In vivo biochemistry: applications for small molecule biosensors in plant biology

Quantifying Plant Signaling Pathways by Integrating Luminescence-Based Biosensors and Mathematical Modeling

Plants have evolved intricate signaling pathways, which operate as networks governed by feedback to deal with stressors. Nevertheless, the sophisticated molecular mechanisms underlying these routes still need to be comprehended, and experimental validation poses significant challenges and expenses. Consequently, computational hypothesis evaluation gains prominence in understanding plant signaling dynamics. Biosensors are genetically modified to emit light when exposed to a particular hormone, such as abscisic acid (ABA), enabling quantification. We developed computational models to simulate the relationship between ABA concentrations and bioluminescent sensors utilizing the Hill equation and ordinary differential equations (ODEs), aiding better hypothesis development regarding plant signaling. Based on simulation results, the luminescence intensity was recorded for a concentration of 47.646 RLUs for 1.5 μmol, given the specified parameters and model assumptions. This method enhances our understanding of plant signaling pathways at the cellular level, offering significant benefits to the scientific community in a cost-effective manner. The alignment of these computational predictions with experimental results emphasizes the robustness of our approach, providing a cost-effective means to validate mathematical models empirically. The research intended to correlate the bioluminescence of biosensors with plant signaling and its mathematical models for quantified detection of specific plant hormone ABA.

Fluorescent proteins and genetically encoded biosensors

The genetically encoded fluorescent sensors convert chemical and physical signals into light. They are powerful tools for the visualisation of physiological processes in living cells and freely moving animals. The fluorescent protein is the reporter module of a genetically encoded biosensor. In this study, we first review the history of the fluorescent protein in full emission spectra on a structural basis. Then, we discuss the design of the genetically encoded biosensor. Finally, we briefly review several major types of genetically encoded biosensors that are currently widely used based on their design and molecular targets, which may be useful for the future design of fluorescent biosensors.

In vivo visualization of nitrate dynamics using a genetically encoded fluorescent biosensor

Nitrate (NO₃^-) uptake and distribution are critical to plant life. Although the upstream regulation of NO₃^- uptake and downstream responses to NO₃^- in a variety of cells have been well studied, it is still not possible to directly visualize the spatial and temporal distribution of NO₃^- with high resolution at the cellular level. Here, we report a nuclear-localized, genetically encoded fluorescent biosensor, which we named NitraMeter3.0, for the quantitative visualization of NO₃^- distribution in Arabidopsis thaliana. This biosensor tracked the spatiotemporal distribution of NO₃^- along the primary root axis and disruptions by genetic mutation of transport (low NO₃^- uptake) and assimilation (high NO₃^- accumulation). The developed biosensor effectively monitors NO₃^- concentrations at the cellular level in real time and spatiotemporal changes during the plant life cycle.

Nanosensor Applications in Plant Science

Plant science is a major research topic addressing some of the most important global challenges we face today, including energy and food security. Plant science has a role in the production of staple foods and materials, as well as roles in genetics research, environmental management, and the synthesis of high-value compounds such as pharmaceuticals or raw materials for energy production. Nanosensors-selective transducers with a characteristic dimension that is nanometre in scale-have emerged as important tools for monitoring biological processes such as plant signalling pathways and metabolism in ways that are non-destructive, minimally invasive, and capable of real-time analysis. A variety of nanosensors have been used to study different biological processes; for example, optical nanosensors based on Förster resonance energy transfer (FRET) have been used to study protein interactions, cell contents, and biophysical parameters, and electrochemical nanosensors have been used to detect redox reactions in plants. Nanosensor applications in plants include nutrient determination, disease assessment, and the detection of proteins, hormones, and other biological substances. The combination of nanosensor technology and plant sciences has the potential to be a powerful alliance and could support the successful delivery of the 2030 Sustainable Development Goals. However, a lack of knowledge regarding the health effects of nanomaterials and the high costs of some of the raw materials required has lessened their commercial impact.

Concept of Fluorescent Transport Activity Biosensor for the Characterization of the Arabidopsis NPF1.3 Activity of Nitrate

The NRT1/PTR FAMILY (NPF) in Arabidopsis (Arabidopsis thaliana) plays a major role as a nitrate transporter. The first nitrate transporter activity biosensor NiTrac1 converted the dual-affinity nitrate transceptor NPF6.3 into fluorescence activity sensors. To test whether this approach is transferable to other members of this family, screening for genetically encoded fluorescence transport activity sensor was performed with the member of the NPF family in Arabidopsis. In this study, NPF1.3, an uncharacterized member of NPF in Arabidopsis, was converted into a transporter activity biosensor NiTrac-NPF1.3 that responds specifically to nitrate. The emission ratio change of NiTrac-NPF1.3 triggered by the addition of nitrate reveals the important function of NPF1.3 in nitrate transport in Arabidopsis. A functional analysis of Xenopus laevis oocytes confirmed that NPF1.3 plays a role as a nitrate transporter. This new technology is applicable in plant and medical research.

Integration of nutrient and water availabilities via auxin into the root developmental program

In most soils, the spatial distribution of nutrients and water in the rooting zone of plants is heterogeneous and changes over time. To access localized resources more efficiently, plants induce foraging responses by modulating individual morphological root traits, such as the length of the primary root or the number and length of lateral roots. These adaptive responses require the integration of exogenous and endogenous nutrient- or water-related signals into the root developmental program. Recent studies corroborated a central role of auxin in shaping root architectural traits in response to fluctuating nutrient and water availabilities. In this review, we highlight current knowledge on nutrient- and water-related developmental processes that impact root foraging and involve auxin as a central player. A deeper understanding and exploitation of these auxin-related processes and mechanisms promises advances in crop breeding for higher resource efficiency.

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.

Review: The Next Steps in Crop Improvement: Adoption of Emerging Strategies to Identify Bottlenecks in Sugar Flux

Sugar allocation in plants is the fundamental process that transports sugar from source to sink tissues and has a dramatic impact on crop yields. Controlling sugar allocation is required to increase crop yields, as well as biomass for biofuel production. Successful examples have demonstrated that genetic engineering of sugar partitioning offers a promising strategy to achieve this goal. However, improvement has thus far been limited by gaps in understanding of the underlying mechanisms controlling the allocation of sugars. The dynamics of sugar partitioning are minimally predictable under different conditions, between species, or in response to abiotic stresses. Here, we discuss four methodologies that have not been sufficiently exploited for the identification of bottlenecks in sugar flux. Furthermore, we suggest how these strategies can be used and combined to provide the insight needed to maximize crop yields or biomass, especially under conditions of environmental stress.

Enhancement of Probe Density in DNA Sensing by Tuning the Exponential Growth Regime of Polyelectrolyte Multilayers

Surface-based biosensing devices benefit from a dedicated design of the probe layer present at the transducing interface. The layer architecture, its physicochemical properties, and the embedding of the receptor sites affect the probability of binding the analyte. Here, the enhancement of the probe density at the sensing interface by tuning the exponential growth regime of polyelectrolyte multilayers (PEMs) is presented. PEMs were made of poly-l-lysine (PLL), with appended clickable dibenzocyclooctyne (DBCO) groups and oligo(ethylene glycol) chains, and poly(styrene sulfonate) (PSS). The DNA probe loading and target hybridization efficiencies of the PEMs were evaluated as a function of the PLL layer number and the growth regime by a quartz crystal microbalance (QCM). An amplification factor of 25 in the target DNA detection was found for a 33-layer exponentially grown PEM compared to a monolayer. A Voigt-based model showed that DNA probe binding to the DBCO groups is more efficient in the open, exponentially grown films, while the hybridization efficiencies appeared to be high for all layer architectures. These results show the potential of such engineered gel-like structures to increase the detection of bio-relevant analytes in biosensing systems.

Imaging of the Lactate/Pyruvate Ratio Using a Genetically Encoded Förster Resonance Energy Transfer Indicator

The ratio between the cytosolic concentrations of lactate and pyruvate is a direct readout of the balance between glycolysis and mitochondrial oxidative metabolism. Current approaches do not allow detection of the lactate/pyruvate ratio in a single readout with high spatial/temporal resolution in living systems. Using a Förster resonance energy transfer (FRET)-based screening strategy, we found that the orphan transcriptional factor LutR from Bacillus licheniformis is an endogenous sensor of the lactate/pyruvate ratio, suitable for use as a binding moiety to develop a lactate/pyruvate ratio FRET-based genetically encoded indicator, Lapronic. The sensitivity of the indicator to lactate and pyruvate was characterized through changes in the fluorescence FRET ratio and validated with isothermal titration calorimetry. Lapronic was insensitive to physiological pH and temperature and did not respond to structurally related molecules acetate and β-hydroxybutyrate or cofactors NAD⁺ and NADH. Lapronic was expressed in HEK 293 cells showing a homogeneous cytosolic localization and was also targeted to the mitochondrial matrix. A calibration protocol was designed to quantitatively assess the lactate/pyruvate ratio in intact mammalian cells. Purified protein from Escherichia coli showed robust stability over time and was found suitable for lactate/pyruvate ratio detection in biological samples. We envision that Lapronic will be of practical interest for basic and applied research.

FRET kinase sensor development reveals SnRK2/OST1 activation by ABA but not by MeJA and high CO2 during stomatal closure

Sucrose-non-fermenting-1-related protein kinase-2s (SnRK2s) are critical for plant abiotic stress responses, including abscisic acid (ABA) signaling. Here, we develop a genetically encoded reporter for SnRK2 kinase activity. This sensor, named SNACS, shows an increase in the ratio of yellow to cyan fluorescence emission by OST1/SnRK2.6-mediated phosphorylation of a defined serine residue in SNACS. ABA rapidly increases FRET efficiency in N. benthamiana leaf cells and Arabidopsis guard cells. Interestingly, protein kinase inhibition decreases FRET efficiency in guard cells, providing direct experimental evidence that basal SnRK2 activity prevails in guard cells. Moreover, in contrast to ABA, the stomatal closing stimuli, elevated CO2 and MeJA, did not increase SNACS FRET ratios. These findings and gas exchange analyses of quintuple/sextuple ABA receptor mutants show that stomatal CO2 signaling requires basal ABA and SnRK2 signaling, but not SnRK2 activation. A recent model that CO2 signaling is mediated by PYL4/PYL5 ABA-receptors could not be supported here in two independent labs. We report a potent approach for real-time live-cell investigations of stress signaling.

Imaging Mitochondrial Functions: from Fluorescent Dyes to Genetically-Encoded Sensors

Mitochondria are multifunctional organelles that are crucial to cell homeostasis. They constitute the major site of energy production for the cell, they are key players in signalling pathways using secondary messengers such as calcium, and they are involved in cell death and redox balance paradigms. Mitochondria quickly adapt their dynamics and biogenesis rates to meet the varying energy demands of the cells, both in normal and in pathological conditions. Therefore, understanding simultaneous changes in mitochondrial functions is crucial in developing mitochondria-based therapy options for complex pathological conditions such as cancer, neurological disorders, and metabolic syndromes. To this end, fluorescence microscopy coupled to live imaging represents a promising strategy to track these changes in real time. In this review, we will first describe the commonly available tools to follow three key mitochondrial functions using fluorescence microscopy: Calcium signalling, mitochondrial dynamics, and mitophagy. Then, we will focus on how the development of genetically-encoded fluorescent sensors became a milestone for the understanding of these mitochondrial functions. In particular, we will show how these tools allowed researchers to address several biochemical activities in living cells, and with high spatiotemporal resolution. With the ultimate goal of tracking multiple mitochondrial functions simultaneously, we will conclude by presenting future perspectives for the development of novel genetically-encoded fluorescent biosensors.

"Second-generation" fluorogenic RNA-based sensors

A fluorogenic aptamer can specifically interact with a fluorophore to activate its fluorescence. These nucleic acid-based fluorogenic modules have been dramatically developed over the past decade, and have been used as versatile reporters in the sensor development and for intracellular imaging. In this review, we summarize the design principles, applications, and challenges of the first-generation fluorogenic RNA-based sensors. Moreover, we discuss some strategies to develop next-generation biosensors with improved sensitivity, selectivity, quantification property, and eukaryotic robustness. Using genetically encoded catalytic hairpin assembly strategy as an example, we further introduce a standard protocol to design, characterize, and apply these fluorogenic RNA-based sensors for in vitro detection and cellular imaging of target biomolecules. By incorporating natural RNA machineries, nucleic acid nanotechnology, and systematic evolution approaches, next-generation fluorogenic RNA-based devices can be potentially engineered to be widely applied in cell biology and biomedicine.

Sugar Partitioning between Ustilago maydis and Its Host Zea mays L during Infection

The basidiomycete Ustilago maydis causes smut disease in maize (Zea mays) by infecting all plant aerial tissues. The infection causes leaf chlorosis and stimulates the plant to produce nutrient-rich niches (i.e. tumors), where the fungus can proliferate and complete its life cycle. Previous studies have recorded high accumulation of soluble sugars and starch within these tumors. Using interdisciplinary approaches, we found that the sugar accumulation within tumors coincided with the differential expression of plant sugars will eventually be exported transporters and the proton/sucrose symporter Sucrose Transporter1 To accumulate plant sugars, the fungus deploys its own set of sugar transporters, generating a sugar gradient within the fungal cytosol, recorded by expressing a cytosolic glucose (Glc) Förster resonance energy transfer sensor. Our measurements indicated likely elevated Glc levels in hyphal tips during infection. Growing infected plants under dark conditions led to decreased plant sugar levels and loss of the fungal tip Glc gradient, supporting a tight link between fungal sugar acquisition and host supplies. Finally, the fungal infection causes a strong imbalance in plant sugar distribution, ultimately impacting seed set and yield.

Consequences of Heterogeneous Crowding on an Enzymatic Reaction: A Residence Time Monte Carlo Approach

Translational diffusion of a free substrate in crowded metabolically active spaces such as cell cytoplasm or mitochondrial matrix is punctuated by collisions and nonspecific interactions with soluble/immobile macromolecules/macrostructures in a variety of shapes/sizes. It is not understood how such disruptions alter enzyme reaction kinetics in such spaces. A novel Monte Carlo (MC) technique, "residence time MC", has been developed to study the kinetics of a simple enzyme-substrate reaction in a crowded milieu using a single immobile enzyme in the midst of diffusing substrates and products. The reaction time lost while the substrate nonspecifically interacts or is transiently trapped with ambient macromolecules is quantified by introducing the residence time "tau". Tau scales with the size of crowding macromolecules but makes the knowledge of their shape redundant. The residence time thus presents a convenient parameter to realistically mimic the sticky surroundings encountered by a diffusing substrate in heterogeneously crowded physiological spaces. Results reveal that for identical substrate concentration and excluded volume, increase in tau significantly diminished enzymatic product yield and reaction rate, slowed down substrate/product diffusion, and prolonged their relaxation times. A smooth transition from the anomalous subdiffusive motion to normal diffusion at long time limits was observed irrespective of the value of tau. The predictions from the model are shown to be in qualitative agreement with in vitro experimental data revealing the rate of alkaline phosphatase-catalyzed hydrolysis of p-nitrophenyl phosphate in the midst of 40/500/2000 kDa dextrans. Our findings from the residence time MC model also attempt to rationalize previously unexplained experimental observations in crowded enzyme kinetics literature. Furthermore, major insights to emerge from this study are the reasons why free diffusion of the substrate in crowded physiological spaces is detrimental to enzyme function. It is argued that organized enzyme clusters such as "metabolon" may perhaps exist to regulate the substrate translocation in such sticky physiological spaces to maintain optimal enzyme function. In summary, this work provides key insights explaining why absence of substrate channeling can dramatically slow down enzyme reaction rate in crowded metabolically active spaces.

Plant Nanobionics: Application of Nanobiosensors in Plant Biology

Nanobiosensors (NBSs) are a class of chemical sensors which are sensitive to a physical or chemical stimulus (heat, acidity, metabolism transformations) that conveys information about vital processes. NBSs detect physiological signals and convert them into standardized signals, often electrical, to be quantified from analog to digital. NBSs are classified according to the transducer element (electrochemical, piezoelectric, optical, and thermal) in accordance with biorecognition principle (enzyme recognition, affinity immunoassay, whole sensors, DNA). NBSs have varied forms, depending on the degree of interpretation of natural processes in plants. Plant nanobionics uses mathematical models based on qualitative and less quantitative records. NBSs can give information about endogenous concentrations or endogenous fluxes of signaling molecules (phytohormones). The properties of NBSs are temporal and spatial resolution, the ability of being used without significantly interfering with the system. NBSs with the best properties are the optically genetically coded NBSs, but each NBS needs specific development efforts. NBS technologies using antibodies as a recognition domain are generic and tend to be more invasive, and there are examples of their use in plant nanobionics. Through opportunities that develop along with technologies, we hope that more and more NBSs will become available for plant nanobionics. The main advantages of NBSs are short analysis time, low-cost tests and portability, real-time measurements, and remote control.

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.

An in Vivo Imaging Assay Detects Spatial Variability in Glucose Release from Plant Roots

Plants secrete a plethora of metabolites into the rhizosphere that allow them to obtain nutrients necessary for growth and modify microbial communities around the roots. Plants release considerable amounts of photosynthetically fixed carbon into the rhizosphere; hence, it is important to understand how carbon moves from the roots into the rhizosphere. Approaches used previously to address this question involved radioactive tracers, fluorescent probes, and biosensors to study sugar movement in the roots and into the rhizosphere. Although quite effective for studying sugar movement, it has been challenging to obtain data on spatial and temporal variability in sugar exudation using these techniques. In this study, we developed a gel-based enzyme-coupled colorimetric and fluorometric assay to image glucose (Glc) in vivo and used this assay to show that there is spatial variability in Glc release from plant roots. We found that the primary roots of maize (Zea mays) released more Glc from the base of the root than from the root tip and that the Glc release rate is reduced in response to water stress. These findings were confirmed independently by quantifying Glc release in well-watered and water-stressed maize primary roots using high-performance anion-exchange chromatography. Additionally, we demonstrated differential patterns of Glc exudation in different monocot and eudicot plant species. These findings and their implications on root-rhizosphere interactions are discussed.

On the Promising Role of Enzyme Activity Assay in Interpreting Comparative Proteomic Data in Plants

Comparative proteomics is widely used to detect protein changes, especially differential abundance proteins (DAPs) that are involved in plant responses to development, disease, or environment. Once DAPs are identified, it is essential to validate any change in their abundance, and their role in the biological process under study. In addition to common confirmation by quantitative RT-PCR, immunoblot, and multiple reaction monitoring analysis, it has been proposed that enzyme activity assay (EAA) can be complementary to the standard proteomics results, especially regarding the elucidation of protein (enzyme) function and the mechanism of enzyme-associated biochemical or metabolic pathways. The enzymes discussed here are the DAPs identified in comparative plant proteomics. Despite the small number of enzymes in a proteome, they often make up a substantial proportion of the DAPs identified in comparative studies. Currently, only a few studies have performed EAA to complement the interpretation of proteomic data, especially activity-based protein profiling. This viewpoint aims to arouse the attention of proteomic researchers on the promising role of EAA in plant proteomics and highlights the need for high-throughput assays of enzyme activities in comparative plant proteomics.

Dual-flow-RootChip reveals local adaptations of roots towards environmental asymmetry at the physiological and genetic levels

Roots grow in highly dynamic and heterogeneous environments. Biological activity as well as uneven nutrient availability or localized stress factors result in diverse microenvironments. Plants adapt their root morphology in response to changing environmental conditions, yet it remains largely unknown to what extent developmental adaptations are based on systemic or cell-autonomous responses. We present the dual-flow-RootChip, a microfluidic platform for asymmetric perfusion of Arabidopsis roots to investigate root-environment interactions under simulated environmental heterogeneity. Applications range from investigating physiology, root hair development and calcium signalling upon selective exposure to environmental stresses to tracing molecular uptake, performing selective drug treatments and localized inoculations with microbes. Using the dual-flow-RootChip, we revealed cell-autonomous adaption of root hair development under asymmetric phosphate (Pi) perfusion, with unexpected repression in root hair growth on the side exposed to low Pi and rapid tip-growth upregulation when Pi concentrations increased. The asymmetric root environment further resulted in an asymmetric gene expression of RSL4, a key transcriptional regulator of root hair growth. Our findings demonstrate that roots possess the capability to locally adapt to heterogeneous conditions in their environment at the physiological and transcriptional levels. Being able to generate asymmetric microenvironments for roots will help further elucidate decision-making processes in root-environment interactions.

Transitioning to the Next Phase: The Role of Sugar Signaling throughout the Plant Life Cycle

Developmental transitions depend on the availability of sufficient carbon resources, which is sensed by sugar signaling pathways for high and low carbon availability.

In vivo gibberellin gradients visualized in rapidly elongating tissues

The phytohormone gibberellin (GA) is a key regulator of plant growth and development. Although the upstream regulation and downstream responses to GA vary across cells and tissues, developmental stages and environmental conditions, the spatiotemporal distribution of GA in vivo remains unclear. Using a combinatorial screen in yeast, we engineered an optogenetic biosensor, GIBBERELLIN PERCEPTION SENSOR 1 (GPS1), that senses nanomolar levels of bioactive GAs. Arabidopsis thaliana plants expressing a nuclear localized GPS1 report on GAs at the cellular level. GA gradients were correlated with gradients of cell length in rapidly elongating roots and dark-grown hypocotyls. In roots, accumulation of exogenously applied GA also correlated with cell length, intimating that a root GA gradient can be established independently of GA biosynthesis. In hypocotyls, GA levels were reduced in a phytochrome interacting factor (pif) quadruple mutant in the dark and increased in a phytochrome double mutant in the light, indicating that PIFs elevate GA in the dark and that phytochrome inhibition of PIFs could lower GA in the light. As GA signalling directs hypocotyl elongation largely through promoting PIF activity, PIF promotion of GA accumulation represents a positive feedback loop within the molecular framework driving rapid hypocotyl growth.

Quantitatively Understanding Plant Signaling: Novel Theoretical-Experimental Approaches

With the need to respond to and integrate a multitude of external and internal stimuli, plant signaling is highly complex, exhibiting signaling component redundancy and high interconnectedness between individual pathways. We review here novel theoretical-experimental approaches in manipulating plant signaling towards the goal of a comprehensive understanding and targeted quantitative control of plant processes. We highlight approaches taken in the field of synthetic biology used in other systems and discuss their applicability in plants. Finally, we introduce existing tools for the quantitative analysis and monitoring of plant signaling and the integration of experimentally obtained quantitative data into mathematical models. Incorporating principles of synthetic biology into plant sciences more widely will lead this field forward in both fundamental and applied research.

Advances in methods for identification and characterization of plant transporter function

Transport proteins are crucial for cellular function at all levels. Numerous importers and exporters facilitate transport of a diverse array of metabolites and ions intra- and intercellularly. Identification of transporter function is essential for understanding biological processes at both the cellular and organismal level. Assignment of a functional role to individual transporter proteins or to identify a transporter with a given substrate specificity has notoriously been challenging. Recently, major advances have been achieved in function-driven screens, phenotype-driven screens, and in silico-based approaches. In this review, we highlight examples that illustrate how new technology and tools have advanced identification and characterization of plant transporter functions.

PII Protein-Derived FRET Sensors for Quantification and Live-Cell Imaging of 2-Oxoglutarate

The citric acid cycle intermediate 2-oxoglutarate (2-OG, a.k.a. alpha-ketoglutarate) links the carbon and nitrogen metabolic pathways and can provide information on the metabolic status of cells. In recent years, it has become exceedingly clear that 2-OG also acts as a master regulator of diverse biologic processes in all domains of life. Consequently, there is a great demand for time-resolved data on 2-OG fluctuations that can’t be adequately addressed using established methods like mass spectrometry-based metabolomics analysis. Therefore, we set out to develop a novel intramolecular 2-OG FRET sensor based on the signal transduction protein P_II from Synechococcus elongatus PCC 7942. We created two variants of the sensor, with a dynamic range for 2-OG from 0.1 µM to 0.1 mM or from 10 µM to 10 mM. As proof of concept, we applied the sensors to determine in situ glutamine:2-oxoglutarate aminotransferase (GOGAT) activity in Synechococcus elongatus PCC 7942 cells and measured 2-OG concentrations in cell extracts from Escherichia coli in vitro. Finally, we could show the sensors’ functionality in living human cell lines, demonstrating their potential in the context of mechanistic studies and drug screening.

Effective antibodies immobilization and functionalized nanoparticles in a quartz-crystal microbalance-based immunosensor for the detection of parathion

BACKGROUND

Biosensor-based detection provides a rapid and low-cost alternative to conventional analytical methods for revealing the presence of the contaminants in water as well as solid matrices. Although important to be detected, small analytes (few hundreds of Daltons) are an issue in biosensing since the signal they induce in the transducer, and specifically in a Quartz-Crystal Microbalance, is undetectable. A pesticide like parathion (M = 292 Da) is a typical example of contaminant for which a signal amplification procedure is desirable.

METHODS/FINDINGS

The ballasting of the analyte by gold nanoparticles has been already applied to heavy target as proteins or bacteria to improve the limit of detection. In this paper, we extend the application of such a method to small analytes by showing that once the working surface of a Quartz-Crystal Microbalance (QCM) has been properly functionalized, a limit of detection lower than 1 ppb is reached for parathion. The effective surface functionalization is achieved by immobilizing antibodies upright oriented on the QCM gold surface by a simple photochemical technique (Photonic Immobilization Technique, PIT) based on the UV irradiation of the antibodies, whereas a simple protocol provided by the manufacturer is applied to functionalize the gold nanoparticles. Thus, in a non-competitive approach, the small analyte is made detectable by weighing it down through a "sandwich protocol" with a second antibody tethered to heavy gold nanoparticles. The immunosensor has been proved to be effective against the parathion while showing no cross reaction when a mixture of compounds very similar to parathion is analyzed.

CONCLUSION/SIGNIFICANCE

The immunosensor described in this paper can be easily applied to any small molecule for which polyclonal antibodies are available since both the functionalization procedure of the QCM probe surface and gold nanoparticle can be applied to any IgG, thereby making our device of general application in terms of target analyte.

Increasing Nitrogen Fixation and Seed Development in Soybean Requires Complex Adjustments of Nodule Nitrogen Metabolism and Partitioning Processes

Legumes are able to access atmospheric di-nitrogen (N2) through a symbiotic relationship with rhizobia that reside within root nodules. In soybean, following N2 fixation by the bacteroids, ammonia is finally reduced in uninfected cells to allantoin and allantoic acid [1]. These ureides present the primary long-distance transport forms of nitrogen (N), and are exported from nodules via the xylem for shoot N supply. Transport of allantoin and allantoic acid out of nodules requires the function of ureide permeases (UPS1) located in cells adjacent to the vasculature [2, 3]. We expressed a common bean UPS1 transporter in cortex and endodermis cells of soybean nodules and found that delivery of N from nodules to shoot, as well as seed set, was significantly increased. In addition, the number of transgenic nodules was increased and symbiotic N2 fixation per nodule was elevated, indicating that transporter function in nodule N export is a limiting step in bacterial N acquisition. Further, the transgenic nodules showed considerable increases in nodule N assimilation, ureide synthesis, and metabolite levels. This suggests complex adjustments of nodule N metabolism and partitioning processes in support of symbiotic N2 fixation. We propose that the transgenic UPS1 plants display metabolic and allocation plasticity to overcome N2 fixation and seed yield limitations. Overall, it is demonstrated that transporter function in N export from nodules is a key step for enhancing atmospheric N2 fixation and nodule function and for improving shoot N nutrition and seed development in legumes.

Biosensors and their applications - A review

The various types of biosensors such as enzyme-based, tissue-based, immunosensors, DNA biosensors, thermal and piezoelectric biosensors have been deliberated here to highlight their indispensable applications in multitudinous fields. Some of the popular fields implementing the use of biosensors are food industry to keep a check on its quality and safety, to help distinguish between the natural and artificial; in the fermentation industry and in the saccharification process to detect precise glucose concentrations; in metabolic engineering to enable in vivo monitoring of cellular metabolism. Biosensors and their role in medical science including early stage detection of human interleukin-10 causing heart diseases, rapid detection of human papilloma virus, etc. are important aspects. Fluorescent biosensors play a vital role in drug discovery and in cancer. Biosensor applications are prevalent in the plant biology sector to find out the missing links required in metabolic processes. Other applications are involved in defence, clinical sector, and for marine applications.

Quantitative Imaging of FRET-Based Biosensors for Cell- and Organelle-Specific Analyses in Plants

Genetically encoded Förster resonance energy transfer (FRET)-based biosensors have been used to report relative concentrations of ions and small molecules, as well as changes in protein conformation, posttranslational modifications, and protein-protein interactions. Changes in FRET are typically quantified through ratiometric analysis of fluorescence intensities. Here we describe methods to evaluate ratiometric imaging data acquired through confocal microscopy of a FRET-based inorganic phosphate biosensor in different cells and subcellular compartments of Arabidopsis thaliana. Linear regression was applied to donor, acceptor, and FRET-derived acceptor fluorescence intensities obtained from images of multiple plants to estimate FRET ratios and associated location-specific spectral correction factors with high precision. FRET/donor ratios provided a combination of high dynamic range and precision for this biosensor when applied to the cytosol of both root and leaf cells, but lower precision when this ratiometric method was applied to chloroplasts. We attribute this effect to quenching of donor fluorescence because high precision was achieved with FRET/acceptor ratios and thus is the preferred ratiometric method for this organelle. A ligand-insensitive biosensor was also used to distinguish nonspecific changes in FRET ratios. These studies provide a useful guide for conducting quantitative ratiometric studies in live plants that is applicable to any FRET-based biosensor.

Shoot-root carbon allocation, sugar signalling and their coupling with nitrogen uptake and assimilation

Roots and shoots are distantly located but functionally interdependent. The growth and development of these two organ systems compete for energy and nutrient resource, and yet, they keep a dynamic balance with each other for growth and development. The success of such a relationship depends on efficient root-shoot communication. Aside from the well-known signalling processes mediated by hormones such as auxin and cytokinin, sugars have recently been shown to act as a rapid signal to co-ordinate root and shoot development in response to endogenous and exogenous clues, in parallel to their function as carbon and energy resources for biomass production. New findings from studies on vascular fluids have provided molecular insights into the role of sugars in long-distance communications between shoot and root. In this review, we discussed phloem- and xylem- translocation of sugars and the impacts of sugar allocation and signalling on balancing root-shoot development. Also, we have taken the shoot-root carbon-nitrogen allocation as an example to illustrate the communication between the two organs through multi-layer root-shoot-root signalling circuits, comprising sugar, nitrogen, cytokinin, auxin and vascular small peptide signals.

The biosensor toolbox for plant developmental biology

Plant development is highly interconnected with the metabolic state of tissues and cells. Current research efforts focus on the identification of the links and mechanisms that govern the interplay between metabolic and gene-regulatory networks. Genetically encoded sensors that allow detection of small molecules in vivo and at high spatio-temporal resolution promise to be the tools of choice for quantifying and visualizing the dynamics of metabolite flux in plants. We provide an overview about current approaches to measure signaling molecules, such as hormones, calcium and sugars, as well as for monitoring the metabolic state via energy equivalents and pH. Biosensors show great potential to address questions of plant development but there are also limitations where alternative approaches are needed.

The Arabidopsis vacuolar sugar transporter SWEET2 limits carbon sequestration from roots and restricts Pythium infection

Plant roots secrete a significant portion of their assimilated carbon into the rhizosphere. The putative sugar transporter SWEET2 is highly expressed in Arabidopsis roots. Expression patterns of SWEET2-β-glucuronidase fusions confirmed that SWEET2 accumulates highly in root cells and thus may contribute to sugar secretion, specifically from epidermal cells of the root apex. SWEET2-green fluorescent protein fusions localized to the tonoplast, which engulfs the major sugar storage compartment. Functional analysis of SWEET2 activity in yeast showed low uptake activity for the glucose analog 2-deoxyglucose, consistent with a role in the transport of glucose across the tonoplast. Loss-of-function sweet2 mutants showed reduced tolerance to excess glucose, lower glucose accumulation in leaves, and 15-25% higher glucose-derived carbon efflux from roots, suggesting that SWEET2 has a role in preventing the loss of sugar from root tissue. SWEET2 root expression was induced more than 10-fold during Pythium infection. Importantly, sweet2 mutants were more susceptible to the oomycete, showing impaired growth after infection. We propose that root-expressed vacuolar SWEET2 modulates sugar secretion, possibly by reducing the availability of glucose sequestered in the vacuole, thereby limiting carbon loss to the rhizosphere. Moreover, the reduced availability of sugar in the rhizosphere due to SWEET2 activity contributes to resistance to Pythium.

Binary 2in1 Vectors Improve in Planta (Co)localization and Dynamic Protein Interaction Studies

Fluorescence-based protein-protein interaction techniques are vital tools for understanding in vivo cellular functions on a mechanistic level. However, only under the condition of highly efficient (co)transformation and accumulation can techniques such as Förster resonance energy transfer (FRET) realize their potential for providing highly accurate and quantitative interaction data. FRET as a fluorescence-based method unifies several advantages, such as measuring in an in vivo environment, real-time context, and the ability to include transient interactions as well as detecting the mere proximity of proteins. Here, we introduce a novel vector set that incorporates the benefit of the recombination-based 2in1 cloning system with the latest state-of-the-art fluorescent proteins for optimal coaccumulation and FRET output studies. We demonstrate its utility across a range of methods. Merging the 2in1 cloning system with new-generation FRET fluorophore pairs allows for enhanced detection, speeds up the preparation of clones, and enables colocalization studies and the identification of meaningful protein-protein interactions in vivo.

Concepts in bio-molecular spectroscopy: vibrational case studies on metalloenzymes

Challenges and chances in bio-molecular spectroscopy are exemplified by vibrational case studies on metalloenzymes.

Moving toward a comprehensive map of central plant metabolism

Decades of intensive study have led to the discovery of the main pathways involved in central metabolism but only some of the pathways and regulatory networks in which they are embedded. In this review, we discuss techniques used to assemble these pathways into a systems biology framework that can enable accurate modeling of the response of central metabolism to changes, including ways to perturb metabolic systems and assemble the resulting data into a meaningful network. Critically, these networks are of such size and complexity that it is possible to derive them only if data from different groups can be comprehensively and meaningfully combined. We conclude that it is essential to establish common standards for the description of experimental conditions and data collection and to store this information in databases to which the whole community can contribute.

Metabolic engineering to enhance the value of plants as green factories

The promise of plants to serve as the green factories of the future is ever increasing. Plants have been used traditionally for construction, energy, food and feed. Bioactive compounds primarily derived from specialized plant metabolism continue to serve as important scaffold molecules for pharmaceutical drug production. Yet, the past few years have witnessed a growing interest on plants as the ultimate harvesters of carbon and energy from the sun, providing carbohydrate and lipid biofuels that would contribute to balancing atmospheric carbon. How can the metabolic output from plants be increased even further, and what are the bottlenecks? Here, we present what we perceive to be the main opportunities and challenges associated with increasing the efficiency of plants as chemical factories. We offer some perspectives on when it makes sense to use plants as production systems because the amount of biomass needed makes any other system unfeasible. However, there are other instances in which plants serve as great sources of biological catalysts, yet are not necessarily the best-suited systems for production. We also present emerging opportunities for manipulating plant genomes to make plant synthetic biology a reality.

Synthetic metabolons for metabolic engineering

It has been proposed that enzymes can associate into complexes (metabolons) that increase the efficiency of metabolic pathways by channelling substrates between enzymes. Metabolons may increase flux by increasing the local concentration of intermediates, decreasing the concentration of enzymes needed to maintain a given flux, directing the products of a pathway to a specific subcellular location or minimizing the escape of reactive intermediates. Metabolons can be formed by relatively loose non-covalent protein-protein interaction, anchorage to membranes, and (in bacteria) by encapsulation of enzymes in protein-coated microcompartments. Evidence that non-coated metabolons are effective at channelling substrates is scarce and difficult to obtain. In plants there is strong evidence that small proportions of glycolytic enzymes are associated with the outside of mitochondria and are effective in substrate channelling. More recently, synthetic metabolons, in which enzymes are scaffolded to synthetic proteins or nucleic acids, have been expressed in microorganisms and these provide evidence that scaffolded enzymes are more effective than free enzymes for metabolic engineering. This provides experimental evidence that metabolons may have a general advantage and opens the way to improving the outcome of metabolic engineering in plants by including synthetic metabolons in the toolbox.

Plant biologists FRET over stress

Two independent research labs have developed fluorescent biosensors to report the levels of the stress hormone, abscisic acid, within cells in living plants in real-time.

Abscisic acid dynamics in roots detected with genetically encoded FRET sensors

Cytosolic hormone levels must be tightly controlled at the level of influx, efflux, synthesis, degradation and compartmentation. To determine ABA dynamics at the single cell level, FRET sensors (ABACUS) covering a range ∼0.2–800 µM were engineered using structure-guided design and a high-throughput screening platform. When expressed in yeast, ABACUS1 detected concentrative ABA uptake mediated by the AIT1/NRT1.2 transporter. Arabidopsis roots expressing ABACUS1-2µ (K_d∼2 µM) and ABACUS1-80µ (K_d∼80 µM) respond to perfusion with ABA in a concentration-dependent manner. The properties of the observed ABA accumulation in roots appear incompatible with the activity of known ABA transporters (AIT1, ABCG40). ABACUS reveals effects of external ABA on homeostasis, that is, ABA-triggered induction of ABA degradation, modification, or compartmentation. ABACUS can be used to study ABA responses in mutants and quantitatively monitor ABA translocation and regulation, and identify missing components. The sensor screening platform promises to enable rapid fine-tuning of the ABA sensors and engineering of plant and animal hormone sensors to advance our understanding of hormone signaling.

DOI:http://dx.doi.org/10.7554/eLife.01741.001

Plants are able to respond to detrimental changes in their environment—when, for example, water becomes scarce or the soil becomes too salty—in ways that minimize stress and damage caused by these changes. Hormones are chemicals that trigger the plant’s response under these circumstances.

Abscisic acid is the hormone that regulates how plants respond to drought and salt stress, and also controls growth and development. In the past, it was possible to measure the average level of this hormone in a given tissue, but not the level in individual cells in a living plant, nor in specific compartments within a cell. Moreover, it was difficult to follow directly how abscisic acid moved between the plant cells, tissues or organs.

Now, Jones et al. (and independently Waadt et al.) have developed tools that can measure the levels of abscisic acid within defined compartments of individual cells in living plants and in real time. The plants were genetically engineered to produce sensor proteins with two properties: they can bind to abscisic acid in a reversible manner, and they contain two ‘reporters’ that fluoresce at different wavelengths. Shining light onto the plant at a specific wavelength that is only absorbed by one of the reporters causes both of the reporters on the sensor proteins to fluoresce. However, the two reporters fluoresce differently when the sensor binds to abscisic acid. Specifically, one reporter fluoresces more and the other less. Hence, measuring the ratio of these two wavelengths in the light that is given off by the sensor proteins can be used as a measure of the concentration of abscisic acid in a plant cell.

Jones et al. used a high-throughput platform to engineer five sensor proteins that detect abscisic acid over a wide range of concentrations. Using these ‘ABACUS’ sensors in living plants could track the uptake of abscisic acid into root cells, and revealed that the concentration of the hormone inside the cell stayed below the levels provided on the outside. Since known abscisic acid-transporters are capable of raising the hormone concentration inside a cell above that provided on the outside, abscisic acid transport into plant roots may occur via as-yet-undiscovered transporter proteins. Jones et al. also show that root cells rapidly eliminate abscisic acid, and that adding extra abscisic acid to the roots increases the rate of elimination within minutes.

Plants were also engineered to target the sensor proteins specifically to the cell nucleus. In the future, targeting these sensors to the cell wall should allow tracking of the cell-to-cell movement of this hormone. Further aims include using ABACUS to track abscisic acid in plants undergoing stress, and to use the high-throughput platform to develop new sensors to track other hormones in living organisms (including animals).

DOI:http://dx.doi.org/10.7554/eLife.01741.002

Dynamic imaging of cytosolic zinc in Arabidopsis roots combining FRET sensors and RootChip technology

Zinc plays a central role in all living cells as a cofactor for enzymes and as a structural element enabling the adequate folding of proteins. In eukaryotic cells, metals are highly compartmentalized and chelated. Although essential to characterize the mechanisms of Zn(2+) homeostasis, the measurement of free metal concentrations in living cells has proved challenging and the dynamics are difficult to determine. Our work combines the use of genetically encoded Förster resonance energy transfer (FRET) sensors and a novel microfluidic technology, the RootChip, to monitor the dynamics of cytosolic Zn(2+) concentrations in Arabidopsis root cells. Our experiments provide estimates of cytosolic free Zn(2+) concentrations in Arabidopsis root cells grown under sufficient (0.4 nM) and excess (2 nM) Zn(2+) supply. In addition, monitoring the dynamics of cytosolic [Zn(2+) ] in response to external supply suggests the involvement of high- and low-affinity uptake systems as well as release from internal stores. In this study, we demonstrate that the combination of genetically encoded FRET sensors and microfluidics provides an attractive tool to monitor the dynamics of cellular metal ion concentrations over a wide concentration range in root cells.

Development of FRET biosensors for mammalian and plant systems

Genetically encoded biosensors are increasingly used in visualising signalling processes in different organisms. Sensors based on green fluorescent protein technology are providing a great opportunity for using Förster resonance energy transfer (FRET) as a tool that allows for monitoring dynamic processes in living cells. The development of these FRET biosensors requires careful selection of fluorophores, substrates and recognition domains. In this review, we will discuss recent developments, strategies to create and optimise FRET biosensors and applications of FRET-based biosensors for use in the two major eukaryotic kingdoms and elaborate on different methods for FRET detection.

Mitochondrial biosensors

Biosensors offer an innovative tool for measuring the dynamics of a wide range of metabolites in living organisms. Biosensors are genetically encoded, and thus can be specifically targeted to specific compartments of organelles by fusion to proteins or targeting sequences. Mitochondria are central to eukaryotic cell metabolism and present a complex structure with multiple compartments. Over the past decade, genetically encoded sensors for molecules involved in energy production, reactive oxygen species and secondary messengers have helped to unravel key aspects of mitochondrial physiology. To date, sensors for ATP, NADH, pH, hydrogen peroxide, superoxide anion, redox state, cAMP, calcium and zinc have been used in the matrix, intermembrane space and in the outer membrane region of mitochondria of animal and plant cells. This review summarizes the different types of sensors employed in mitochondria and their main limits and advantages, and it provides an outlook for the future application of biosensor technology in studying mitochondrial biology.

Fluorescent labeling and confocal microscopic imaging of chloroplasts and non-green plastids

While chlorophyll has served as an excellent label for plastids in green tissue, the development of fluorescent proteins has allowed their ready visualization in all tissues of the plants, revealing new features of their morphology and motility. Gene regulatory sequences in plastid transgenes can be optimized through the use of fluorescent protein reporters. Fluorescent labeling of plastids simultaneously with other subcellular locations reveals dynamic interactions and mutant phenotypes. Transient expression of fluorescent protein fusions is particularly valuable to determine whether or not a protein of unknown function is targeted to the plastid. Particle bombardment and agroinfiltration methods described here are convenient for imaging fluorescent proteins in plant organelles. With proper selection of fluorophores for labeling the components of the plant cell, confocal microscopy can produce extremely informative images at high resolution at depths not feasible by standard epifluorescence microscopy.

The use of nanoscale fluorescence microscopic to decipher cell wall modifications during fungal penetration

Plant diseases are one of the most studied subjects in the field of plant science due to their impact on crop yield and food security. Our increased understanding of plant-pathogen interactions was mainly driven by the development of new techniques that facilitated analyses on a subcellular and molecular level. The development of labeling technologies, which allowed the visualization and localization of cellular structures and proteins in live cell imaging, promoted the use of fluorescence and laser-scanning microscopy in the field of plant-pathogen interactions. Recent advances in new microscopic technologies opened their application in plant science and in the investigation of plant diseases. In this regard, in planta Förster/Fluorescence resonance energy transfer has demonstrated to facilitate the measurement of protein-protein interactions within the living tissue, supporting the analysis of regulatory pathways involved in plant immunity and putative host-pathogen interactions on a nanoscale level. Localization microscopy, an emerging, non-invasive microscopic technology, will allow investigations with a nanoscale resolution leading to new possibilities in the understanding of molecular processes.

Development and properties of genetically encoded pH sensors in plants

Fluorescent proteins (FPs) have given access to a large choice of live imaging techniques and have thereby profoundly modified our view of plant cells. Together with technological improvement of imaging, they have opened the possibility to monitor physico-chemical changes within cells. For this purpose, a new generation of FPs has been engineered. For instance, pHluorin, a point mutated version of green fluorescent protein, allows to get local pH estimates. In this paper, we will describe how genetically encoded sensors can be used to measure pH in the microenvironment of living tissues and subsequently discuss the role of pH in (i) exocytosis, (ii) ion uptake by plant roots, (iii) cell growth, and (iv) protein trafficking.