Sense and sensibility: the use of fluorescent protein-based genetically encoded biosensors in plants

Ion Channels in Electrical Signaling in Higher Plants

Electrical signals (ESs) appearing in plants under the action of various external factors play an important role in adaptation to changing environmental conditions. Generation of ES in higher plant cells is associated with activation of Ca2+, K+, and anion fluxes, as well as with changes in the activity of plasma membrane H+-ATPase. In the present review, molecular nature of the ion channels contributing to ESs transmission in higher plants is analyzed based on comparison of the data from molecular-genetic and electrophysiological studies. Based on such characteristics of ion channels as selectivity, activation mechanism, and intracellular and tissue localization, those ion channels that meet the requirements for potential participation in ES generation were selected from a wide variety of ion channels in higher plants. Analysis of the data of experimental studies performed on mutants with suppressed or enhanced expression of a certain channel gene revealed those channels whose activation contributes to ESs formation. The channels responsible for Ca2+ flux during generation of ESs include channels of the GLR family, for K+ flux - GORK, for anions - MSL. Consideration of the prospects of further studies suggests the need to combine electrophysiological and genetic approaches along with analysis of ion concentrations in intact plants within a single study.

Calcium Signaling in Plant-Insect Interactions

In plant-insect interactions, calcium (Ca²⁺) variations are among the earliest events associated with the plant perception of biotic stress. Upon herbivory, Ca²⁺ waves travel long distances to transmit and convert the local signal to a systemic defense program. Reactive oxygen species (ROS), Ca²⁺ and electrical signaling are interlinked to form a network supporting rapid signal transmission, whereas the Ca²⁺ message is decoded and relayed by Ca²⁺-binding proteins (including calmodulin, Ca²⁺-dependent protein kinases, annexins and calcineurin B-like proteins). Monitoring the generation of Ca²⁺ signals at the whole plant or cell level and their long-distance propagation during biotic interactions requires innovative imaging techniques based on sensitive sensors and using genetically encoded indicators. This review summarizes the recent advances in Ca²⁺ signaling upon herbivory and reviews the most recent Ca²⁺ imaging techniques and methods.

Live Imaging of Abscisic Acid Dynamics Using Genetically Encoded Fluorescence Resonance Energy Transfer (FRET )-Based ABA Biosensors

The phytohormone abscisic acid (ABA) regulates various aspects of plant physiology, growth, and development to maintain a balanced plant water status. Cellular ABA levels are regulated through the combined activities of biosynthesis, catabolism, and transport proteins and depend on the developmental stage, the cell-type and on environmental conditions. Genetically encoded Förster (fluorescence) Resonance Energy Transfer (FRET)-based ABA-responsive biosensors enable the direct monitoring of ABA dynamics in intact plants. Thus, ABA biosensor-based in vivo imaging can provide novel insights about the spatiotemporal patterns of biosynthesis- and transport-dependent ABA dynamics that are required for the regulation of seed dormancy and germination, root growth and hydrotropism, and stomatal closure under water limiting conditions. Here, I describe a protocol for the in vivo analysis of ABA in 5-day-old Arabidopsis seedlings (roots) expressing the FRET-based ABA biosensor ABAleonSD1-3L21.

Optimizing the Protein Fluorescence Reporting System for Somatic Embryogenesis Regeneration Screening and Visual Labeling of Functional Genes in Cotton

Protein fluorescence reporting systems are of crucial importance to in-depth life science research, providing systematic labeling tools for visualization of microscopic biological activities in vivo and revolutionizing basic research. Cotton somatic cell regeneration efficiency is low, causing difficulty in cotton transformation. It is conducive to screening transgenic somatic embryo using the fluorescence reporting system. However, available fluorescence labeling systems in cotton are currently limited. To optimize the fluorescence reporting system of cotton with an expanded range of available fluorescent proteins, we selected 11 fluorescent proteins covering red, green, yellow, and cyan fluorescence colors and expressed them in cotton. Besides mRuby2 and G3GFP, the other nine fluorescent proteins (mCherry, tdTomato, sfGFP, Clover, EYFP, YPet, mVenus, mCerulean, and ECFP) were stably and intensely expressed in transgenic callus and embryo, and inherited in different cotton organs derive from the screened embryo. In addition, transgenic cotton expressing tdTomato appears pink under white light, not only for callus and embryo tissues but also various organs of mature plants, providing a visual marker in the cotton genetic transformation process, accelerating the evaluation of transgenic events. Further, we constructed transgenic cotton expressing mCherry-labeled organelle markers in vivo that cover seven specific subcellular compartments: plasma membrane, endoplasmic reticulum, tonoplast, mitochondrion, plastid, Golgi apparatus, and peroxisome. We also provide a simple and highly efficient strategy to quickly determine the subcellular localization of uncharacterized proteins in cotton cells using organelle markers. Lastly, we built the first cotton stomatal fluorescence reporting system using stomata-specific expression promoters (ProKST1, ProGbSLSP, and ProGC1) to drive Clover expression. The optimized fluorescence labeling system for transgenic somatic embryo screening and functional gene labeling in this study offers the potential to accelerating somatic cell regeneration efficiency and the in vivo monitoring of diverse cellular processes in cotton.

Multiparameter in vivo imaging in plants using genetically encoded fluorescent indicator multiplexing

Biological processes are highly dynamic, and during plant growth, development, and environmental interactions, they occur and influence each other on diverse spatiotemporal scales. Understanding plant physiology on an organismic scale requires analyzing biological processes from various perspectives, down to the cellular and molecular levels. Ideally, such analyses should be conducted on intact and living plant tissues. Fluorescent protein (FP)-based in vivo biosensing using genetically encoded fluorescent indicators (GEFIs) is a state-of-the-art methodology for directly monitoring cellular ion, redox, sugar, hormone, ATP and phosphatidic acid dynamics, and protein kinase activities in plants. The steadily growing number of diverse but technically compatible genetically encoded biosensors, the development of dual-reporting indicators, and recent achievements in plate-reader-based analyses now allow for GEFI multiplexing: the simultaneous recording of multiple GEFIs in a single experiment. This in turn enables in vivo multiparameter analyses: the simultaneous recording of various biological processes in living organisms. Here, we provide an update on currently established direct FP-based biosensors in plants, discuss their functional principles, and highlight important biological findings accomplished by employing various approaches of GEFI-based multiplexing. We also discuss challenges and provide advice for FP-based biosensor analyses in plants.

Unraveling the roles of plant specialized metabolites: using synthetic biology to design molecular biosensors

Plants are a rich source of specialized metabolites with a broad range of bioactivities and many applications in human daily life. Over the past decades significant progress has been made in identifying many such metabolites in different plant species and in elucidating their biosynthetic pathways. However, the biological roles of plant specialized metabolites remain elusive and proposed functions lack an identified underlying molecular mechanism. Understanding the roles of specialized metabolites frequently is hampered by their dynamic production and their specific spatiotemporal accumulation within plant tissues and organs throughout a plant's life cycle. In this review, we propose the employment of strategies from the field of Synthetic Biology to construct and optimize genetically encoded biosensors that can detect individual specialized metabolites in a standardized and high-throughput manner. This will help determine the precise localization of specialized metabolites at the tissue and single-cell levels. Such information will be useful in developing complete system-level models of specialized plant metabolism, which ultimately will demonstrate how the biosynthesis of specialized metabolites is integrated with the core processes of plant growth and development.

Spatiotemporal Quantification of Cytosolic pH in Arabidopsis Pollen Tubes

Ion-specific probes and fluorescent indicators have been key in establishing the role of ion signaling, namely calcium, protons, and anions, in plant development, providing a robust approach for monitoring spatiotemporal changes in intracellular ion dynamics. The integration of protons/pH in signaling mechanisms is especially important as reports of their biological functions continue to expand; however, attaining quantitative estimates with high spatiotemporal resolution in single cells poses a major research challenge. Here, we detail the use of the genetically encoded pH-sensitive pHluorin reporter expressed in Arabidopsis thaliana pollen tubes to assess cytosolic measurements with calibration to provide actual pH values. This technique enabled us to identify critical phenotypes and establish the importance of tip-focused pH gradient for pollen tube growth, although it can be adapted to other experimental systems.

An optimized genetically encoded dual reporter for simultaneous ratio imaging of Ca2+ and H+ reveals new insights into ion signaling in plants

Whereas the role of calcium ions (Ca2+ ) in plant signaling is well studied, the physiological significance of pH-changes remains largely undefined. Here we developed CapHensor, an optimized dual-reporter for simultaneous Ca2+ and pH ratio-imaging and studied signaling events in pollen tubes (PTs), guard cells (GCs), and mesophyll cells (MCs). Monitoring spatio-temporal relationships between membrane voltage, Ca2+ - and pH-dynamics revealed interconnections previously not described. In tobacco PTs, we demonstrated Ca2+ -dynamics lag behind pH-dynamics during oscillatory growth, and pH correlates more with growth than Ca2+ . In GCs, we demonstrated abscisic acid (ABA) to initiate stomatal closure via rapid cytosolic alkalization followed by Ca2+ elevation. Preventing the alkalization blocked GC ABA-responses and even opened stomata in the presence of ABA, disclosing an important pH-dependent GC signaling node. In MCs, a flg22-induced membrane depolarization preceded Ca2+ -increases and cytosolic acidification by c. 2 min, suggesting a Ca2+ /pH-independent early pathogen signaling step. Imaging Ca2+ and pH resolved similar cytosol and nuclear signals and demonstrated flg22, but not ABA and hydrogen peroxide to initiate rapid membrane voltage-, Ca2+ - and pH-responses. We propose close interrelation in Ca2+ - and pH-signaling that is cell type- and stimulus-specific and the pH having crucial roles in regulating PT growth and stomata movement.

Current and future advances in fluorescence-based visualization of plant cell wall components and cell wall biosynthetic machineries

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.

Flow Cytometry and Sorting in Arabidopsis

Flow cytometry and sorting represents a valuable and mature experimental platform for the analysis of cellular populations. Applications involving higher plants started to emerge around 40 years ago and are now widely employed both to provide unique information regarding basic and applied questions in the biosciences and to advance agricultural productivity in practical ways. Further development of this platform is being actively pursued, and this promises additional progress in our understanding of the interactions of cells within complex tissues and organs. Higher plants offer unique challenges in terms of flow cytometric analysis, first since their organs and tissues are, almost without exception, three-dimensional assemblies of different cell types held together by tough cell walls, and, second, because individual plant cells are generally larger than those of mammals.This chapter, which updates work last reviewed in 2014 [Galbraith DW (2014) Flow cytometry and sorting in Arabidopsis. In: Sanchez Serrano JJ, Salinas J (eds) Arabidopsis Protocols, 3rd ed. Methods in molecular biology, vol 1062. Humana Press, Totowa, pp 509-537], describes the application of techniques of flow cytometry and sorting to the model plant species Arabidopsis thaliana, in particular emphasizing (a) fluorescence labeling in vivo of specific cell types and of subcellular components, (b) analysis using both conventional cytometers and spectral analyzers, (c) fluorescence-activated sorting of protoplasts and nuclei, and (d) transcriptome analyses using sorted protoplasts and nuclei, focusing on population analyses at the level of single protoplasts and nuclei. Since this is an update, details of new experimental methods are emphasized.

Long-term live-cell imaging techniques for visualizing pavement cell morphogenesis

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.

Plant Molecular Responses to Potato Virus Y: A Continuum of Outcomes from Sensitivity and Tolerance to Resistance

Potato virus Y (PVY) is the most economically important virus affecting potato production. PVY manipulates the plant cell machinery in order to successfully complete the infecting cycle. On the other side, the plant activates a sophisticated multilayer immune defense response to combat viral infection. The balance between these mechanisms, depending on the plant genotype and environment, results in a specific outcome that can be resistance, sensitivity, or tolerance. In this review, we summarize and compare the current knowledge on molecular events, leading to different phenotypic outcomes in response to PVY and try to link them with the known molecular mechanisms.

The ThSOS3 Gene Improves the Salt Tolerance of Transgenic Tamarix hispida and Arabidopsis thaliana

The salt overly sensitive (SOS) signal transduction pathway is one of the most highly studied salt tolerance pathways in plants. However, the molecular mechanism of the salt stress response in Tamarix hispida has remained largely unclear. In this study, five SOS genes (ThSOS1-ThSOS5) from T. hispida were cloned and characterized. The expression levels of most ThSOS genes significantly changed after NaCl, PEG₆₀₀₀, and abscisic acid (ABA) treatment in at least one organ. Notably, the expression of ThSOS3 was significantly downregulated after 6 h under salt stress. To further analyze ThSOS3 function, ThSOS3 overexpression and RNAi-mediated silencing were performed using a transient transformation system. Compared with controls, ThSOS3-overexpressing transgenic T. hispida plants exhibited greater reactive oxygen species (ROS)-scavenging capability and antioxidant enzyme activity, lower malondialdehyde (MDA) and H₂O₂ levels, and lower electrolyte leakage rates under salt stress. Similar results were obtained for physiological parameters in transgenic Arabidopsis, including H₂O₂ and MDA accumulation, superoxide dismutase (SOD) and peroxidase (POD) activity, and electrolyte leakage. In addition, transgenic Arabidopsis plants overexpressing ThSOS3 displayed increased root growth and fresh weight gain under salt stress. Together, these data suggest that overexpression of ThSOS3 confers salt stress tolerance on plants by enhancing antioxidant enzyme activity, improving ROS-scavenging capability, and decreasing the MDA content and lipid peroxidation of cell membranes. These results suggest that ThSOS3 might play an important physiological role in salt tolerance in transgenic T. hispida plants. This study provides a foundation for further elucidation of salt tolerance mechanisms involving ThSOSs in T. hispida.

Multiparametric real-time sensing of cytosolic physiology links hypoxia responses to mitochondrial electron transport

Hypoxia regularly occurs during plant development and can be induced by the environment through, for example, flooding. To understand how plant tissue physiology responds to progressing oxygen restriction, we aimed to monitor subcellular physiology in real time and in vivo. We establish a fluorescent protein sensor-based system for multiparametric monitoring of dynamic changes in subcellular physiology of living Arabidopsis thaliana leaves and exemplify its applicability for hypoxia stress. By monitoring cytosolic dynamics of magnesium adenosine 5'-triphosphate, free calcium ion concentration, pH, NAD redox status, and glutathione redox status in parallel, linked to transcriptional and metabolic responses, we generate an integrated picture of the physiological response to progressing hypoxia. We show that the physiological changes are surprisingly robust, even when plant carbon status is modified, as achieved by sucrose feeding or extended night. Inhibition of the mitochondrial respiratory chain causes dynamics of cytosolic physiology that are remarkably similar to those under oxygen depletion, highlighting mitochondrial electron transport as a key determinant of the cellular consequences of hypoxia beyond the organelle. A broadly applicable system for parallel in vivo sensing of plant stress physiology is established to map out the physiological context under which both mitochondrial retrograde signalling and low oxygen signalling occur, indicating shared upstream stimuli.

The plant immune system in heterogeneous environments

The plant immune system inhibits pathogen growth and contributes to shaping a healthy microbial community in the plant body. Plants must appropriately respond to both microbial signals and abiotic factors that are diverse in time and space, and thus, proper integration of these inputs at local and systemic levels is of crucial importance for optimal plant responses and fitness in nature. Here, we review our current knowledge of three properties of the plant immune system, resilience, tunability, and balance, which enable plants to deal with complex cocktails of environmental factors. We also discuss future challenges on the path towards a comprehensive understanding of the interactions between plant immunity and pathogenic, non-pathogenic, and beneficial microbes.

Calcineurin B-Like Proteins CBL4 and CBL10 Mediate Two Independent Salt Tolerance Pathways in Arabidopsis

In Arabidopsis, the salt overly sensitive (SOS) pathway, consisting of calcineurin B-like protein 4 (CBL4/SOS3), CBL-interacting protein kinase 24 (CIPK24/SOS2) and SOS1, has been well defined as a crucial mechanism to control cellular ion homoeostasis by extruding Na⁺ to the extracellular space, thus conferring salt tolerance in plants. CBL10 also plays a critical role in salt tolerance possibly by the activation of Na⁺ compartmentation into the vacuole. However, the functional relationship of the SOS and CBL10-regulated processes remains unclear. Here, we analyzed the genetic interaction between CBL4 and CBL10 and found that the cbl4 cbl10 double mutant was dramatically more sensitive to salt as compared to the cbl4 and cbl10 single mutants, suggesting that CBL4 and CBL10 each directs a different salt-tolerance pathway. Furthermore, the cbl4 cbl10 and cipk24 cbl10 double mutants were more sensitive than the cipk24 single mutant, suggesting that CBL10 directs a process involving CIPK24 and other partners different from the SOS pathway. Although the cbl4 cbl10, cipk24 cbl10, and sos1 cbl10 double mutants showed comparable salt-sensitive phenotype to sos1 at the whole plant level, they all accumulated much lower Na⁺ as compared to sos1 under high salt conditions, suggesting that CBL10 regulates additional unknown transport processes that play distinct roles from the SOS1 in Na⁺ homeostasis.

What Drives Symbiotic Calcium Signalling in Legumes? Insights and Challenges of Imaging

We review the contribution of bioimaging in building a coherent understanding of Ca 2 + signalling during legume-bacteria symbiosis. Currently, two different calcium signals are believed to control key steps of the symbiosis: a Ca 2 + gradient at the tip of the legume root hair is involved in the development of an infection thread, while nuclear Ca 2 + oscillations, the hallmark signal of this symbiosis, control the formation of the root nodule, where bacteria fix nitrogen. Additionally, different Ca 2 + spiking signatures have been associated with specific infection stages. Bioimaging is intrinsically a cross-disciplinary area that requires integration of image recording, processing and analysis. We used experimental examples to critically evaluate previously-established conclusions and draw attention to challenges caused by the varying nature of the signal-to-noise ratio in live imaging. We hypothesise that nuclear Ca 2 + spiking is a wide-range signal involving the entire root hair and that the Ca 2 + signature may be related to cytoplasmic streaming.

Evidence That Ion-Based Signaling Initiating at the Cell Surface Can Potentially Influence Chromatin Dynamics and Chromatin-Bound Proteins in the Nucleus

We have developed tools and performed pilot experiments to test the hypothesis that an intracellular ion-based signaling pathway, provoked by an extracellular stimulus acting at the cell surface, can influence interphase chromosome dynamics and chromatin-bound proteins in the nucleus. The experimental system employs chromosome-specific fluorescent tags and the genome-encoded fluorescent pH sensor SEpHluorinA227D, which has been targeted to various intracellular membranes and soluble compartments in root cells of Arabidopsis thaliana. We are using this system and three-dimensional live cell imaging to visualize whether fluorescent-tagged interphase chromosome sites undergo changes in constrained motion concurrently with reductions in membrane-associated pH elicited by extracellular ATP, which is known to trigger a cascade of events in plant cells including changes in calcium ion concentrations, pH, and membrane potential. To examine possible effects of the proposed ion-based signaling pathway directly at the chromatin level, we generated a pH-sensitive fluorescent DNA-binding protein that allows pH changes to be monitored at specific genomic sites. Results obtained using these tools support the existence of a rapid, ion-based signaling pathway that initiates at the cell surface and reaches the nucleus to induce alterations in interphase chromatin mobility and the surrounding pH of chromatin-bound proteins. Such a pathway could conceivably act under natural circumstances to allow external stimuli to swiftly influence gene expression by affecting interphase chromosome movement and the structures and/or activities of chromatin-associated proteins.

Seeing is better than believing: visualization of membrane transport in plants

Recently, the plant transport field has shifted their research focus toward a more integrative investigation of transport networks thought to provide the basis for long-range transport routes. Substantial progress was provided by of a series of elegant techniques that allow for a visualization or prediction of substrate movements in plant tissues in contrast to established quantitative methods offering low spatial resolution. These methods are critically evaluated in respect to their spatio-temporal resolution, invasiveness, dynamics and overall quality. Current limitations of transport route predictions-based on transporter locations and transport modeling are addressed. Finally, the potential of new tools that have not yet been fully implemented into plant research is indicated.