitive parts of the sample. Specifically in these parts, the high-power STED laser is deactivated automatically to prevent local damage. Guided STED nanoscopy finally allows super-resolution imaging of the whole Plasmodium life cycle, enabling multicolour imaging of blood-stage malaria parasites with resolutions down to 35 nm without sample destruction.
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Affiliation(s)
| | - Jörn Heine
- Abberior Instruments GmbH, 37077, Göttingen, Germany
| | - Alan F Cowman
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Michał Pasternak
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia.
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Shaw SL, Thoms D, Powers J. Structured illumination approaches for super-resolution in plant cells. Microscopy (Oxf) 2019; 68:37-44. [PMID: 30295787 DOI: 10.1093/jmicro/dfy043] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 09/17/2018] [Accepted: 10/01/2018] [Indexed: 11/14/2022] Open
Abstract
The advent of super-resolution techniques in biological microscopy has opened new frontiers for exploring the molecular distribution of proteins and small molecules in cells. Improvements in optical design and innovations in the approaches for the collection of fluorescence emission have produced substantial gains in signal from chemical labels and fluorescent proteins. Structuring the illumination to elicit fluorescence from specific or even random patterns allows the extraction of higher order spatial frequencies from specimens labeled with conventional probes. Application of this approach to plant systems for super-resolution imaging has been relatively slow owing in large part to aberrations incurred when imaging through the plant cell wall. In this brief review, we address the use of two prominent methods for generating super-resolution images in living plant specimens and discuss future directions for gaining better access to these techniques.
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Affiliation(s)
- Sidney L Shaw
- Department of Biology, Light Microscopy Imaging Center, Indiana University, Bloomington, IN, USA
| | - David Thoms
- Department of Biology, Light Microscopy Imaging Center, Indiana University, Bloomington, IN, USA
| | - James Powers
- Department of Biology, Light Microscopy Imaging Center, Indiana University, Bloomington, IN, USA
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Vavrdová T, ˇSamaj J, Komis G. Phosphorylation of Plant Microtubule-Associated Proteins During Cell Division. FRONTIERS IN PLANT SCIENCE 2019; 10:238. [PMID: 30915087 PMCID: PMC6421500 DOI: 10.3389/fpls.2019.00238] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 02/12/2019] [Indexed: 05/20/2023]
Abstract
Progression of mitosis and cytokinesis depends on the reorganization of cytoskeleton, with microtubules driving the segregation of chromosomes and their partitioning to two daughter cells. In dividing plant cells, microtubules undergo global reorganization throughout mitosis and cytokinesis, and with the aid of various microtubule-associated proteins (MAPs), they form unique systems such as the preprophase band (PPB), the acentrosomal mitotic spindle, and the phragmoplast. Such proteins include nucleators of de novo microtubule formation, plus end binding proteins involved in the regulation of microtubule dynamics, crosslinking proteins underlying microtubule bundle formation and members of the kinesin superfamily with microtubule-dependent motor activities. The coordinated function of such proteins not only drives the continuous remodeling of microtubules during mitosis and cytokinesis but also assists the positioning of the PPB, the mitotic spindle, and the phragmoplast, affecting tissue patterning by controlling cell division plane (CDP) orientation. The affinity and the function of such proteins is variably regulated by reversible phosphorylation of serine and threonine residues within the microtubule binding domain through a number of protein kinases and phosphatases which are differentially involved throughout cell division. The purpose of the present review is to provide an overview of the function of protein kinases and protein phosphatases involved in cell division regulation and to identify cytoskeletal substrates relevant to the progression of mitosis and cytokinesis and the regulation of CDP orientation.
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Vavrdová T, Šamajová O, Křenek P, Ovečka M, Floková P, Šnaurová R, Šamaj J, Komis G. Multicolour three dimensional structured illumination microscopy of immunolabeled plant microtubules and associated proteins. PLANT METHODS 2019; 15:22. [PMID: 30899319 PMCID: PMC6408805 DOI: 10.1186/s13007-019-0406-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 02/26/2019] [Indexed: 05/04/2023]
Abstract
BACKGROUND In the present work, we provide an account of structured illumination microscopy (SIM) imaging of fixed and immunolabeled plant probes. We take advantage of SIM, to superresolve intracellular structures at a considerable z-range and circumvent its low temporal resolution capacity during the study of living samples. Further, we validate the protocol for the imaging of fixed transgenic material expressing fluorescent protein-based markers of different subcellular structures. RESULTS Focus is given on 3D imaging of bulky subcellular structures, such as mitotic and cytokinetic microtubule arrays as well as on the performance of SIM using multichannel imaging and the quantitative correlations that can be deduced. As a proof of concept, we provide a superresolution output on the organization of cortical microtubules in wild-type and mutant Arabidopsis cells, including aberrant preprophase microtubule bands and phragmoplasts in a cytoskeletal mutant devoid of the p60 subunit of the microtubule severing protein KATANIN and refined details of cytoskeletal aberrations in the mitogen activated protein kinase (MAPK) mutant mpk4. We further demonstrate, in a qualitative and quantitative manner, colocalizations between MPK6 and unknown dually phosphorylated and activated MAPK species and we follow the localization of the microtubule associated protein 65-3 (MAP65-3) in telophase and cytokinetic microtubular arrays. CONCLUSIONS 3D SIM is a powerful, versatile and adaptable microscopy method for elucidating spatial relationships between subcellular compartments. Improved methods of sample preparation aiming to the compensation of refractive index mismatches, allow the use of 3D SIM in the documentation of complex plant cell structures, such as microtubule arrays and the elucidation of their interactions with microtubule associated proteins.
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Affiliation(s)
- T. Vavrdová
- Department of Cell Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University Olomouc, Olomouc, Czech Republic
| | - O. Šamajová
- Department of Cell Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University Olomouc, Olomouc, Czech Republic
| | - P. Křenek
- Department of Cell Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University Olomouc, Olomouc, Czech Republic
| | - M. Ovečka
- Department of Cell Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University Olomouc, Olomouc, Czech Republic
| | - P. Floková
- Department of Cell Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University Olomouc, Olomouc, Czech Republic
| | - R. Šnaurová
- Department of Cell Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University Olomouc, Olomouc, Czech Republic
| | - J. Šamaj
- Department of Cell Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University Olomouc, Olomouc, Czech Republic
| | - G. Komis
- Department of Cell Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University Olomouc, Olomouc, Czech Republic
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45
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Reski R. Quantitative moss cell biology. CURRENT OPINION IN PLANT BIOLOGY 2018; 46:39-47. [PMID: 30036707 DOI: 10.1016/j.pbi.2018.07.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 06/14/2018] [Accepted: 07/05/2018] [Indexed: 06/08/2023]
Abstract
Research on mosses has provided answers to many fundamental questions in the life sciences, with the model moss Physcomitrella patens spearheading the field. Recent breakthroughs in cell biology were obtained in the quantification of chlorophyll fluorescence, signalling via calcium waves, the creation of designer organelles, gene identification in cellular reprogramming, reproduction via motile sperm and egg cells, asymmetric cell division, visualization of the actin cytoskeleton, identification of genes responsible for the shift from 2D to 3D growth, the structure and importance of the cell wall, and in the live imaging and modelling of protein networks in general. Highly standardized growth conditions, simplicity of most moss tissues, and an outstandingly efficient gene editing facilitate quantitative moss cell biology.
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Affiliation(s)
- Ralf Reski
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany; BIOSS - Centre for Biological Signalling Studies, University of Freiburg, Schänzlestr. 18, 79104 Freiburg, Germany; SGBM - Spemann Graduate School of Biology and Medicine, University of Freiburg, Albertstr. 19A, 79104 Freiburg, Germany; FIT - Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany.
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46
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Kaiserli E, Perrella G, Davidson ML. Light and temperature shape nuclear architecture and gene expression. CURRENT OPINION IN PLANT BIOLOGY 2018; 45:103-111. [PMID: 29909288 PMCID: PMC6250907 DOI: 10.1016/j.pbi.2018.05.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 05/29/2018] [Accepted: 05/31/2018] [Indexed: 05/10/2023]
Abstract
Environmental stimuli play a major role in modulating growth and development throughout the life-cycle of a plant. Quantitative and qualitative variations in light and temperature trigger changes in gene expression that ultimately shape plant morphology for adaptation and survival. Although the phenotypic and transcriptomic basis of plant responses to the constantly changing environment have been examined for decades, the relationship between global changes in nuclear architecture and adaption to environmental stimuli is just being uncovered. This review presents recent discoveries investigating how changes in light and temperature trigger changes in chromatin structure and nuclear organization with a focus on the role of gene repositioning and chromatin accessibility in regulating gene expression.
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Affiliation(s)
- Eirini Kaiserli
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, Bower Building, University of Glasgow, Glasgow G12 8QQ, UK.
| | - Giorgio Perrella
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, Bower Building, University of Glasgow, Glasgow G12 8QQ, UK
| | - Mhairi Lh Davidson
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, Bower Building, University of Glasgow, Glasgow G12 8QQ, UK
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47
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Ovečka M, von Wangenheim D, Tomančák P, Šamajová O, Komis G, Šamaj J. Multiscale imaging of plant development by light-sheet fluorescence microscopy. NATURE PLANTS 2018; 4:639-650. [PMID: 30185982 DOI: 10.1038/s41477-018-0238-2] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 07/31/2018] [Indexed: 05/21/2023]
Abstract
Light-sheet fluorescence microscopy (LSFM) methods collectively represent the major breakthrough in developmental bio-imaging of living multicellular organisms. They are becoming a mainstream approach through the development of both commercial and custom-made LSFM platforms that are adjusted to diverse biological applications. Based on high-speed acquisition rates under conditions of low light exposure and minimal photo-damage of the biological sample, these methods provide ideal means for long-term and in-depth data acquisition during organ imaging at single-cell resolution. The introduction of LSFM methods into biology extended our understanding of pattern formation and developmental progress of multicellular organisms from embryogenesis to adult body. Moreover, LSFM imaging allowed the dynamic visualization of biological processes under almost natural conditions. Here, we review the most important, recent biological applications of LSFM methods in developmental studies of established and emerging plant model species, together with up-to-date methods of data editing and evaluation for modelling of complex biological processes. Recent applications in animal models push LSFM into the forefront of current bio-imaging approaches. Since LSFM is now the single most effective method for fast imaging of multicellular organisms, allowing quantitative analyses of their long-term development, its broader use in plant developmental biology will likely bring new insights.
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Affiliation(s)
- Miroslav Ovečka
- Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University Olomouc, Olomouc, Czech Republic
| | - Daniel von Wangenheim
- Plant Sciences Division, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, UK
| | - Pavel Tomančák
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Olga Šamajová
- Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University Olomouc, Olomouc, Czech Republic
| | - George Komis
- Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University Olomouc, Olomouc, Czech Republic
| | - Jozef Šamaj
- Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University Olomouc, Olomouc, Czech Republic.
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48
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Shahid M, Pinelli E, Dumat C. Tracing trends in plant physiology and biochemistry: Need of databases from genetic to kingdom level. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2018; 127:630-635. [PMID: 29747147 DOI: 10.1016/j.plaphy.2018.04.030] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2018] [Revised: 04/21/2018] [Accepted: 04/23/2018] [Indexed: 05/01/2023]
Abstract
With the rapid advancement in technologies over recent decades, abundant data regarding plant physiological/biochemical responses to stress conditions are now available. Comparing plant stress responses using latest statistical software and analytical models can trace very interesting and useful trends in literature data, which can be of high use for future research and policy making. This model study uses principal component analysis (PCA) to compare physiological/biochemical responses of Vicia faba plant against Pb stress chelated by ethylenediaminetetraacetic acid (EDTA) or citric acid (CA). PCA confirmed the descriptive analysis and divided all the treatments into two main groups: toxic (Pb alone, Pb-CA-a and Pb-CA-b), and non-toxic (control, EDTA-b, CA-b, Pb-EDTA-a and Pb-EDTA-b) treatments. PCA analysis further revealed the effectiveness of different plant physiological/biochemical responses under Pb stress: glutathione reductase (GR) and ascorbate peroxidase (APX) are the main enzymes reacting against Pb toxicity in relation with Pb uptake by V. faba roots, while GR reacts alone in leaves. It is proposed, using latest statistical tests and software, that the comparison and correlation of physiological responses and analytical techniques can be applied at various levels and types of stresses and responses of living organisms to develop a larger dataset based on existing literature. The trends marked out can be correlated with biochemical and physiological processes/mechanisms taking place at genetic-cellular level.
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Affiliation(s)
- Muhammad Shahid
- Department of Environmental Sciences, COMSATS Institute of Information Technology, Vehari, Pakistan.
| | - Eric Pinelli
- Université de Toulouse, INP-ENSAT, Av. de l'Agrobiopôle, 31326 Castanet-Tolosan, France; UMR 5245 CNRS-INP-UPS, EcoLab (Laboratoire d'écologie fonctionnelle), 31326 Castanet-Tolosan, France
| | - Camille Dumat
- Centre d'Etude et de Recherche Travail Organisation Pouvoir (CERTOP), UMR5044, Université J. Jaurès - Toulouse II, 5 Allée Antonio Machado, 31058 Toulouse Cedex 9, France
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Voiniciuc C, Pauly M, Usadel B. Monitoring Polysaccharide Dynamics in the Plant Cell Wall. PLANT PHYSIOLOGY 2018; 176:2590-2600. [PMID: 29487120 PMCID: PMC5884611 DOI: 10.1104/pp.17.01776] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 02/07/2018] [Indexed: 05/18/2023]
Abstract
New technologies reveal the deposition and remodeling of plant cell wall polysaccharides and their impact on plant development.
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Affiliation(s)
- Cătălin Voiniciuc
- Institute for Plant Cell Biology and Biotechnology and Cluster of Excellence on Plant Sciences, Heinrich Heine University, 40225 Duesseldorf, Germany
| | - Markus Pauly
- Institute for Plant Cell Biology and Biotechnology and Cluster of Excellence on Plant Sciences, Heinrich Heine University, 40225 Duesseldorf, Germany
| | - Björn Usadel
- Institute for Biology I, BioSC, RWTH Aachen University, 52074 Aachen, Germany
- Forschungszentum Jülich, IBG-2 Plant Sciences, 52428 Juelich, Germany
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50
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Sinclair R, Rosquete MR, Drakakaki G. Post-Golgi Trafficking and Transport of Cell Wall Components. FRONTIERS IN PLANT SCIENCE 2018; 9:1784. [PMID: 30581448 PMCID: PMC6292943 DOI: 10.3389/fpls.2018.01784] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 11/16/2018] [Indexed: 05/13/2023]
Abstract
The cell wall, a complex macromolecular composite structure surrounding and protecting plant cells, is essential for development, signal transduction, and disease resistance. This structure is also integral to cell expansion, as its tensile resistance is the primary balancing mechanism against internal turgor pressure. Throughout these processes, the biosynthesis, transport, deposition, and assembly of cell wall polymers are tightly regulated. The plant endomembrane system facilitates transport of polysaccharides, polysaccharide biosynthetic and modifying enzymes and glycoproteins through vesicle trafficking pathways. Although a number of enzymes involved in cell wall biosynthesis have been identified, comparatively little is known about the transport of cell wall polysaccharides and glycoproteins by the endomembrane system. This review summarizes our current understanding of trafficking of cell wall components during cell growth and cell division. Emerging technologies, such as vesicle glycomics, are also discussed as promising avenues to gain insights into the trafficking of structural polysaccharides to the apoplast.
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